diff --git a/.gitattributes b/.gitattributes index 3e35a0d8496..d08df52f0a1 100644 --- a/.gitattributes +++ b/.gitattributes @@ -4,4 +4,7 @@ *.mzml binary *.mzxml binary +# Vendor API archives are binary; never normalize line endings (would corrupt them) +*.7z binary + *.sh text eol=lf \ No newline at end of file diff --git a/pwiz/data/common/cv.cpp b/pwiz/data/common/cv.cpp index 335f230e519..c9bac572632 100644 --- a/pwiz/data/common/cv.cpp +++ b/pwiz/data/common/cv.cpp @@ -66,7 +66,7 @@ const TermInfo termInfos_[] = {PEFF_DbSource, "PEFF:0000012", "DbSource", "PEFF keyword for the source of the database file.", false}, {PEFF_DbVersion, "PEFF:0000013", "DbVersion", "PEFF keyword for the database version (release date) according to database provider.", false}, {PEFF_DbDate_OBSOLETE, "PEFF:0000014", "DbDate", "PEFF keyword for the database date (release or file date of the source) according to database provider.", true}, - {PEFF_NumberOfEntries, "PEFF:0000015", "NumberOfEntries", "PEFF keyword for the sumber of sequence entries in the database.", false}, + {PEFF_NumberOfEntries, "PEFF:0000015", "NumberOfEntries", "PEFF keyword for the number of sequence entries in the database.", false}, {PEFF_Conversion, "PEFF:0000016", "Conversion", "PEFF keyword for the description of the conversion from original format to this current one.", false}, {PEFF_SequenceType, "PEFF:0000017", "SequenceType", "PEFF keyword for the molecular type of the sequences.", false}, {PEFF_SpecificKey, "PEFF:0000018", "SpecificKey", "PEFF keyword for database specific keywords not included in the current controlled vocabulary.", false}, @@ -88,7 +88,7 @@ const TermInfo termInfos_[] = {PEFF_Processed, "PEFF:0001010", "Processed", "PEFF keyword for information on how the full length original protein sequence can be processed into shorter components such as signal peptides and chains.", false}, {PEFF_Variant_OBSOLETE, "PEFF:0001011", "Variant", "Sequence variation (substitution, insertion, deletion).", true}, {PEFF_ModResPsi, "PEFF:0001012", "ModResPsi", "PEFF keyword for the modified residue with PSI-MOD identifier.", false}, - {PEFF_ModRes, "PEFF:0001013", "ModRes", "PEFF keyword for the modified residue without aPSI-MOD or UniMod identifier.", false}, + {PEFF_ModRes, "PEFF:0001013", "ModRes", "PEFF keyword for the modified residue without a PSI-MOD or Unimod identifier.", false}, {PEFF_AltAC, "PEFF:0001014", "AltAC", "PEFF keyword for the Alternative Accession Code.", false}, {PEFF_SeqStatus, "PEFF:0001015", "SeqStatus", "PEFF keyword for the sequence status. Complete or Fragment.", false}, {PEFF_CC, "PEFF:0001016", "CC", "PEFF keyword for the entry associated comment.", false}, @@ -102,7 +102,7 @@ const TermInfo termInfos_[] = {PEFF_Crc64, "PEFF:0001024", "Crc64", "PEFF keyword for the Sequence checksum in crc64.", false}, {PEFF_Domain, "PEFF:0001025", "Domain", "PEFF keyword for the sequence range of a domain.", false}, {PEFF_ID, "PEFF:0001026", "ID", "PEFF keyword for the UniProtKB specific Protein identifier ID; a UniProtKB term.", false}, - {PEFF_ModResUnimod, "PEFF:0001027", "ModResUnimod", "PEFF keyword for the modified residue with UniMod identifier.", false}, + {PEFF_ModResUnimod, "PEFF:0001027", "ModResUnimod", "PEFF keyword for the modified residue with Unimod identifier.", false}, {PEFF_VariantSimple, "PEFF:0001028", "VariantSimple", "PEFF keyword for the simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term.", false}, {PEFF_VariantComplex, "PEFF:0001029", "VariantComplex", "PEFF keyword for a sequence variation that is more complex than a single amino acid change or change to a stop codon.", false}, {PEFF_Proteoform, "PEFF:0001030", "Proteoform", "PEFF keyword for the proteoforms of this protein, constructed as a set of annotation identifiers.", false}, @@ -253,8 +253,8 @@ const TermInfo termInfos_[] = {MS_Shimadzu_instrument_model, "MS:1000124", "Shimadzu instrument model", "Shimadzu corporation instrument model.", false}, {MS_Thermo_Finnigan_instrument_model, "MS:1000125", "Thermo Finnigan instrument model", "ThermoFinnigan from Thermo Electron Corporation instrument model.", false}, {MS_Waters_instrument_model, "MS:1000126", "Waters instrument model", "Waters Corporation instrument model.", false}, - {MS_centroid_spectrum, "MS:1000127", "centroid spectrum", "Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset.", false}, - {MS_profile_spectrum, "MS:1000128", "profile spectrum", "A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis.", false}, + {MS_centroid_spectrum, "MS:1000127", "centroid spectrum", "A spectrum representation in which each peak is recorded as a single discrete data point at a distinct coordinate value (e.g. m/z; wavelength; drift time) with a corresponding intensity.", false}, + {MS_profile_spectrum, "MS:1000128", "profile spectrum", "A spectrum representation in which ion signal for each peak is recorded as a distribution of intensity values across the coordinate range (e.g. m/z; wavelength; drift time).", false}, {MS_negative_scan, "MS:1000129", "negative scan", "Polarity of the scan is negative.", false}, {MS_positive_scan, "MS:1000130", "positive scan", "Polarity of the scan is positive.", false}, {MS_number_of_detector_counts, "MS:1000131", "number of detector counts", "The number of counted events observed in one or a group of elements of a detector.", false}, @@ -2249,7 +2249,7 @@ const TermInfo termInfos_[] = {MS_number_of_precursor_ion_observations, "MS:1002228", "number of precursor ion observations", "The number of times the specific precursor ion has been observed in a series of SRM experiments.", false}, {MS_ProteomeDiscoverer_Mascot_Significance_Middle, "MS:1002229", "ProteomeDiscoverer:Mascot:Significance Middle", "Calculated relaxed significance when performing a decoy search for high-confidence peptides.", false}, {MS_ProteomeDiscoverer_Mascot_Significance_High, "MS:1002230", "ProteomeDiscoverer:Mascot:Significance High", "Calculated relaxed significance when performing a decoy search for medium-confidence peptides.", false}, - {MS_regular_expressions_for_a_GUID, "MS:1002231", "regular expressions for a GUID", "([A-Fa-f0-9]\\{8\\}-([A-Fa-f0-9]\\{4\\}-)\\{3\\}[A-Fa-f0-9]\\{12\\}).", false}, + {MS_regular_expressions_for_a_GUID, "MS:1002231", "regular expressions for a GUID", "([A-Fa-f0-9]\\\\{8\\\\}-([A-Fa-f0-9]\\\\{4\\\\}-)\\\\{3\\\\}[A-Fa-f0-9]\\\\{12\\\\}).", false}, {MS_ProteomeDiscoverer_Default_FDR_calculator, "MS:1002232", "ProteomeDiscoverer:Default FDR calculator", "The default FDR calculator as globally unique identifier (GUID).", false}, {MS_ProteomeDiscoverer_SEQUEST_Low_resolution_spectra_contained, "MS:1002233", "ProteomeDiscoverer:SEQUEST:Low resolution spectra contained", "Flag indicating if low-resolution spectra are taken into consideration.", false}, {MS_selected_precursor_m_z, "MS:1002234", "selected precursor m/z", "Mass-to-charge ratio of a precursor ion selected for fragmentation.", false}, @@ -2498,7 +2498,7 @@ const TermInfo termInfos_[] = {MS_mean_ion_mobility_drift_time_array, "MS:1002477", "mean ion mobility drift time array", "Array of population mean ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array.", false}, {MS_mean_charge_array, "MS:1002478", "mean charge array", "Array of mean charge values where the mean charge is calculated as a weighted mean of the charges of individual peaks that are aggregated into a processed spectrum.", false}, {MS_regular_expression, "MS:1002479", "regular expression", "Regular expression.", false}, - {MS_regular_expression_for_a_digital_object_identifier__DOI_, "MS:1002480", "regular expression for a digital object identifier (DOI)", "(10[.][0-9]\\{4,\\}(?:[.][0-9]+)*/(?:(?![\\\"&\\'<>])[^ \\t\\\\r\\n\\\\v\\\\f])+).", false}, + {MS_regular_expression_for_a_digital_object_identifier__DOI_, "MS:1002480", "regular expression for a digital object identifier (DOI)", "(10[.][0-9]\\\\{4,\\\\}(?:[.][0-9]+)*/(?:(?![\\\\\\\"&\\\\'<>])[^ \\\\t\\\\r\\\\n\\\\v\\\\f])+).", false}, {MS_higher_energy_beam_type_collision_induced_dissociation, "MS:1002481", "higher energy beam-type collision-induced dissociation", "A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV.", false}, {MS_statistical_threshold, "MS:1002482", "statistical threshold", "Estimated statistical threshold.", false}, {MS_PSM_level_statistical_threshold, "MS:1002483", "PSM-level statistical threshold", "Estimated statistical threshold at PSM-level.", false}, @@ -2523,7 +2523,7 @@ const TermInfo termInfos_[] = {MS_no_peptide_level_threshold, "MS:1002502", "no peptide-level threshold", "Indicating that no peptide-level threshold was used.", false}, {MS_PSM_is_used_for_peptide_level_scoring, "MS:1002503", "PSM is used for peptide-level scoring", "Flags a PSM that it is used for peptide-level scoring.", false}, {MS_modification_index, "MS:1002504", "modification index", "The order of modifications to be referenced elsewhere in the document.", false}, - {MS_regular_expression_for_modification_localization_scoring, "MS:1002505", "regular expression for modification localization scoring", "(?[0-9]+):(?[01][.][0-9]+(?:[Ee][+\\-]?[0-9]+)?):(?[0-9]+(?:[|][0-9]+)*):(?true|false)", false}, + {MS_regular_expression_for_modification_localization_scoring, "MS:1002505", "regular expression for modification localization scoring", "(?[0-9]+):(?[01][.][0-9]+(?:[Ee][+\\\\-]?[0-9]+)?):(?[0-9]+(?:[|][0-9]+)*):(?true|false)", false}, {MS_modification_position_score, "MS:1002506", "modification position score", "Modification position score.", false}, {MS_modification_rescoring_false_localization_rate, "MS:1002507", "modification rescoring:false localization rate", "Mod position score: false localization rate.", false}, {MS_crosslinking_attribute, "MS:1002508", "crosslinking attribute", "Crosslinking attribute.", false}, @@ -2828,7 +2828,7 @@ const TermInfo termInfos_[] = {MS_adduct_ion_attribute, "MS:1002809", "adduct ion attribute", "Nonphysical characteristic attributed to an adduct ion.", false}, {MS_adduct_ion_X_m_z, "MS:1002810", "adduct ion X m/z", "Theoretical m/z of the X component in the adduct (addition product) M+X or M-X. This term was formerly called 'adduct ion mass', but it is not really a mass. It corresponds to the column mislabelled as 'mass' at https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator.", false}, {MS_adduct_ion_isotope, "MS:1002811", "adduct ion isotope", "Isotope of the matrix molecule M of an adduct formation.", false}, - {MS_Regular_expression_for_adduct_ion_formula, "MS:1002812", "Regular expression for adduct ion formula", "(\\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\\][:digit:]{0,1}[+-]).", false}, + {MS_Regular_expression_for_adduct_ion_formula, "MS:1002812", "Regular expression for adduct ion formula", "(\\\\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\\\\][:digit:]{0,1}[+-]).", false}, {MS_adduct_ion_formula, "MS:1002813", "adduct ion formula", "Adduct formation formula of the form M+X or M-X, as constrained by the provided regular expression.", false}, {MS_volt_second_per_square_centimeter, "MS:1002814", "volt-second per square centimeter", "An electrical mobility unit that equals the speed [cm/s] an ion reaches when pulled through a gas by a Voltage[V] over a certain distance [cm].", false}, {MS_inverse_reduced_ion_mobility, "MS:1002815", "inverse reduced ion mobility", "Ion mobility measurement for an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This might refer to the central value of a bin into which all ions within a narrow range of mobilities have been aggregated.", false}, @@ -3222,7 +3222,7 @@ const TermInfo termInfos_[] = {MS_constituent_spectrum_file, "MS:1003203", "constituent spectrum file", "Spectrum data file from which (at least) a subset of spectra were extracted from. Should use USI notation mzspec:PXDxxxx:msRunName if possible, or a URI if USI notation is not possible.", false}, {MS_constituent_identification_file, "MS:1003204", "constituent identification file", "Identification file where (at least) a subset of identifications were extracted from. Should use a URI if possible", false}, {MS_constituent_library_file, "MS:1003205", "constituent library file", "Source library URI which(at least) a subset of spectra were extracted from.", false}, - {MS_library_creation_log, "MS:1003206", "library creation log", "String of logging information generated when the library was constructed from its constituent files. Multiple lines should be separated with escaped \\n", false}, + {MS_library_creation_log, "MS:1003206", "library creation log", "String of logging information generated when the library was constructed from its constituent files. Multiple lines should be separated with escaped \\\\n", false}, {MS_library_creation_software, "MS:1003207", "library creation software", "Library creation software", false}, {MS_experimental_precursor_monoisotopic_m_z, "MS:1003208", "experimental precursor monoisotopic m/z", "The measured or inferred m/z (as reported by the mass spectrometer acquisition software or post-processing software) of the monoisotopic peak of the precursor ion based on the MSn-1 spectrum.", false}, {MS_monoisotopic_m_z_deviation, "MS:1003209", "monoisotopic m/z deviation", "The measured monoisotopic m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical monoisotopic m/z of the analyte assigned to the spectrum.", false}, @@ -3404,7 +3404,7 @@ const TermInfo termInfos_[] = {MS_CompoundDb, "MS:1003388", "CompoundDb", "Bioconductor package CompoundDb for creation, usage and maintenance of public or library-specific annotation databases and spectra libraries.", false}, {MS_mzTab_M, "MS:1003389", "mzTab-M", "Expanded tabular result format for metabolomics experiments reporting quantitative summary data, MS features and identification evidence.", false}, {MS_crosslinker_cleavage_characteristics, "MS:1003390", "crosslinker cleavage characteristics", "Signifies that the crosslinker is cleavable and on cleavage can leave a given stub. The pattern specifies three slots ::.", false}, - {MS_crosslinker_cleavage_regular_expression, "MS:1003391", "crosslinker cleavage regular expression", "^(?[A-Za-z]):(?[+-]?[0-9]+(\\.[0-9]+)?([eE][+-]?[0-9]+(\\.[0-9]+)?)?):(?[A-Za-z]+)$", false}, + {MS_crosslinker_cleavage_regular_expression, "MS:1003391", "crosslinker cleavage regular expression", "^(?[A-Za-z]):(?[+-]?[0-9]+(\\\\.[0-9]+)?([eE][+-]?[0-9]+(\\\\.[0-9]+)?)?):(?[A-Za-z]+)$", false}, {MS_search_modification_id, "MS:1003392", "search modification id", "A unique identifier within an in mzIdentML document denoting a search modification rule. The same modification may be present multiple times with different id values to reflect different specificities or neutral losses.", false}, {MS_search_modification_id_ref, "MS:1003393", "search modification id ref", "A reference to a `search modification id` in the current mzIdentML document that defines the properties of this modification instance.", false}, {MS_SelexION_separation_voltage, "MS:1003394", "SelexION separation voltage", "RF voltage applied in the SelexION device to separate ions in trajectory based on the difference in their mobility between the high field and low field portions of the applied RF.", false}, @@ -3607,7 +3607,7 @@ const TermInfo termInfos_[] = {MS_ultra_high_performance_liquid_chromatography_system, "MS:1003592", "ultra-high performance liquid chromatography system", "A system for Ultra-High Performance Liquid Chromatography (UHPLC), an advanced form of high-performance liquid chromatography designed to achieve significantly faster, higher-resolution, and more sensitive separations. It is primarily achieved by innovations in particle chemistry and systemation capable of handling ultra-high pressures.", false}, {MS_fast_protein_liquid_chromatography_system, "MS:1003593", "fast protein liquid chromatography system", "A system for Fast Protein Liquid Chromatography (FPLC), a versatile and widely used medium-pressure chromatography technique primarily employed for the separation and purification of biomolecules, especially proteins. It operates under low to moderate pressures, making it suitable for labile proteins and other large biomolecules that might be denatured by the high pressures and organic solvents often used in high-performance liquid chromatography.", false}, {MS_three_dimensional_liquid_chromatography_system, "MS:1003594", "three-dimensional liquid chromatography system", "A system for Three-dimensional liquid chromatography (3D-LC), an advanced separation technique that combines three distinct liquid chromatography (LC) methods to achieve significantly enhanced separation power for complex mixtures, particularly in fields like proteomics.", false}, - {MS_planar_chomatography_system, "MS:1003595", "planar chomatography system", "A system for on-line planar chomatography.", false}, + {MS_planar_chromatography_system, "MS:1003595", "planar chromatography system", "A system for on-line planar chromatography.", false}, {MS_thin_layer_chromatography_system, "MS:1003596", "thin layer chromatography system", "A system for on-line Thin Layer Chromatography (TLC), based upon a widely used, simple, and cost-effective analytical technique for separating and identifying components in a mixture.", false}, {MS_high_performance_thin_layer_chromatography_system, "MS:1003597", "high-performance thin layer chromatography system", "A system for on-line High-Performance Thin Layer Chromatography (HPTLC), an advanced and refined version of traditional Thin Layer Chromatography (TLC), designed to offer significantly improved performance in terms of resolution, sensitivity, and reproducibility. It utilizes finer and more uniformly sized stationary phase particles, leading to more efficient separations and more accurate quantitative analysis.", false}, {MS_two_dimensional_liquid_chromatography_system, "MS:1003598", "two-dimensional liquid chromatography system", "A system for two-dimensional liquid chromatography (2D-LC), also often referred to as LC-LC or LC×LC, an advanced analytical technique that combines two different liquid chromatography methods in series to achieve enhanced separation of complex mixtures. It offers significantly higher resolving power and peak capacity compared to conventional one-dimensional liquid chromatography (1D-LC).", false}, @@ -3744,8 +3744,6 @@ const TermInfo termInfos_[] = {MS_Agilent_gas_chromatography_system_model, "MS:1003731", "Agilent gas chromatography system model", "Agilent Technologies gas chromatography system model.", false}, {MS_6890N, "MS:1003732", "6890N", "Agilent 6890N gas chromatograph.", false}, {MS_gas_chromatography_mass_spectrometry_system, "MS:1003733", "gas chromatography mass spectrometry system", "A gas chromatography mass spectrometry system (GC–MS) integrates a gas chromatograph for volatile analyte separation with a mass spectrometer for ionization and detection, enabling sensitive qualitative or quantitative analysis.", false}, - {MS_gas_chromatography_mass_spectrometry_system_model, "MS:1003734", "gas chromatography mass spectrometry system model", "Gas chromatography mass spectrometry system model name not including the vendor's name.", false}, - {MS_Shimadzu_gas_chromatography_mass_spectrometry_system_model, "MS:1003735", "Shimadzu gas chromatography mass spectrometry system model", "Shimadzu Corporation gas chromatography mass spectrometry system model.", false}, {MS_separation_system, "MS:1003737", "separation system", "A system to effect separation of compounds.", false}, {MS_5975C, "MS:1003738", "5975C", "Agilent 5975C gas chromatograph.", false}, {MS_5975T, "MS:1003739", "5975T", "Agilent 5975T gas chromatograph.", false}, @@ -3771,26 +3769,50 @@ const TermInfo termInfos_[] = {MS_TRACE_GC_Ultra, "MS:1003759", "TRACE GC Ultra", "Thermo TRACE GC Ultra gas chromatograph.", false}, {MS_FOCUS_GC, "MS:1003760", "FOCUS GC", "Thermo FOCUS GC gas chromatograph.", false}, {MS_instrument_class, "MS:1003761", "instrument class", "Instruments classified based on their architecture with respect to mass analyzers.", false}, - {MS_triple_quadrupole, "MS:1003762", "triple quadrupole", "A triple quadrupole mass spectrometer (TQMS; QqQ) is a tandem mass spectrometry (MS/MS) system that employs three linear quadrupoles in series to achieve highly selective and sensitive targeted quantification of specific compounds. The first quadrupole (Q1) may select a precursor ion, the second (Q2) induces fragmentation via collision-induced dissociation (CID), and the third (Q3) monitors specific product ions, typically through Multiple Reaction Monitoring (MRM).", false}, - {MS_quadrupole_time_of_flight, "MS:1003763", "quadrupole time-of-flight", "A quadrupole time-of-flight (Q-TOF) mass spectrometer is a hybrid instrument that combines a quadrupole mass filter with a time-of-flight (TOF) mass analyzer to provide both highly accurate mass measurements and fragmentation data. The quadrupole may be used to select a specific precursor ion which is then fragmented, and the resulting product ions are measured by the TOF analyzer, providing high resolution and mass accuracy for structural elucidation and quantification.", false}, - {MS_ion_trap_time_of_flight, "MS:1003764", "ion trap time-of-flight", "An ion trap time-of-flight (IT-TOF) mass spectrometer is a hybrid instrument that uses an ion trap to accumulate, store, and often fragment ions, which are then periodically injected into a time-of-flight (TOF) mass analyzer for high-resolution mass analysis. This combination allows for sensitive MSn experiments (multiple stages of mass spectrometry) within the ion trap for structural elucidation and provides high mass accuracy and resolution via the TOF component.", false}, - {MS_triple_quadrupole_linear_ion_trap, "MS:1003765", "triple quadrupole linear ion trap", "A triple quadrupole linear ion trap (QqLIT) mass spectrometer is a hybrid instrument that can operate as a conventional triple quadrupole for high-sensitivity quantification (e.g., in Multiple Reaction Monitoring mode) or as a linear ion trap for qualitative analysis, such as MSn experiments and structural elucidation. The final quadrupole (Q3) of the system can be rapidly switched between functioning as a mass-resolving filter and a high-capacity linear ion trap, allowing for both precise quantification and comprehensive structural information to be acquired in a single analytical run.", false}, - {MS_quadrupole_fourier_transform_ion_cyclotron_resonance, "MS:1003766", "quadrupole fourier transform ion cyclotron resonance", "A quadrupole Fourier-transform ion cyclotron resonance (Q-FT-ICR) mass spectrometer is a hybrid instrument that uses an initial quadrupole for ion guiding or mass filtering before the ions are introduced into a Penning trap, where the mass analysis occurs. Once in the Penning trap, the ions' mass-to-charge ratios (m/z) are determined with ultra-high resolution and mass accuracy by measuring their unique cyclotron frequencies in a strong magnetic field and converting the resulting image current signal into a mass spectrum via a Fourier transform. ", false}, - {MS_quadrupole_ion_mobility_time_of_flight, "MS:1003767", "quadrupole ion mobility time-of-flight", "A quadrupole ion mobility time-of-flight (Q-IMS-TOF) mass spectrometer is a hybrid instrument that adds an ion mobility spectrometry (IMS) cell between the quadrupole and the time-of-flight (TOF) analyzer, providing an additional dimension of separation based on ion size, shape, and charge in a buffer gas. This configuration allows for the separation of isobars and isomers that have the same mass-to-charge ratio (m/z) but different three-dimensional structures, which significantly enhances analytical confidence for complex samples such as in proteomics, environmental analysis, and drug screening.", false}, - {MS_ion_trap_orbitrap, "MS:1003768", "ion trap orbitrap", "A hybrid instrument that combines an ion trap for ion storage and fragmentation with an Orbitrap mass analyzer for high-resolution, accurate-mass (HRAM) detection.", false}, - {MS_quadrupole_orbitrap, "MS:1003769", "quadrupole orbitrap", "A quadrupole Orbitrap mass spectrometer is a hybrid instrument that uses a quadrupole mass filter for precursor ion selection, a collision cell for fragmentation, followed by an Orbitrap mass analyzer which determines the precise mass-to-charge ratios of ions with high resolution and mass accuracy via Fourier transform.", false}, - {MS_quadrupole_ion_trap_orbitrap, "MS:1003770", "quadrupole ion trap orbitrap", "A mass spectrometer that integrates a quadrupole mass filter, a linear ion trap, and an Orbitrap mass analyzer to provide precursor ion selection, multiple-stage fragmentation (MSn), and ultra-high resolution mass analysis.", false}, - {MS_quadrupole_orbitrap_astral, "MS:1003771", "quadrupole orbitrap astral", "A instrument that integrates a quadrupole mass filter, an Orbitrap mass analyzer, and the ASTRAL analyzer for high performance in ion selection, high-resolution analysis, and high-speed, high-sensitivity MS2 measurements.", false}, + {MS_triple_quadrupole_instrument, "MS:1003762", "triple quadrupole instrument", "A tandem instrument that employs three quadrupoles in series, where the first (Q1) acts as a mass filter for precursor ion selection, the second (q2) serves as a collision cell for fragmentation, and the third (Q3) as a mass filter for product ion detection.", false}, + {MS_quadrupole_time_of_flight_instrument, "MS:1003763", "quadrupole time-of-flight instrument", "A hybrid instrument that combines a quadrupole mass filter for precursor ion selection with a time-of-flight mass analyzer for high-resolution, accurate-mass detection of product ions.", false}, + {MS_ion_trap_time_of_flight_instrument, "MS:1003764", "ion trap time-of-flight instrument", "A hybrid instrument that combines an ion trap for ion accumulation, storage, and fragmentation with a time-of-flight mass analyzer for high-resolution, accurate-mass detection.", false}, + {MS_triple_quadrupole_linear_ion_trap_instrument, "MS:1003765", "triple quadrupole linear ion trap instrument", "A hybrid instrument that combines a triple quadrupole configuration with a linear ion trap, where the third quadrupole can function either as a conventional mass filter or as a linear ion trap for MSn analysis.", false}, + {MS_quadrupole_fourier_transform_ion_cyclotron_resonance_instrument, "MS:1003766", "quadrupole fourier transform ion cyclotron resonance instrument", "A hybrid instrument that combines a quadrupole for ion guiding or mass filtering with a Fourier transform ion cyclotron resonance mass analyzer for ultra-high resolution and mass accuracy.", false}, + {MS_quadrupole_ion_mobility_time_of_flight_instrument, "MS:1003767", "quadrupole ion mobility time-of-flight instrument", "A hybrid instrument that combines a quadrupole mass filter, an ion mobility spectrometry separation cell, and a time-of-flight mass analyzer, enabling separation of ions by size and shape in addition to mass-to-charge ratio.", false}, + {MS_ion_trap_orbitrap_instrument, "MS:1003768", "ion trap orbitrap instrument", "A hybrid instrument that combines an ion trap for ion storage and fragmentation with an Orbitrap mass analyzer for high-resolution, accurate-mass detection.", false}, + {MS_quadrupole_orbitrap_instrument, "MS:1003769", "quadrupole orbitrap instrument", "A hybrid instrument that combines a quadrupole mass filter for precursor ion selection with an Orbitrap mass analyzer for high-resolution, accurate-mass detection.", false}, + {MS_quadrupole_ion_trap_orbitrap_instrument, "MS:1003770", "quadrupole ion trap orbitrap instrument", "A hybrid instrument that combines a quadrupole mass filter, a linear ion trap for MSn fragmentation, and an Orbitrap mass analyzer for high-resolution, accurate-mass detection.", false}, + {MS_quadrupole_orbitrap_astral_instrument, "MS:1003771", "quadrupole orbitrap astral instrument", "A hybrid instrument that combines a quadrupole mass filter, an Orbitrap mass analyzer, and an asymmetric track lossless (ASTRAL) analyzer for high-resolution analysis and high-speed MS/MS measurements.", false}, {MS_mixed_polarity_acquisition, "MS:1003774", "mixed polarity acquisition", "The scans of a run include both positive and negative polarity acquisitions in a pattern that is not strictly alternating, such as discrete blocks of each polarity, irregular switching sequences, or other non-alternating arrangements.", false}, {MS_secondary_electrospray_ionization, "MS:1003775", "secondary electrospray ionization", "Secondary electrospray ionization (SESI) is an atmospheric pressure ionization (API) technique that uses a primary nano-electrospray plume of solvent ions to ionize neutral gaseous molecules in the gas phase via efficient proton transfer reactions. Operating at atmospheric pressure, SESI allows for the sensitive and real-time detection of volatile organic compounds (VOCs) and vapors with minimal sample preparation, making it ideal for applications like breath analysis and environmental monitoring.", false}, + {MS_acquisition_polarity, "MS:1003776", "acquisition polarity", "The ion polarity configuration used during data acquisition of a sample run.", false}, {MS_zstd_compression, "MS:1003780", "zstd compression", "Zstandard compression, a fast, modern, general purpose lossless compression algorithm.", false}, {MS_byte_shuffled_zstd_compression, "MS:1003781", "byte-shuffled zstd compression", "Byte shuffle transform followed by Zstandard compression.", false}, {MS_dictionary_encoded_zstd_compression, "MS:1003782", "dictionary-encoded zstd compression", "Dictionary encoding followed by Zstandard compression using a sorted dictionary with separately byte-shuffled values and indices.", false}, {MS_MS_Numpress_linear_prediction_compression_followed_by_zstd_compression, "MS:1003783", "MS-Numpress linear prediction compression followed by zstd compression", "Compression using MS-Numpress linear prediction compression and Zstandard .", false}, {MS_MS_Numpress_positive_integer_compression_followed_by_zstd_compression, "MS:1003784", "MS-Numpress positive integer compression followed by zstd compression", "Compression using MS-Numpress positive integer compression and Zstandard.", false}, {MS_MS_Numpress_short_logged_float_compression_followed_by_zstd_compression, "MS:1003785", "MS-Numpress short logged float compression followed by zstd compression", "Compression using MS-Numpress short logged float compression and Zstandard.", false}, + {MS_electrophoretic_separation, "MS:1003786", "electrophoretic separation", "Electrophoretic separation is a technique in which charged analytes are separated by differential migration in an applied electric field.", false}, + {MS_capillary_electrophoresis, "MS:1003787", "capillary electrophoresis", "Capillary electrophoresis (CE) is an electrophoretic separation technique performed in narrow-bore capillaries, in which analytes migrate through an electrolyte solution under the influence of an electric field and separate according to their electrophoretic mobility.", false}, + {MS_electrochromatography, "MS:1003788", "electrochromatography", "Electrochromatography is a liquid chromatography technique in which the mobile phase is driven through a stationary phase by electroosmotic flow generated by an applied electric field, combining electrophoretic migration with chromatographic retention.", false}, + {MS_ion_pair_reversed_phase_chromatography, "MS:1003789", "ion-pair reversed phase chromatography", "Ion-pair reversed-phase chromatography is a reversed-phase chromatography technique in which an ion-pairing reagent is added to the mobile phase to enable retention and separation of charged or ionizable analytes on a nonpolar stationary phase.", false}, + {MS_supercritical_fluid_chromatography, "MS:1003790", "supercritical fluid chromatography", "Supercritical fluid chromatography (SFC) is a separation technique in which the mobile phase is a fluid above and relatively close to its critical temperature and pressure.", false}, {MS_TSQ_Certis, "MS:1003800", "TSQ Certis", "Thermo Scientific TSQ Certis Triple Quadrupole MS.", false}, {MS_AccurateMassSearch, "MS:1003801", "AccurateMassSearch", "OpenMS TOPP tool to assemble metabolite features from singleton mass traces.", false}, + {MS_Ionoptika_instrument_model, "MS:1003802", "Ionoptika instrument model", "Ionoptika Ltd. instrument model.", false}, + {MS_Ionoptika_software, "MS:1003803", "Ionoptika software", "Ionoptika software for data acquisition and analysis.", false}, + {MS_Ionoptika_J105, "MS:1003804", "Ionoptika J105", "Ionoptika J105 time-of-flight secondary ion mass spectrometer.", false}, + {MS_J_Series_III, "MS:1003805", "J Series III", "Ionoptika J Series III time-of-flight secondary ion mass spectrometer.", false}, + {MS_NeoSIMS, "MS:1003806", "NeoSIMS", "Ionoptika software for data acquisition.", false}, + {MS_Ionoptika_Image_Analyser, "MS:1003807", "Ionoptika Image Analyser", "Ionoptika software for image data analysis.", false}, + {MS_J105_Ionoptika_Mass_Imager, "MS:1003808", "J105 Ionoptika Mass Imager", "Ionoptika J105 software for mass spectrometry imaging data analysis.", false}, + {MS_IoDataConverter, "MS:1003809", "IoDataConverter", "Ionoptika software for converting Ionoptika data formats to imzML or HDF5.", false}, + {MS_Ionoptika_V1_format, "MS:1003810", "Ionoptika V1 format", "Ionoptika data format generated by J105 TOF-SIMS instrument.", false}, + {MS_Ionoptika_V3_format, "MS:1003811", "Ionoptika V3 format", "Ionoptika data format generated by J105 TOF-SIMS instrument.", false}, + {MS_lambda_max, "MS:1003812", "lambda max", "The wavelength of maximum absorbance for a substance. This is analogous to the base peak m/z for UV-Vis spectroscopy.", false}, + {MS_list_of_doubles, "MS:1003813", "list of doubles", "A list of xsd:double.", false}, + {MS_coordinate_spacing_model, "MS:1003820", "coordinate spacing model", "Defines a model for calculating or correcting the spacing between points along a continuous dimension.", false}, + {MS_polynomial_delta_coordinate_interpolation, "MS:1003821", "polynomial delta coordinate interpolation", "A coordinate spacing model that predicts the next coordinate as a function of a low degree polynomial on the current coordinate, for instance a 2nd degree $x_{i + 1} = (a*x_i^2 + b*x_i + c) + x_i$. It is assumed that the parameters are inferred from the value list and the number implies the polynomial degree.", false}, + {MS_grid_coordinate_interpolation, "MS:1003822", "grid coordinate interpolation", "A coordinate spacing model that uses some form of interpolation to calculate coordinate values between a fixed minimum and maximum value. This includes formula for (potentially lossily) converting a coordinate to an integer index and vice-versa. The grid model and recalibration function parameters are given by the value list. The recalibration function may be the identity function, or a more complex model defined in a child term.", false}, + {MS_linear_grid_interpolation, "MS:1003824", "linear grid interpolation", "A coordinate spacing model that uses linear interpolation to map grid indices to coordinates $x_i = f_x(b + i * a)$ where $f$ is some recalibration function.", false}, + {MS_square_root_grid_interpolation, "MS:1003825", "square root grid interpolation", "A coordinate spacing model that maps grid indices to coordinates $x_i = f_x((b + i * a)^2)$ where $f$ is some recalibration function. The square root of the coordinate is linear with respect to the index. This mirrors the formula relating time-of-flight to m/z, $t = k\\\\sqrt{m/z}$", false}, + {MS_coordinate_grid_encoding, "MS:1003826", "coordinate grid encoding", "This array stores indices or spans into some form of coordinate space model rather than the coordinates themselves, and that grid is stored externally from this data array. The objective being that these coordinates are more compact to store than the raw coordinates themselves. The value of this parameter is the grid identifier, if there are multiple to choose from. A separate coordinate spacing model parameter will signify what form of coordinate space model is used.", false}, {MS_zero_intensity_point_trimming, "MS:1003901", "zero intensity point trimming", "Apply an algorithm to remove excess zero intensity value data points from a spectrum. Data may be retained for interperatbility such as retaining only zeros that flank non-zero intensity value data points from a profile spectrum..", false}, {MS_zero_intensity_point_trimming_interpolation, "MS:1003902", "zero intensity point trimming interpolation", "A zero intensity point trimming algorithm that interpolates the m/z coordinate values from the local data or an estimated model.", false}, {MS_analysis, "MS:1003903", "analysis", "A strategy for mass spectrometry-based analysis that defines whether analytes are predetermined or discovered during acquisition.", false}, @@ -3798,7 +3820,100 @@ const TermInfo termInfos_[] = {MS_targeted_analysis, "MS:1003905", "targeted analysis", "An analytical approach in which a predefined set of analytes is measured, typically enabling quantitative determination.", false}, {MS_semi_targeted_analysis, "MS:1003906", "semi-targeted analysis", "An analytical approach combining targeted monitoring of predefined analytes with simultaneous untargeted data acquisition.", false}, {MS_parallel_reaction_monitoring, "MS:1003907", "parallel reaction monitoring", "Parallel Reaction Monitoring (PRM) utilizes high-resolution, accurate-mass mass spectrometry, typically a quadrupole orbitrap or quadrupole time-of-flight instrument, to isolate specific precursor ions and detect all resulting product ions in parallel. Unlike Selected Reaction Monitoring (SRM), which filters for pre-selected transitions, PRM acquires full MS/MS spectra for each target, thereby eliminating the need for transition optimization and providing high specificity through high-resolution interference rejection.", false}, - {MS_Agilent_gas_chromatography_mass_spectrometry_system_model, "MS:1003914", "Agilent gas chromatography mass spectrometry system model", "Agilent Technologies gas chromatography mass spectrometry system model.", false}, + {MS_centroid_peak, "MS:1003908", "centroid peak", "A peak represented as a single discrete data point defined by a distinct coordinate value (e.g. m/z; wavelength; drift time) and a corresponding intensity value.", false}, + {MS_two_dimensional_gas_chromatography, "MS:1003915", "two-dimensional gas chromatography", "Comprehensive two-dimensional gas chromatography (GCxGC) is a multidimensional separation technique that utilizes two columns with different stationary phases connected by a modulator, which traps, focuses and reinjects fractions from the first column to the second. This approach leads to a 2D chromatogram offering higher peak capacity and separation power.", false}, + {MS_SpectroSwiss_software, "MS:1003916", "SpectroSwiss software", "SpectroSwiss software for mass spectrometry data processing and analysis.", false}, + {MS_Peak_by_Peak, "MS:1003917", "Peak-by-Peak", "SpectroSwiss software for Fourier transform mass spectrometry (FTMS) data processing and analysis, providing advanced workflows including the processing of unreduced, transient data.", false}, + {MS_chromatographic_column, "MS:1003920", "chromatographic column", "A tube or housing containing a stationary phase, through which a mobile phase flows to achieve chromatographic separation of analytes.", false}, + {MS_liquid_chromatographic_column, "MS:1003921", "liquid chromatographic column", "A chromatographic column designed for use with a liquid mobile phase, housing a stationary phase for analyte separation.", false}, + {MS_chromatographic_stationary_phase, "MS:1003922", "chromatographic stationary phase", "The immobile phase in a chromatographic system with which analytes interact differentially, enabling separation based on chemical or physical properties.", false}, + {MS_chromatographic_stationary_phase_attribute, "MS:1003923", "chromatographic stationary phase attribute", "Chromatographic stationary phase properties that are associated with a value.", false}, + {MS_pore_size, "MS:1003924", "pore size", "The average diameter of the pores within the particles of the stationary phase, typically represented in angstroms (Å)", false}, + {MS_particle_diameter, "MS:1003925", "particle diameter", "The average diameter of the solid particles that constitute the stationary phase.", false}, + {MS_chromatographic_column_attribute, "MS:1003926", "chromatographic column attribute", "Properties of the chromatographic column hardware that are associated with a value.", false}, + {MS_column_length, "MS:1003927", "column length", "The length of the chromatographic column, representing the path length available for separation.", false}, + {MS_column_internal_diameter, "MS:1003928", "column internal diameter", "The inner diameter of the chromatographic column.", false}, + {MS_particle_porosity, "MS:1003929", "particle porosity", "The porosity of the particles composing the chromatographic stationary phase.", false}, + {MS_fully_porous, "MS:1003930", "fully porous", "A chromatographic stationary phase particle with pores distributed throughout its entire volume.", false}, + {MS_superficially_porous, "MS:1003931", "superficially porous", "A chromatographic stationary phase particle consisting of a solid, non-porous core surrounded by a porous shell.", false}, + {MS_non_porous, "MS:1003932", "non-porous", "A solid chromatographic stationary phase particle without internal pores.", false}, + {MS_support_material, "MS:1003933", "support material", "The base material from which the chromatographic stationary phase is constructed.", false}, + {MS_silica_based, "MS:1003934", "silica-based", "A chromatographic stationary phase constructed from silica particles, optionally with surface chemical modification.", false}, + {MS_hybrid_particle, "MS:1003935", "hybrid particle", "A chromatographic stationary phase constructed from organic-inorganic hybrid particles, such as ethylene-bridged hybrid (BEH), providing enhanced chemical stability and pH range.", false}, + {MS_polymer_based, "MS:1003936", "polymer-based", "A chromatographic stationary phase constructed from organic polymer particles such as polystyrene-divinylbenzene or methacrylate-based polymers.", false}, + {MS_monolithic, "MS:1003937", "monolithic", "A chromatographic stationary phase consisting of a single continuous porous rod rather than packed discrete particles.", false}, + {MS_porous_graphitic_carbon, "MS:1003938", "porous graphitic carbon", "A chromatographic stationary phase composed of porous graphitic carbon, providing strong retention of polar compounds and chemical robustness across a wide pH range.", false}, + {MS_trap_column, "MS:1003939", "trap column", "A short chromatographic column used for on-line sample loading, concentration, and desalting prior to separation on the analytical column.", false}, + {MS_guard_column, "MS:1003940", "guard column", "A short protective chromatographic column placed upstream of the analytical column to capture contaminants and extend analytical column lifetime.", false}, + {MS_analytical_column, "MS:1003941", "analytical column", "The primary chromatographic column in which analyte separation occurs.", false}, + {MS_gas_chromatographic_column, "MS:1003943", "gas chromatographic column", "A chromatographic column designed for use with a gaseous mobile phase.", false}, + {MS_chromatographic_column_role, "MS:1003944", "chromatographic column role", "The functional role of a chromatographic column within the separation workflow.", false}, + {MS_chromatographic_column_type, "MS:1003945", "chromatographic column type", "The type of chromatographic column classified by the mobile phase it is designed to operate with.", false}, + {MS_tandem_time_of_flight_instrument, "MS:1003946", "tandem time-of-flight instrument", "A tandem instrument that combines two time-of-flight mass analyzers in series, where the first selects precursor ions and the second analyzes fragment ions produced by collision-induced dissociation or post-source decay.", false}, + {MS_magnetic_sector_ion_trap_instrument, "MS:1003947", "magnetic sector ion trap instrument", "A hybrid instrument that combines a double-focusing magnetic sector analyzer for high-resolution precursor ion selection with an ion trap for MSn fragmentation analysis.", false}, + {MS_fourier_transform_ion_cyclotron_resonance_instrument, "MS:1003948", "fourier transform ion cyclotron resonance instrument", "An instrument that uses a Fourier transform ion cyclotron resonance mass analyzer as its primary means of mass analysis.", false}, + {MS_magnetic_sector_instrument, "MS:1003949", "magnetic sector instrument", "An instrument that uses a magnetic sector mass analyzer as its primary means of mass analysis.", false}, + {MS_quadrupole_instrument, "MS:1003950", "quadrupole instrument", "An instrument that uses a single quadrupole mass analyzer as its primary means of mass analysis.", false}, + {MS_time_of_flight_instrument, "MS:1003951", "time-of-flight instrument", "An instrument that uses a time-of-flight mass analyzer as its primary means of mass analysis.", false}, + {MS_ion_trap_instrument, "MS:1003952", "ion trap instrument", "An instrument that uses an ion trap mass analyzer as its primary means of mass analysis.", false}, + {MS_orbitrap_instrument, "MS:1003953", "orbitrap instrument", "An instrument that uses an Orbitrap mass analyzer as its primary means of mass analysis.", false}, + {MS_argon_gas_cluster_ion_beam, "MS:1003954", "argon gas cluster ion beam", "Argon gas cluster ion beam (Ar GCIB) bombardment uses a focused beam of large argon cluster ions, typically [Ar500]+ to [Ar10000]+, accelerated to high energies to sputter and generate secondary ions from a surface, enabling molecular depth profiling and imaging of organic and biological materials with reduced subsurface damage compared to monatomic ion beams.", false}, + {MS_singly_charged_bismuth_trimer_liquid_metal_ion_gun, "MS:1003955", "singly charged bismuth trimer liquid metal ion gun", "A beam of singly charged bismuth trimer ([Bi3]+) ions for desorption and ionisation from a surface, providing high spatial resolution imaging and enhanced molecular secondary ion yields compared to monatomic primary ion beams.", false}, + {MS_doubly_charged_bismuth_trimer_liquid_metal_ion_gun, "MS:1003956", "doubly charged bismuth trimer liquid metal ion gun", "A beam of doubly charged bismuth trimer ([Bi3]2+) ions for desorption and ionisation from a surface. Ions achieve a higher velocity at a given acceleration voltage compared to singly charged [Bi3]+, resulting in enhanced secondary ion yields for surface analysis.", false}, + {MS_two_dimensional_liquid_chromatography, "MS:1003957", "two-dimensional liquid chromatography", "Two-dimensional liquid chromatography (2D-LC) is a multidimensional separation technique that couples two liquid chromatography columns with different selectivities, such as strong cation exchange and reversed phase, connected by a switching valve or modulator to provide significantly higher peak capacity and resolving power for complex mixtures than one-dimensional liquid chromatography.", false}, + {MS_bismuth_liquid_metal_ion_gun, "MS:1003958", "bismuth liquid metal ion gun", "Bismuth liquid metal ion gun (Bi LMIG) bombardment uses a focused beam of bismuth ions emitted from a liquid metal ion source to desorb and ionize molecules from a surface. The LMIG source generates a diversity of monomers and clusters, which are filtered prior to the sample in order to select the specific ionisation characteristics.", false}, + {MS_gas_cluster_ion_beam, "MS:1003959", "gas cluster ion beam", "A gas cluster ion beam (GCIB) is an ion source that generates and accelerates large aggregates of gas atoms or molecules to high energies. The low energy per constituent atom minimizes surface damage and molecular fragmentation, making it highly effective for molecular depth profiling and the analysis of fragile organic and biological materials.", false}, + {MS_liquid_metal_ion_gun, "MS:1003960", "liquid metal ion gun", "A liquid metal ion gun (LMIG) is an ion source that extracts and ionizes a thin layer of liquid metal from a fine heated needle using a high-voltage electric field. It produces a high-brightness, tightly focused beam of metal ions or clusters, enabling high-resolution imaging and analysis in Secondary Ion Mass Spectrometry (SIMS).", false}, + {MS_Thermo_Scientific_software, "MS:1003961", "Thermo Scientific software", "Thermo Scientific software for data acquisition and analysis.", false}, + {MS_TraceFinder, "MS:1003962", "TraceFinder", "Thermo Scientific software for targeted quantitative and screening analysis of LC-MS, GC-MS, and IC-MS data, supporting automated data acquisition, processing, and reporting for diverse workflows.", false}, + {MS_FreeStyle, "MS:1003963", "FreeStyle", "Thermo Scientific software for interactive qualitative visualization and review of mass spectrometry data, including chromatographic peak detection, spectral library searching, and high-resolution deconvolution.", false}, + {MS_Chromeleon_CDS, "MS:1003964", "Chromeleon CDS", "Thermo Scientific enterprise chromatography data system with integrated mass spectrometry instrument control and data processing, supporting GC-MS, LC-MS, and IC-MS platforms with GxP/21 CFR Part 11 compliance.", false}, + {MS_Mass_Frontier, "MS:1003965", "Mass Frontier", "Thermo Scientific software for mass spectral interpretation and structural elucidation of small molecules, featuring the HighChem fragmentation library, fragmentation prediction, and spectral tree searching.", false}, + {MS_LipidSearch, "MS:1003966", "LipidSearch", "Thermo Scientific software for automated identification of lipid molecular species from LC-MS and LC-MS/MS data using a comprehensive database of predicted lipid ion fragments.", false}, + {MS_mzVault, "MS:1003967", "mzVault", "Thermo Scientific software for offline storage, searching, and management of high-resolution accurate-mass spectral libraries, including curated mzCloud content and user-generated in-house libraries.", false}, + {MS_SIEVE, "MS:1003968", "SIEVE", "Thermo Scientific software for label-free differential expression analysis of LC-MS and GC-MS data, providing chromatographic alignment, feature detection, and statistical comparison for proteomics and metabolomics.", false}, + {MS_BioPharma_Finder, "MS:1003969", "BioPharma Finder", "Thermo Scientific software for complex biotherapeutic characterization by LC-MS, supporting intact protein analysis, peptide mapping, oligonucleotide analysis, multi-attribute method workflows, and top-down or middle-down approaches.", false}, + {MS_ion_mobility_quadrupole_time_of_flight_instrument, "MS:1003970", "ion mobility quadrupole time-of-flight instrument", "An instrument that uses an ion mobility analyzer followed by a quadrupole mass filter and a time-of-flight mass analyzer as its primary means of mass analysis.", false}, + {MS_ion_trap_fourier_transform_ion_cyclotron_resonance_instrument, "MS:1003971", "ion trap fourier transform ion cyclotron resonance instrument", "An instrument that uses a linear ion trap coupled to a fourier transform ion cyclotron resonance mass analyzer as its primary means of mass analysis.", false}, + {MS_quadrupole_ion_trap_instrument, "MS:1003972", "quadrupole ion trap instrument", "An instrument that uses a quadrupole mass filter followed by an ion trap mass analyzer as its primary means of mass analysis.", false}, + {MS_LECO_PEG_format, "MS:1003973", "LECO PEG format", "Proprietary binary data format with extension '.peg', used by LECO ChromaTOF software to store raw and processed data from LECO Pegasus series mass spectrometers.", false}, + {MS_JEOL_JPF_format, "MS:1003974", "JEOL JPF format", "Proprietary binary data format with extension '.jpf', used by JEOL mass spectrometry systems and associated data processing software to store mass spectral data.", false}, + {MS_peak_group, "MS:1003975", "peak group", "A collection of co-eluting chromatographic peaks with matching profiles, derived from a single source analyte. Examples include: related product ion peaks of a single precursor; related peaks derived from different adducts, multimers or isotopologues of a given analyte; and related peaks derived from in-source fragmentation of a given analyte.", false}, + {MS_retention_time_window_target, "MS:1003976", "retention time window target", "The reference retention time from which a retention time window is defined. The target may be derived from a predicted, expected, observed, or user-specified retention time.", false}, + {MS_Monocle, "MS:1003977", "Monocle", "A software program for converting Thermo Scientific RAW file format to mzXML, mzML, or CSV with improved monoisotopic mass estimation. Monocle was originally developed at the Gygi Lab at Harvard Medical School.", false}, + {MS_______DE______AFILMV___P__, "MS:1003978", "(?<=[^DE])(?=[AFILMV][^P])", "Regular expression for Thermolysin.", false}, + {MS_Thermolysin, "MS:1003979", "Thermolysin", "Thermostable extracellular metalloendopeptidase containing four calcium ions", false}, + {MS_____AEFILTVWY__, "MS:1003980", "(?=[AEFILTVWY])", "Regular expression for peptidase K.", false}, + {MS_peptidase_K, "MS:1003981", "peptidase K", "Peptidase from the mold Tritirachium album Limber", false}, + {MS_____N____G_, "MS:1003982", "(?<=N)(?=G)", "Regular expression for hydroxylamine.", false}, + {MS_hydroxylamine, "MS:1003983", "hydroxylamine", "NH2OH", false}, + {MS_amino_acid_confidence_level, "MS:1003984", "amino acid confidence level", "The confidence level of the PSM assignment per amino acid, where 0 is not confident and 1 is maximally confident.", false}, + {MS_peptidoform_token_confidence_level, "MS:1003985", "peptidoform token confidence level", "The confidence level of the PSM assignment per peptidoform token, so separately for each amino acid and modification, where 0 is not confident and 1 is maximally confident.", false}, + {MS_protein_sequence, "MS:1003986", "protein sequence", "The protein sequence of a protein in a database.", false}, + {MS_Orbitrap_Tribrid_Apex, "MS:1003987", "Orbitrap Tribrid Apex", "Thermo Scientific Orbitrap Tribrid Apex mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers.", false}, + {MS_Xevo_MRT_P10, "MS:1003988", "Xevo MRT P10", "Waters Xevo MRT P10 quadrupole - multi-reflecting time-of-flight mass spectrometer.", false}, + {MS_Cyclic_IMS_P20, "MS:1003989", "Cyclic IMS P20", "Waters Cyclic IMS P20 multipass cyclic ion mobility quadrupole time-of-flight mass spectrometer.", false}, + {MS_Orbitrap_Excedion, "MS:1003990", "Orbitrap Excedion", "Thermo Scientific Orbitrap Excedion mass spectrometer.", false}, + {MS_novus_V55, "MS:1003991", "novus V55", "SCIEX novus V55 triple quadrupole mass spectrometer.", false}, + {MS_9500_Triple_Quadrupole_ICP_MS, "MS:1003992", "9500 Triple Quadrupole ICP-MS", "Agilent 9500 Triple Quadrupole ICP-MS inductively coupled plasma triple quadrupole mass spectrometer.", false}, + {MS_InfinityLab_Pro_iQ, "MS:1003993", "InfinityLab Pro iQ", "Agilent InfinityLab Pro iQ single quadrupole LC mass detector.", false}, + {MS_ion_mobility_quadrupole_FT_ICR_instrument, "MS:1003994", "ion mobility quadrupole FT-ICR instrument", "Instrument class combining trapped ion mobility spectrometry (TIMS) with a quadrupole mass filter and fourier transform ion cyclotron resonance (magnetic resonance) mass analysis.", false}, + {MS_timsMRMS, "MS:1003995", "timsMRMS", "Bruker timsMRMS instrument combining trapped ion mobility spectrometry with magnetic resonance (FT-ICR) mass spectrometry.", false}, + {MS_DeepNovo, "MS:1003996", "DeepNovo", "DeepNovo is a deep-learning based de novo peptide sequencer for DDA.", false}, + {MS_DeepNovo_DIA, "MS:1003997", "DeepNovo-DIA", "DeepNovo is a deep-learning based de novo peptide sequencer for DDA and DIA.", false}, + {MS_PointNovo, "MS:1003998", "PointNovo", "PointNovo is neural network based de novo peptide sequencing model.", false}, + {MS_PGPointNovo, "MS:1003999", "PGPointNovo", "PGPointNovo is a modification of PointNovo that allows parallel processing and a better optimization strategy.", false}, + {MS_BiATNovo, "MS:1004000", "BiATNovo", "BiATNovo an attention based bidirectional de novo peptide sequencing software.", false}, + {MS_NovoB, "MS:1004001", "NovoB", "NovoB a transformer based bidirectional de novo peptide sequencing software.", false}, + {MS_PepNet, "MS:1004002", "PepNet", "PepNet a convolutional neural network de novo peptide sequencing software.", false}, + {MS__xCF__x80__HelixNovo, "MS:1004003", "π-HelixNovo", "π-HelixNovo a transformer based de novo peptide sequencing software.", false}, + {MS__xCF__x80__PrimeNovo, "MS:1004004", "π-PrimeNovo", "π-PrimeNovo a non-autoregressive de novo peptide sequencing software.", false}, + {MS_PowerNovo, "MS:1004005", "PowerNovo", "PowerNovo a BERT and transformer ensemble de novo peptide sequencing software.", false}, + {MS_pUniFind, "MS:1004006", "pUniFind", "pUniFind a open modification de novo peptide sequencing and rescoring software.", false}, + {MS_Sage, "MS:1004007", "Sage", "A database search based peptide identification software with retention time prediction, quantification, rescoring, and false discovery rate control.", false}, + {MS_BiblioSpec_Spectrum_Sequence_List, "MS:1004008", "BiblioSpec Spectrum Sequence List", "Tabular result format for proteomics and small molecule experiments, saved with extension '.ssl'.", false}, + {MS_ProteoScape, "MS:1004009", "ProteoScape", "Bruker ProteoScape is a GPU-powered platform delivering parallel computing capabilities and real-time database search results for bottom-up proteomics.", false}, + {MS_Stitch, "MS:1004010", "Stitch", "Template-based assembly of PSMs for de novo protein sequencing.", false}, {NCIT_Number_of_Occurrences, "NCIT:3150827", "Number of Occurrences", "The number of times something happened.", false}, {MS_PSI_MS_CV_Quality_Control_Vocabulary, "MS:4000000", "PSI-MS CV Quality Control Vocabulary", "PSI Quality Control controlled vocabulary term.", false}, {MS_QC_metric, "MS:4000001", "QC metric", "Parent term for QC metrics, each metric MUST have this as an ancestor in its is_a relations.", false}, @@ -5549,6 +5664,15 @@ const TermInfo termInfos_[] = {UNIMOD_b_type_ion, "UNIMOD:2132", "b-type-ion", "Dehydration of C-terminus as reaction inside the mass spectrometer.", false}, {UNIMOD_PnTAG, "UNIMOD:2135", "PnTAG", "6-Phosphonohexanoylation.", false}, {UNIMOD_DMA_PEG3, "UNIMOD:2136", "DMA-PEG3", "DimethylaminoPEG3ylation.", false}, + {UNIMOD_HCCA_Lys, "UNIMOD:2138", "HCCA-Lys", "Lysine labelled with HCCA tag.", false}, + {UNIMOD_Phosphocholine, "UNIMOD:2139", "Phosphocholine", "Serine/Threonine/Tyrosine of a protein becomes posttranslationally modified with a phosphocholine moiety..", false}, + {UNIMOD_Methyl_13C_1_2H_2_, "UNIMOD:2140", "Methyl:13C(1)2H(2)", "Heavy-Methyl:13C(1)2H(2).", false}, + {UNIMOD_c_type_ion, "UNIMOD:2141", "c-type-ion", "Cleavage at the N atom from the N+1 residue as reaction inside the mass spectrometer.", false}, + {UNIMOD_x_type_ion, "UNIMOD:2142", "x-type-ion", "Cleavage at the carbonyl from the N-1 residue as reaction inside the mass spectrometer.", false}, + {UNIMOD_z_type_ion, "UNIMOD:2143", "z-type-ion", "Ammonia loss from N-terminus as reaction inside the mass spectrometer.", false}, + {UNIMOD_Dehydromethionine, "UNIMOD:2144", "Dehydromethionine", "Intramolecular cyclization product of N-terminal methionine, forming a five-membered azasulfonium ion where the sulfur atom bonds to the amine group.", false}, + {UNIMOD_Label_2H_8_, "UNIMOD:2146", "Label:2H(8)", "SILAC: Lysine_D8.", false}, + {UNIMOD_imidazolone, "UNIMOD:2147", "imidazolone", "Imidazolone from 3-DG.", false}, {UO_unit, "UO:0000000", "unit", "A unit of measurement is a standardized quantity of a physical quality.", false}, {UO_length_unit, "UO:0000001", "length unit", "A unit which is a standard measure of the distance between two points.", false}, {UO_mass_unit, "UO:0000002", "mass unit", "A unit which is a standard measure of the amount of matter/energy of a physical object.", false}, @@ -6258,19 +6382,15 @@ CVIDPair relationsIsA_[] = {MS_electrospray_ionization, MS_ionization_type}, {MS_fast_atom_bombardment_ionization, MS_ionization_type}, {MS_matrix_assisted_laser_desorption_ionization, MS_desorption_ionization}, - {MS_negative_polarity_acquisition, MS_data_file_content}, - {MS_positive_polarity_acquisition, MS_data_file_content}, + {MS_negative_polarity_acquisition, MS_acquisition_polarity}, + {MS_positive_polarity_acquisition, MS_acquisition_polarity}, {MS_axial_ejection_linear_ion_trap, MS_linear_ion_trap}, {MS_fourier_transform_ion_cyclotron_resonance, MS_mass_analyzer_type}, - {MS_fourier_transform_ion_cyclotron_resonance, MS_instrument_class}, {MS_magnetic_sector, MS_mass_analyzer_type}, - {MS_magnetic_sector, MS_instrument_class}, {MS_quadrupole, MS_mass_analyzer_type}, - {MS_quadrupole, MS_instrument_class}, {MS_quadrupole_ion_trap, MS_ion_trap}, {MS_radial_ejection_linear_ion_trap, MS_linear_ion_trap}, {MS_time_of_flight, MS_mass_analyzer_type}, - {MS_time_of_flight, MS_instrument_class}, {MS_baseline, MS_resolution_measurement_method}, {MS_full_width_at_half_maximum, MS_resolution_measurement_method}, {MS_ten_percent_valley, MS_resolution_measurement_method}, @@ -6314,70 +6434,130 @@ CVIDPair relationsIsA_[] = {MS_post_source_decay, MS_dissociation_method}, {MS_surface_induced_dissociation, MS_dissociation_method}, {MS_normalized_collision_energy, MS_precursor_activation_attribute}, + {MS_4000_QTRAP, MS_triple_quadrupole_linear_ion_trap_instrument}, {MS_4000_QTRAP, MS_SCIEX_instrument_model}, + {MS_4700_Proteomics_Analyzer, MS_tandem_time_of_flight_instrument}, {MS_4700_Proteomics_Analyzer, MS_Applied_Biosystems_instrument_model}, + {MS_apex_IV, MS_fourier_transform_ion_cyclotron_resonance_instrument}, {MS_apex_IV, MS_Bruker_Daltonics_apex_series}, + {MS_apex_Q, MS_quadrupole_fourier_transform_ion_cyclotron_resonance_instrument}, {MS_apex_Q, MS_Bruker_Daltonics_apex_series}, + {MS_API_150EX, MS_quadrupole_instrument}, {MS_API_150EX, MS_SCIEX_instrument_model}, + {MS_API_150EX_Prep, MS_quadrupole_instrument}, {MS_API_150EX_Prep, MS_SCIEX_instrument_model}, + {MS_API_2000, MS_triple_quadrupole_instrument}, {MS_API_2000, MS_SCIEX_instrument_model}, + {MS_API_3000, MS_triple_quadrupole_instrument}, {MS_API_3000, MS_SCIEX_instrument_model}, + {MS_API_4000, MS_triple_quadrupole_instrument}, {MS_API_4000, MS_SCIEX_instrument_model}, + {MS_autoflex_II, MS_time_of_flight_instrument}, {MS_autoflex_II, MS_Bruker_Daltonics_flex_series}, + {MS_autoflex_TOF_TOF, MS_tandem_time_of_flight_instrument}, {MS_autoflex_TOF_TOF, MS_Bruker_Daltonics_flex_series}, + {MS_Auto_Spec_Ultima_NT, MS_magnetic_sector_instrument}, {MS_Auto_Spec_Ultima_NT, MS_Waters_instrument_model}, + {MS_BioTOF_II, MS_time_of_flight_instrument}, {MS_BioTOF_II, MS_Bruker_Daltonics_BioTOF_series}, + {MS_BioTOF_Q, MS_quadrupole_time_of_flight_instrument}, {MS_BioTOF_Q, MS_Bruker_Daltonics_BioTOF_series}, + {MS_DELTA_plusAdvantage, MS_magnetic_sector_instrument}, {MS_DELTA_plusAdvantage, MS_Thermo_Finnigan_instrument_model}, + {MS_DELTAplusXP, MS_magnetic_sector_instrument}, {MS_DELTAplusXP, MS_Thermo_Finnigan_instrument_model}, + {MS_esquire_4000, MS_ion_trap_instrument}, {MS_esquire_4000, MS_Bruker_Daltonics_esquire_series}, + {MS_esquire_6000, MS_ion_trap_instrument}, {MS_esquire_6000, MS_Bruker_Daltonics_esquire_series}, + {MS_explorer, MS_fourier_transform_ion_cyclotron_resonance_instrument}, {MS_explorer, MS_IonSpec_instrument_model}, + {MS_GCT, MS_time_of_flight_instrument}, {MS_GCT, MS_Waters_instrument_model}, + {MS_HCT, MS_ion_trap_instrument}, {MS_HCT, MS_Bruker_Daltonics_HCT_Series}, + {MS_HCTplus, MS_ion_trap_instrument}, {MS_HCTplus, MS_Bruker_Daltonics_HCT_Series}, + {MS_HiRes_ESI, MS_fourier_transform_ion_cyclotron_resonance_instrument}, {MS_HiRes_ESI, MS_IonSpec_instrument_model}, + {MS_HiRes_MALDI, MS_fourier_transform_ion_cyclotron_resonance_instrument}, {MS_HiRes_MALDI, MS_IonSpec_instrument_model}, + {MS_IsoPrime, MS_magnetic_sector_instrument}, {MS_IsoPrime, MS_Waters_instrument_model}, + {MS_IsoProbe, MS_magnetic_sector_instrument}, {MS_IsoProbe, MS_Waters_instrument_model}, + {MS_IsoProbe_T, MS_magnetic_sector_instrument}, {MS_IsoProbe_T, MS_Waters_instrument_model}, + {MS_LCQ_Advantage, MS_ion_trap_instrument}, {MS_LCQ_Advantage, MS_Thermo_Finnigan_instrument_model}, + {MS_LCQ_Classic, MS_ion_trap_instrument}, {MS_LCQ_Classic, MS_Thermo_Finnigan_instrument_model}, + {MS_LCQ_Deca_XP_Plus, MS_ion_trap_instrument}, {MS_LCQ_Deca_XP_Plus, MS_Thermo_Finnigan_instrument_model}, + {MS_M_LDI_L, MS_time_of_flight_instrument}, {MS_M_LDI_L, MS_Waters_instrument_model}, + {MS_M_LDI_LR, MS_time_of_flight_instrument}, {MS_M_LDI_LR, MS_Waters_instrument_model}, + {MS_MAT253, MS_magnetic_sector_instrument}, {MS_MAT253, MS_Finnigan_MAT_instrument_model}, + {MS_MAT900XP, MS_magnetic_sector_instrument}, {MS_MAT900XP, MS_Finnigan_MAT_instrument_model}, + {MS_MAT900XP_Trap, MS_magnetic_sector_ion_trap_instrument}, {MS_MAT900XP_Trap, MS_Finnigan_MAT_instrument_model}, + {MS_MAT95XP, MS_magnetic_sector_instrument}, {MS_MAT95XP, MS_Finnigan_MAT_instrument_model}, + {MS_MAT95XP_Trap, MS_magnetic_sector_ion_trap_instrument}, {MS_MAT95XP_Trap, MS_Finnigan_MAT_instrument_model}, + {MS_microflex, MS_time_of_flight_instrument}, {MS_microflex, MS_Bruker_Daltonics_flex_series}, + {MS_microTOF_LC, MS_time_of_flight_instrument}, {MS_microTOF_LC, MS_Bruker_Daltonics_micrOTOF_series}, + {MS_neptune, MS_magnetic_sector_instrument}, {MS_neptune, MS_Thermo_Finnigan_instrument_model}, {MS_NG_5400, MS_Waters_instrument_model}, + {MS_OMEGA, MS_fourier_transform_ion_cyclotron_resonance_instrument}, {MS_OMEGA, MS_IonSpec_instrument_model}, + {MS_OMEGA_2001, MS_fourier_transform_ion_cyclotron_resonance_instrument}, {MS_OMEGA_2001, MS_IonSpec_instrument_model}, + {MS_OmniFlex, MS_time_of_flight_instrument}, {MS_OmniFlex, MS_Bruker_Daltonics_flex_series}, {MS_Platform_ICP, MS_Waters_instrument_model}, + {MS_PolarisQ, MS_ion_trap_instrument}, {MS_PolarisQ, MS_Thermo_Finnigan_instrument_model}, {MS_proteomics_solution_1, MS_SCIEX_instrument_model}, + {MS_Q_TRAP, MS_triple_quadrupole_linear_ion_trap_instrument}, {MS_Q_TRAP, MS_SCIEX_instrument_model}, + {MS_Q_Tof_micro, MS_quadrupole_time_of_flight_instrument}, {MS_Q_Tof_micro, MS_Waters_instrument_model}, + {MS_Q_Tof_Ultima, MS_quadrupole_time_of_flight_instrument}, {MS_Q_Tof_Ultima, MS_Waters_instrument_model}, + {MS_QSTAR, MS_quadrupole_time_of_flight_instrument}, {MS_QSTAR, MS_SCIEX_instrument_model}, + {MS_quattro_micro, MS_triple_quadrupole_instrument}, {MS_quattro_micro, MS_Waters_instrument_model}, + {MS_Quattro_Ultima, MS_triple_quadrupole_instrument}, {MS_Quattro_Ultima, MS_Waters_instrument_model}, + {MS_Surveyor_MSQ, MS_quadrupole_instrument}, {MS_Surveyor_MSQ, MS_Thermo_Finnigan_instrument_model}, {MS_SymBiot_I, MS_SCIEX_instrument_model}, {MS_SymBiot_XVI, MS_SCIEX_instrument_model}, + {MS_TEMPUS_TOF, MS_time_of_flight_instrument}, {MS_TEMPUS_TOF, MS_Thermo_Finnigan_instrument_model}, + {MS_TRACE_DSQ, MS_quadrupole_instrument}, {MS_TRACE_DSQ, MS_Thermo_Finnigan_instrument_model}, + {MS_TRITON, MS_magnetic_sector_instrument}, {MS_TRITON, MS_Thermo_Finnigan_instrument_model}, + {MS_TSQ_Quantum, MS_triple_quadrupole_instrument}, {MS_TSQ_Quantum, MS_Thermo_Finnigan_instrument_model}, + {MS_ultima, MS_fourier_transform_ion_cyclotron_resonance_instrument}, {MS_ultima, MS_IonSpec_instrument_model}, + {MS_ultraflex, MS_time_of_flight_instrument}, {MS_ultraflex, MS_Bruker_Daltonics_flex_series}, + {MS_ultraflex_TOF_TOF, MS_tandem_time_of_flight_instrument}, {MS_ultraflex_TOF_TOF, MS_Bruker_Daltonics_flex_series}, + {MS_Voyager_DE_PRO, MS_time_of_flight_instrument}, {MS_Voyager_DE_PRO, MS_Applied_Biosystems_instrument_model}, + {MS_Voyager_DE_STR, MS_time_of_flight_instrument}, {MS_Voyager_DE_STR, MS_Applied_Biosystems_instrument_model}, {MS_selected_ion_monitoring, MS_mass_spectrometry_acquisition_method_aspect}, {MS_selected_ion_monitoring, MS_mass_spectrometry_acquisition_method}, @@ -6407,7 +6587,6 @@ CVIDPair relationsIsA_[] = {MS_glow_discharge_ionization, MS_ionization_type}, {MS_infrared_multiphoton_dissociation, MS_photodissociation}, {MS_ion_trap, MS_mass_analyzer_type}, - {MS_ion_trap, MS_instrument_class}, {MS_Negative_Ion_chemical_ionization, MS_ionization_type}, {MS_neutralization_reionization_mass_spectrometry, MS_ionization_type}, {MS_photoionization, MS_ionization_type}, @@ -6481,38 +6660,41 @@ CVIDPair relationsIsA_[] = {MS_low_energy_collision_induced_dissociation, MS_dissociation_method}, {MS_photodissociation, MS_dissociation_method}, {MS_fast_ion_bombardment, MS_ionization_type}, + {MS_LTQ, MS_ion_trap_instrument}, {MS_LTQ, MS_Thermo_Scientific_instrument_model}, + {MS_LTQ_FT, MS_ion_trap_fourier_transform_ion_cyclotron_resonance_instrument}, {MS_LTQ_FT, MS_Thermo_Scientific_instrument_model}, + {MS_LTQ_Orbitrap, MS_ion_trap_orbitrap_instrument}, {MS_LTQ_Orbitrap, MS_Thermo_Scientific_instrument_model}, + {MS_LXQ, MS_ion_trap_instrument}, {MS_LXQ, MS_Thermo_Scientific_instrument_model}, {MS_ion_selection_attribute, MS_object_attribute}, - {MS_1200_series_LC_MSD_SL, MS_ion_trap}, + {MS_1200_series_LC_MSD_SL, MS_ion_trap_instrument}, {MS_1200_series_LC_MSD_SL, MS_Agilent_instrument_model}, - {MS_6110_Quadrupole_LC_MS, MS_quadrupole}, + {MS_6110_Quadrupole_LC_MS, MS_quadrupole_instrument}, {MS_6110_Quadrupole_LC_MS, MS_Agilent_instrument_model}, - {MS_6120A_Quadrupole_LC_MS, MS_quadrupole}, + {MS_6120A_Quadrupole_LC_MS, MS_quadrupole_instrument}, {MS_6120A_Quadrupole_LC_MS, MS_Agilent_instrument_model}, - {MS_6130_Quadrupole_LC_MS, MS_quadrupole}, + {MS_6130_Quadrupole_LC_MS, MS_quadrupole_instrument}, {MS_6130_Quadrupole_LC_MS, MS_Agilent_instrument_model}, - {MS_6140_Quadrupole_LC_MS, MS_quadrupole}, + {MS_6140_Quadrupole_LC_MS, MS_quadrupole_instrument}, {MS_6140_Quadrupole_LC_MS, MS_Agilent_instrument_model}, - {MS_6210_Time_of_Flight_LC_MS, MS_time_of_flight}, + {MS_6210_Time_of_Flight_LC_MS, MS_time_of_flight_instrument}, {MS_6210_Time_of_Flight_LC_MS, MS_Agilent_instrument_model}, - {MS_6310_Ion_Trap_LC_MS, MS_ion_trap}, + {MS_6310_Ion_Trap_LC_MS, MS_ion_trap_instrument}, {MS_6310_Ion_Trap_LC_MS, MS_Agilent_instrument_model}, - {MS_6320_Ion_Trap_LC_MS, MS_ion_trap}, + {MS_6320_Ion_Trap_LC_MS, MS_ion_trap_instrument}, {MS_6320_Ion_Trap_LC_MS, MS_Agilent_instrument_model}, - {MS_6330_Ion_Trap_LC_MS, MS_ion_trap}, + {MS_6330_Ion_Trap_LC_MS, MS_ion_trap_instrument}, {MS_6330_Ion_Trap_LC_MS, MS_Agilent_instrument_model}, - {MS_6340_Ion_Trap_LC_MS, MS_ion_trap}, + {MS_6340_Ion_Trap_LC_MS, MS_ion_trap_instrument}, {MS_6340_Ion_Trap_LC_MS, MS_Agilent_instrument_model}, - {MS_6410_Triple_Quadrupole_LC_MS, MS_triple_quadrupole}, + {MS_6410_Triple_Quadrupole_LC_MS, MS_triple_quadrupole_instrument}, {MS_6410_Triple_Quadrupole_LC_MS, MS_Agilent_instrument_model}, - {MS_1200_series_LC_MSD_VL, MS_ion_trap}, + {MS_1200_series_LC_MSD_VL, MS_ion_trap_instrument}, {MS_1200_series_LC_MSD_VL, MS_Agilent_instrument_model}, {MS_Thermo_Fisher_Scientific_instrument_model, MS_instrument_model}, {MS_orbitrap, MS_mass_analyzer_type}, - {MS_orbitrap, MS_instrument_class}, {MS_nanospray_inlet, MS_electrospray_inlet}, {MS_source_potential, MS_source_attribute}, {MS_ion_optics_attribute, MS_ion_optics}, @@ -6552,6 +6734,7 @@ CVIDPair relationsIsA_[] = {MS_instrument_serial_number, MS_instrument_attribute}, {MS_file_format_conversion, MS_data_transformation}, {MS_Xcalibur, MS_Thermo_Finnigan_software}, + {MS_Xcalibur, MS_Thermo_Scientific_software}, {MS_Xcalibur, MS_acquisition_software}, {MS_Xcalibur, MS_analysis_software}, {MS_Xcalibur, MS_data_processing_software}, @@ -6593,10 +6776,15 @@ CVIDPair relationsIsA_[] = {MS_Analyst, MS_analysis_software}, {MS_Analyst, MS_data_processing_software}, {MS_Trapper, MS_data_processing_software}, + {MS_LCQ_Deca, MS_ion_trap_instrument}, {MS_LCQ_Deca, MS_Thermo_Finnigan_instrument_model}, + {MS_LTQ_Orbitrap_Discovery, MS_ion_trap_orbitrap_instrument}, {MS_LTQ_Orbitrap_Discovery, MS_Thermo_Scientific_instrument_model}, + {MS_LTQ_Orbitrap_XL, MS_ion_trap_orbitrap_instrument}, {MS_LTQ_Orbitrap_XL, MS_Thermo_Scientific_instrument_model}, + {MS_LTQ_FT_Ultra, MS_ion_trap_fourier_transform_ion_cyclotron_resonance_instrument}, {MS_LTQ_FT_Ultra, MS_Thermo_Scientific_instrument_model}, + {MS_GC_Quantum, MS_triple_quadrupole_instrument}, {MS_GC_Quantum, MS_Thermo_Finnigan_instrument_model}, {MS_mass_spectrometer_file_format, MS_file_format}, {MS_ABI_WIFF_format, MS_mass_spectrometer_file_format}, @@ -6613,6 +6801,7 @@ CVIDPair relationsIsA_[] = {MS_mean_of_spectra, MS_spectra_combination}, {MS_no_compression, MS_binary_data_compression_type}, {MS_source_data_file, MS_spectrum_attribute}, + {MS_LCQ_Fleet, MS_ion_trap_instrument}, {MS_LCQ_Fleet, MS_Thermo_Finnigan_instrument_model}, {MS_MS1_spectrum, MS_mass_spectrum}, {MS_MSn_spectrum, MS_mass_spectrum}, @@ -6641,14 +6830,23 @@ CVIDPair relationsIsA_[] = {MS_ProteinLynx_Global_Server, MS_data_processing_software}, {MS_Shimadzu_MALDI_TOF_instrument_model, MS_Shimadzu_instrument_model}, {MS_Shimadzu_Scientific_Instruments_instrument_model, MS_Shimadzu_instrument_model}, + {MS_LCMS_IT_TOF, MS_ion_trap_time_of_flight_instrument}, {MS_LCMS_IT_TOF, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_LCMS_2010EV, MS_quadrupole_instrument}, {MS_LCMS_2010EV, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_LCMS_2010A, MS_quadrupole_instrument}, {MS_LCMS_2010A, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_AXIMA_CFR_MALDI_TOF, MS_time_of_flight_instrument}, {MS_AXIMA_CFR_MALDI_TOF, MS_Shimadzu_MALDI_TOF_instrument_model}, + {MS_AXIMA_QIT, MS_ion_trap_time_of_flight_instrument}, {MS_AXIMA_QIT, MS_Shimadzu_MALDI_TOF_instrument_model}, + {MS_AXIMA_CFR_plus, MS_time_of_flight_instrument}, {MS_AXIMA_CFR_plus, MS_Shimadzu_MALDI_TOF_instrument_model}, + {MS_AXIMA_Performance_MALDI_TOF_TOF, MS_tandem_time_of_flight_instrument}, {MS_AXIMA_Performance_MALDI_TOF_TOF, MS_Shimadzu_MALDI_TOF_instrument_model}, + {MS_AXIMA_Confidence_MALDI_TOF, MS_time_of_flight_instrument}, {MS_AXIMA_Confidence_MALDI_TOF, MS_Shimadzu_MALDI_TOF_instrument_model}, + {MS_AXIMA_Assurance_Linear_MALDI_TOF, MS_time_of_flight_instrument}, {MS_AXIMA_Assurance_Linear_MALDI_TOF, MS_Shimadzu_MALDI_TOF_instrument_model}, {MS_DTA_format, MS_mass_spectrometer_file_format}, {MS_ProteinLynx_Global_Server_mass_spectrum_XML_format, MS_mass_spectrometer_file_format}, @@ -6670,39 +6868,65 @@ CVIDPair relationsIsA_[] = {MS_basepeak_chromatogram, MS_ion_current_chromatogram}, {MS_low_intensity_threshold, MS_data_processing_parameter}, {MS_high_intensity_threshold, MS_data_processing_parameter}, + {MS_Q_Tof_Premier, MS_quadrupole_time_of_flight_instrument}, {MS_Q_Tof_Premier, MS_Waters_instrument_model}, {MS_possible_charge_state, MS_ion_selection_attribute}, + {MS_DSQ, MS_quadrupole_instrument}, {MS_DSQ, MS_Thermo_Finnigan_instrument_model}, + {MS_ITQ_700, MS_ion_trap_instrument}, {MS_ITQ_700, MS_Thermo_Scientific_instrument_model}, + {MS_ITQ_900, MS_ion_trap_instrument}, {MS_ITQ_900, MS_Thermo_Scientific_instrument_model}, + {MS_ITQ_1100, MS_ion_trap_instrument}, {MS_ITQ_1100, MS_Thermo_Scientific_instrument_model}, + {MS_LTQ_XL_ETD, MS_ion_trap_instrument}, {MS_LTQ_XL_ETD, MS_Thermo_Scientific_instrument_model}, + {MS_LTQ_Orbitrap_XL_ETD, MS_ion_trap_orbitrap_instrument}, {MS_LTQ_Orbitrap_XL_ETD, MS_Thermo_Scientific_instrument_model}, + {MS_DFS, MS_magnetic_sector_instrument}, {MS_DFS, MS_Thermo_Scientific_instrument_model}, + {MS_DSQ_II, MS_quadrupole_instrument}, {MS_DSQ_II, MS_Thermo_Scientific_instrument_model}, + {MS_MALDI_LTQ_XL, MS_ion_trap_instrument}, {MS_MALDI_LTQ_XL, MS_Thermo_Scientific_instrument_model}, + {MS_MALDI_LTQ_Orbitrap, MS_ion_trap_orbitrap_instrument}, {MS_MALDI_LTQ_Orbitrap, MS_Thermo_Scientific_instrument_model}, + {MS_TSQ_Quantum_Access, MS_triple_quadrupole_instrument}, {MS_TSQ_Quantum_Access, MS_Thermo_Scientific_instrument_model}, + {MS_Element_XR, MS_magnetic_sector_instrument}, {MS_Element_XR, MS_Thermo_Scientific_instrument_model}, + {MS_Element_2, MS_magnetic_sector_instrument}, {MS_Element_2, MS_Thermo_Scientific_instrument_model}, + {MS_Element_GD, MS_magnetic_sector_instrument}, {MS_Element_GD, MS_Thermo_Scientific_instrument_model}, {MS_GC_IsoLink, MS_Thermo_Scientific_instrument_model}, + {MS_Exactive, MS_orbitrap_instrument}, {MS_Exactive, MS_Thermo_Scientific_instrument_model}, {MS_Proteome_Discoverer, MS_Thermo_Finnigan_software}, + {MS_Proteome_Discoverer, MS_Thermo_Scientific_software}, {MS_Proteome_Discoverer, MS_analysis_software}, {MS_Proteome_Discoverer, MS_data_processing_software}, + {MS_3200_QTRAP, MS_triple_quadrupole_linear_ion_trap_instrument}, {MS_3200_QTRAP, MS_SCIEX_instrument_model}, + {MS_4800_Plus_MALDI_TOF_TOF, MS_tandem_time_of_flight_instrument}, {MS_4800_Plus_MALDI_TOF_TOF, MS_SCIEX_instrument_model}, + {MS_API_3200, MS_triple_quadrupole_instrument}, {MS_API_3200, MS_SCIEX_instrument_model}, + {MS_API_5000, MS_triple_quadrupole_instrument}, {MS_API_5000, MS_SCIEX_instrument_model}, + {MS_QSTAR_Elite, MS_quadrupole_time_of_flight_instrument}, {MS_QSTAR_Elite, MS_SCIEX_instrument_model}, + {MS_QSTAR_Pulsar, MS_quadrupole_time_of_flight_instrument}, {MS_QSTAR_Pulsar, MS_SCIEX_instrument_model}, + {MS_QSTAR_XL, MS_quadrupole_time_of_flight_instrument}, {MS_QSTAR_XL, MS_SCIEX_instrument_model}, + {MS_4800_Proteomics_Analyzer, MS_tandem_time_of_flight_instrument}, {MS_4800_Proteomics_Analyzer, MS_Applied_Biosystems_instrument_model}, {MS_4000_Series_Explorer_Software, MS_SCIEX_software}, {MS_4000_Series_Explorer_Software, MS_acquisition_software}, {MS_4000_Series_Explorer_Software, MS_analysis_software}, {MS_4000_Series_Explorer_Software, MS_data_processing_software}, + {MS_Xevo_MRT_MS, MS_quadrupole_time_of_flight_instrument}, {MS_Xevo_MRT_MS, MS_Waters_instrument_model}, {MS_GPS_Explorer, MS_SCIEX_software}, {MS_GPS_Explorer, MS_acquisition_software}, @@ -6743,11 +6967,11 @@ CVIDPair relationsIsA_[] = {MS_MultiQuant, MS_SCIEX_software}, {MS_MultiQuant, MS_analysis_software}, {MS_MultiQuant, MS_data_processing_software}, - {MS_6220_Time_of_Flight_LC_MS, MS_time_of_flight}, + {MS_6220_Time_of_Flight_LC_MS, MS_time_of_flight_instrument}, {MS_6220_Time_of_Flight_LC_MS, MS_Agilent_instrument_model}, - {MS_6510_Quadrupole_Time_of_Flight_LC_MS, MS_quadrupole_time_of_flight}, + {MS_6510_Quadrupole_Time_of_Flight_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_6510_Quadrupole_Time_of_Flight_LC_MS, MS_Agilent_instrument_model}, - {MS_6520A_Quadrupole_Time_of_Flight_LC_MS, MS_quadrupole_time_of_flight}, + {MS_6520A_Quadrupole_Time_of_Flight_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_6520A_Quadrupole_Time_of_Flight_LC_MS, MS_Agilent_instrument_model}, {MS_MassHunter_Data_Acquisition, MS_Agilent_software}, {MS_MassHunter_Data_Acquisition, MS_acquisition_software}, @@ -6787,16 +7011,26 @@ CVIDPair relationsIsA_[] = {MS_Bruker_software, MS_software}, {MS_Thermo_Finnigan_software, MS_software}, {MS_Waters_software, MS_software}, + {MS_apex_ultra, MS_quadrupole_fourier_transform_ion_cyclotron_resonance_instrument}, {MS_apex_ultra, MS_Bruker_Daltonics_apex_series}, + {MS_autoflex_III_smartbeam, MS_time_of_flight_instrument}, {MS_autoflex_III_smartbeam, MS_Bruker_Daltonics_flex_series}, {MS_Bruker_Daltonics_HCT_Series, MS_Bruker_Daltonics_instrument_model}, + {MS_HCTultra, MS_ion_trap_instrument}, {MS_HCTultra, MS_Bruker_Daltonics_HCT_Series}, + {MS_HCTultra_PTM, MS_ion_trap_instrument}, {MS_HCTultra_PTM, MS_Bruker_Daltonics_HCT_Series}, + {MS_HCTultra_ETD_II, MS_ion_trap_instrument}, {MS_HCTultra_ETD_II, MS_Bruker_Daltonics_HCT_Series}, + {MS_microflex_LT, MS_time_of_flight_instrument}, {MS_microflex_LT, MS_Bruker_Daltonics_flex_series}, + {MS_micrOTOF, MS_time_of_flight_instrument}, {MS_micrOTOF, MS_Bruker_Daltonics_micrOTOF_series}, + {MS_micrOTOF_Q, MS_quadrupole_time_of_flight_instrument}, {MS_micrOTOF_Q, MS_Bruker_Daltonics_micrOTOF_series}, + {MS_micrOTOF_Q_II, MS_quadrupole_time_of_flight_instrument}, {MS_micrOTOF_Q_II, MS_Bruker_Daltonics_micrOTOF_series}, + {MS_ultraflex_III_TOF_TOF, MS_tandem_time_of_flight_instrument}, {MS_ultraflex_III_TOF_TOF, MS_Bruker_Daltonics_flex_series}, {MS_apexControl, MS_Bruker_software}, {MS_apexControl, MS_acquisition_software}, @@ -6868,14 +7102,19 @@ CVIDPair relationsIsA_[] = {MS_Conversion_to_dta, MS_file_format_conversion}, {MS_Bioworks_SRF_format, MS_mass_spectrometer_file_format}, {MS_Bioworks_SRF_format, MS_intermediate_analysis_format}, + {MS_TSQ_Quantum_Ultra_AM, MS_triple_quadrupole_instrument}, {MS_TSQ_Quantum_Ultra_AM, MS_Thermo_Scientific_instrument_model}, {MS_selected_ion_m_z, MS_ion_selection_attribute}, {MS_retention_time_alignment, MS_data_processing_action}, {MS_high_intensity_data_point_removal, MS_data_filtering}, {MS_completion_time, MS_data_processing_parameter}, + {MS_SSQ_7000, MS_quadrupole_instrument}, {MS_SSQ_7000, MS_Finnigan_MAT_instrument_model}, + {MS_TSQ_7000, MS_triple_quadrupole_instrument}, {MS_TSQ_7000, MS_Finnigan_MAT_instrument_model}, + {MS_TSQ, MS_triple_quadrupole_instrument}, {MS_TSQ, MS_Finnigan_MAT_instrument_model}, + {MS_TSQ_Quantum_Ultra, MS_triple_quadrupole_instrument}, {MS_TSQ_Quantum_Ultra, MS_Thermo_Scientific_instrument_model}, {MS_TOPP_software, MS_analysis_software}, {MS_TOPP_software, MS_data_processing_software}, @@ -6983,8 +7222,11 @@ CVIDPair relationsIsA_[] = {MS_solid_state_laser, MS_laser_type}, {MS_dye_laser, MS_laser_type}, {MS_free_electron_laser, MS_laser_type}, + {MS_LTQ_XL, MS_ion_trap_instrument}, {MS_LTQ_XL, MS_Thermo_Scientific_instrument_model}, + {MS_LTQ_Velos, MS_ion_trap_instrument}, {MS_LTQ_Velos, MS_Thermo_Scientific_instrument_model}, + {MS_LTQ_Velos_ETD, MS_ion_trap_instrument}, {MS_LTQ_Velos_ETD, MS_Thermo_Scientific_instrument_model}, {MS_run_attribute, MS_object_attribute}, {MS_fraction_identifier, MS_run_attribute}, @@ -7055,15 +7297,17 @@ CVIDPair relationsIsA_[] = {MS_calibration_spectrum, MS_spectrum_type}, {MS_Shimadzu_Biotech_nativeID_format, MS_native_spectrum_identifier_format}, {MS_Shimadzu_Biotech_database_entity, MS_mass_spectrometer_file_format}, + {MS_QTRAP_5500, MS_triple_quadrupole_linear_ion_trap_instrument}, {MS_QTRAP_5500, MS_SCIEX_instrument_model}, + {MS_TripleTOF_5600, MS_quadrupole_time_of_flight_instrument}, {MS_TripleTOF_5600, MS_SCIEX_instrument_model}, {MS_protein_modifications, MS_protein_attribute}, {MS_gene_name, MS_protein_attribute}, - {MS_6470A_Triple_Quadrupole_LC_MS, MS_triple_quadrupole}, + {MS_6470A_Triple_Quadrupole_LC_MS, MS_triple_quadrupole_instrument}, {MS_6470A_Triple_Quadrupole_LC_MS, MS_Agilent_instrument_model}, - {MS_6470B_Triple_Quadrupole_LC_MS, MS_triple_quadrupole}, + {MS_6470B_Triple_Quadrupole_LC_MS, MS_triple_quadrupole_instrument}, {MS_6470B_Triple_Quadrupole_LC_MS, MS_Agilent_instrument_model}, - {MS_6495C_Triple_Quadrupole_LC_MS, MS_triple_quadrupole}, + {MS_6495C_Triple_Quadrupole_LC_MS, MS_triple_quadrupole_instrument}, {MS_6495C_Triple_Quadrupole_LC_MS, MS_Agilent_instrument_model}, {MS_SEQUEST_CleavesAt, MS_SEQUEST_input_parameter}, {MS_SEQUEST_ViewCV, MS_SEQUEST_input_parameter}, @@ -7505,6 +7749,7 @@ CVIDPair relationsIsA_[] = {MS_null_terminated_ASCII_string, MS_binary_data_type}, {MS_SCIEX_TOF_TOF_nativeID_format, MS_native_spectrum_identifier_format}, {MS_SCIEX_TOF_TOF_database, MS_mass_spectrometer_file_format}, + {MS_5800_TOF_TOF, MS_tandem_time_of_flight_instrument}, {MS_5800_TOF_TOF, MS_SCIEX_instrument_model}, {MS_SCIEX_TOF_TOF_Series_Explorer_Software, MS_SCIEX_software}, {MS_SCIEX_TOF_TOF_Series_Explorer_Software, MS_acquisition_software}, @@ -7538,6 +7783,7 @@ CVIDPair relationsIsA_[] = {MS_ProteinExtractor_Score, MS_search_engine_specific_score_for_proteins}, {MS_Agilent_MassHunter_nativeID_format, MS_native_spectrum_identifier_format}, {MS_Agilent_MassHunter_format, MS_mass_spectrometer_file_format}, + {MS_TSQ_Vantage, MS_triple_quadrupole_instrument}, {MS_TSQ_Vantage, MS_Thermo_Scientific_instrument_model}, {MS_Sequence_database_filter_types, MS_database_filtering}, {MS_Sequence_database_filters, MS_database_filtering}, @@ -7568,22 +7814,36 @@ CVIDPair relationsIsA_[] = {MS_Bruker_Daltonics_flex_series, MS_Bruker_Daltonics_instrument_model}, {MS_Bruker_Daltonics_BioTOF_series, MS_Bruker_Daltonics_instrument_model}, {MS_Bruker_Daltonics_micrOTOF_series, MS_Bruker_Daltonics_instrument_model}, + {MS_BioTOF, MS_time_of_flight_instrument}, {MS_BioTOF, MS_Bruker_Daltonics_BioTOF_series}, + {MS_BioTOF_III, MS_time_of_flight_instrument}, {MS_BioTOF_III, MS_Bruker_Daltonics_BioTOF_series}, + {MS_UltroTOF_Q, MS_quadrupole_time_of_flight_instrument}, {MS_UltroTOF_Q, MS_Bruker_Daltonics_BioTOF_series}, + {MS_micrOTOF_II, MS_time_of_flight_instrument}, {MS_micrOTOF_II, MS_Bruker_Daltonics_micrOTOF_series}, + {MS_maXis, MS_quadrupole_time_of_flight_instrument}, {MS_maXis, MS_Bruker_Daltonics_maXis_series}, + {MS_amaZon_ETD, MS_ion_trap_instrument}, {MS_amaZon_ETD, MS_Bruker_Daltonics_amaZon_series}, + {MS_microflex_LRF, MS_time_of_flight_instrument}, {MS_microflex_LRF, MS_Bruker_Daltonics_flex_series}, + {MS_ultrafleXtreme, MS_tandem_time_of_flight_instrument}, {MS_ultrafleXtreme, MS_Bruker_Daltonics_flex_series}, {MS_Bruker_Daltonics_amaZon_series, MS_Bruker_Daltonics_instrument_model}, + {MS_amaZon_X, MS_ion_trap_instrument}, {MS_amaZon_X, MS_Bruker_Daltonics_amaZon_series}, {MS_Bruker_Daltonics_maXis_series, MS_Bruker_Daltonics_instrument_model}, {MS_Bruker_Daltonics_solarix_series, MS_Bruker_Daltonics_instrument_model}, + {MS_solariX, MS_quadrupole_fourier_transform_ion_cyclotron_resonance_instrument}, {MS_solariX, MS_Bruker_Daltonics_solarix_series}, + {MS_microflex_II, MS_time_of_flight_instrument}, {MS_microflex_II, MS_Bruker_Daltonics_flex_series}, + {MS_autoflex_II_TOF_TOF, MS_tandem_time_of_flight_instrument}, {MS_autoflex_II_TOF_TOF, MS_Bruker_Daltonics_flex_series}, + {MS_autoflex_III_TOF_TOF_smartbeam, MS_tandem_time_of_flight_instrument}, {MS_autoflex_III_TOF_TOF_smartbeam, MS_Bruker_Daltonics_flex_series}, + {MS_autoflex, MS_time_of_flight_instrument}, {MS_autoflex, MS_Bruker_Daltonics_flex_series}, {MS_Bruker_Daltonics_apex_series, MS_Bruker_Daltonics_instrument_model}, {MS_Shimadzu_Corporation_software, MS_software}, @@ -7778,6 +8038,7 @@ CVIDPair relationsIsA_[] = {MS_ProteomeDiscoverer_Source_Files_old_OBSOLETE, MS_ProteomeDiscoverer_input_parameter}, {MS_ProteomeDiscoverer_WinCyg_reference_database, MS_ProteomeDiscoverer_input_parameter}, {MS_ProteomeDiscoverer_WinCyg_source_files, MS_ProteomeDiscoverer_input_parameter}, + {MS_LTQ_Orbitrap_Velos, MS_ion_trap_orbitrap_instrument}, {MS_LTQ_Orbitrap_Velos, MS_Thermo_Scientific_instrument_model}, {MS_ProteomeDiscoverer_Mascot_Weight_of_A_Ions, MS_ProteomeDiscoverer_input_parameter}, {MS_ProteomeDiscoverer_Mascot_Weight_of_B_Ions, MS_ProteomeDiscoverer_input_parameter}, @@ -7818,29 +8079,51 @@ CVIDPair relationsIsA_[] = {MS_nanoACQUITY_UPLC_with_HDX_Technology, MS_nano_flow_liquid_chromatography_system}, {MS_TRIZAIC_UPLC_nanoTile, MS_Waters_liquid_chromatography_system_model}, {MS_TRIZAIC_UPLC_nanoTile, MS_ultra_performance_liquid_chromatography_system}, + {MS_GCT_Premier, MS_time_of_flight_instrument}, {MS_GCT_Premier, MS_Waters_instrument_model}, + {MS_MALDI_Synapt_G2_HDMS, MS_quadrupole_ion_mobility_time_of_flight_instrument}, {MS_MALDI_Synapt_G2_HDMS, MS_Waters_instrument_model}, + {MS_MALDI_Synapt_G2_MS, MS_quadrupole_time_of_flight_instrument}, {MS_MALDI_Synapt_G2_MS, MS_Waters_instrument_model}, + {MS_MALDI_Synapt_G2_S_HDMS, MS_quadrupole_ion_mobility_time_of_flight_instrument}, {MS_MALDI_Synapt_G2_S_HDMS, MS_Waters_instrument_model}, + {MS_MALDI_Synapt_G2_S_MS, MS_quadrupole_time_of_flight_instrument}, {MS_MALDI_Synapt_G2_S_MS, MS_Waters_instrument_model}, + {MS_MALDI_Synapt_HDMS, MS_quadrupole_ion_mobility_time_of_flight_instrument}, {MS_MALDI_Synapt_HDMS, MS_Waters_instrument_model}, + {MS_MALDI_Synapt_MS, MS_quadrupole_time_of_flight_instrument}, {MS_MALDI_Synapt_MS, MS_Waters_instrument_model}, + {MS_Synapt_G2_HDMS, MS_quadrupole_ion_mobility_time_of_flight_instrument}, {MS_Synapt_G2_HDMS, MS_Waters_instrument_model}, + {MS_Synapt_G2_MS, MS_quadrupole_time_of_flight_instrument}, {MS_Synapt_G2_MS, MS_Waters_instrument_model}, + {MS_Synapt_G2_S_HDMS, MS_quadrupole_ion_mobility_time_of_flight_instrument}, {MS_Synapt_G2_S_HDMS, MS_Waters_instrument_model}, + {MS_Synapt_G2_S_MS, MS_quadrupole_time_of_flight_instrument}, {MS_Synapt_G2_S_MS, MS_Waters_instrument_model}, + {MS_Synapt_HDMS, MS_quadrupole_ion_mobility_time_of_flight_instrument}, {MS_Synapt_HDMS, MS_Waters_instrument_model}, + {MS_Synapt_MS, MS_quadrupole_time_of_flight_instrument}, {MS_Synapt_MS, MS_Waters_instrument_model}, + {MS_Xevo_G2_Q_Tof, MS_quadrupole_time_of_flight_instrument}, {MS_Xevo_G2_Q_Tof, MS_Waters_instrument_model}, + {MS_Xevo_G2_Tof, MS_time_of_flight_instrument}, {MS_Xevo_G2_Tof, MS_Waters_instrument_model}, + {MS_Xevo_Q_Tof, MS_quadrupole_time_of_flight_instrument}, {MS_Xevo_Q_Tof, MS_Waters_instrument_model}, + {MS_3100, MS_quadrupole_instrument}, {MS_3100, MS_Waters_instrument_model}, + {MS_Acquity_SQD, MS_quadrupole_instrument}, {MS_Acquity_SQD, MS_Waters_instrument_model}, + {MS_Acquity_TQD, MS_triple_quadrupole_instrument}, {MS_Acquity_TQD, MS_Waters_instrument_model}, + {MS_Quattro_micro_GC, MS_triple_quadrupole_instrument}, {MS_Quattro_micro_GC, MS_Waters_instrument_model}, {MS_Xevo_TQ_MS, MS_Waters_instrument_model}, - {MS_Xevo_TQ_MS, MS_triple_quadrupole}, + {MS_Xevo_TQ_MS, MS_triple_quadrupole_instrument}, + {MS_Xevo_TQD, MS_triple_quadrupole_instrument}, {MS_Xevo_TQD, MS_Waters_instrument_model}, + {MS_Xevo_TQ_S, MS_triple_quadrupole_instrument}, {MS_Xevo_TQ_S, MS_Waters_instrument_model}, {MS_Mascot_PreferredTaxonomy, MS_Mascot_input_parameter}, {MS_Empower, MS_Waters_software}, @@ -7855,9 +8138,16 @@ CVIDPair relationsIsA_[] = {MS_ChromaTOF_software, MS_data_processing_software}, {MS_ChromaTOF_software, MS_LECO_software}, {MS_LECO_instrument_model, MS_instrument_model}, + {MS_Pegasus_HRT, MS_time_of_flight_instrument}, + {MS_Pegasus_HRT, MS_gas_chromatography_mass_spectrometry_system}, {MS_Pegasus_HRT, MS_LECO_instrument_model}, + {MS_Citius_HRT, MS_time_of_flight_instrument}, {MS_Citius_HRT, MS_LECO_instrument_model}, + {MS_Pegasus, MS_time_of_flight_instrument}, + {MS_Pegasus, MS_gas_chromatography_mass_spectrometry_system}, {MS_Pegasus, MS_LECO_instrument_model}, + {MS_TruTOF, MS_time_of_flight_instrument}, + {MS_TruTOF, MS_gas_chromatography_mass_spectrometry_system}, {MS_TruTOF, MS_LECO_instrument_model}, {MS_quantification_datatype, MS_quantification_information}, {MS_quantification_object_attribute, MS_quantification_information}, @@ -7968,11 +8258,16 @@ CVIDPair relationsIsA_[] = {MS_emPAI_value, MS_protein_level_quantification_datatype}, {MS_APEX_value, MS_protein_level_quantification_datatype}, {MS_retention_time_window_width, MS_retention_time_window_attribute}, + {MS_ISQ, MS_quadrupole_instrument}, {MS_ISQ, MS_Thermo_Scientific_instrument_model}, + {MS_Velos_Plus, MS_ion_trap_instrument}, {MS_Velos_Plus, MS_Thermo_Scientific_instrument_model}, + {MS_Orbitrap_Elite, MS_ion_trap_orbitrap_instrument}, {MS_Orbitrap_Elite, MS_Thermo_Scientific_instrument_model}, + {MS_Q_Exactive, MS_quadrupole_orbitrap_instrument}, {MS_Q_Exactive, MS_Thermo_Scientific_instrument_model}, {MS_PinPoint, MS_Thermo_Finnigan_software}, + {MS_PinPoint, MS_Thermo_Scientific_software}, {MS_PinPoint, MS_analysis_software}, {MS_PinPoint, MS_data_processing_software}, {MS_S_lens_voltage, MS_source_attribute}, @@ -7997,6 +8292,8 @@ CVIDPair relationsIsA_[] = {MS_static_supply_electrospray, MS_electrospray_supply_type}, {MS_fed_supply_electrospray, MS_electrospray_supply_type}, {MS_Collision_cell_exit_potential, MS_precursor_activation_attribute}, + {MS_Pegasus_4D, MS_time_of_flight_instrument}, + {MS_Pegasus_4D, MS_gas_chromatography_mass_spectrometry_system}, {MS_Pegasus_4D, MS_LECO_instrument_model}, {MS_PEAKS_Studio, MS_quantitation_software_name}, {MS_PEAKS_Studio, MS_analysis_software}, @@ -8135,6 +8432,7 @@ CVIDPair relationsIsA_[] = {MS_quantification_file_format, MS_file_format}, {MS_mzQuantML_format, MS_quantification_file_format}, {MS_PAnalyzer, MS_analysis_software}, + {MS_impact, MS_quadrupole_time_of_flight_instrument}, {MS_impact, MS_Bruker_Daltonics_micrOTOF_series}, {MS_ProteomeDiscoverer_1__Static_Modification_OBSOLETE, MS_ProteomeDiscoverer_input_parameter}, {MS_ProteomeDiscoverer_2__Static_Modification_OBSOLETE, MS_ProteomeDiscoverer_input_parameter}, @@ -8336,12 +8634,20 @@ CVIDPair relationsIsA_[] = {MS_liquid_chromatography_separation, MS_chromatography_separation}, {MS_gas_chromatography_separation, MS_chromatography_separation}, {MS_detector_potential, MS_detector_attribute}, + {MS_SQ_Detector_2, MS_quadrupole_instrument}, {MS_SQ_Detector_2, MS_Waters_instrument_model}, + {MS_Xevo_G2_S_Tof, MS_time_of_flight_instrument}, {MS_Xevo_G2_S_Tof, MS_Waters_instrument_model}, + {MS_Xevo_G2_S_QTof, MS_quadrupole_time_of_flight_instrument}, {MS_Xevo_G2_S_QTof, MS_Waters_instrument_model}, + {MS_AutoSpec_Premier, MS_magnetic_sector_instrument}, {MS_AutoSpec_Premier, MS_Waters_instrument_model}, + {MS_Pegasus_III, MS_time_of_flight_instrument}, + {MS_Pegasus_III, MS_gas_chromatography_mass_spectrometry_system}, {MS_Pegasus_III, MS_LECO_instrument_model}, + {MS_maXis_4G, MS_quadrupole_time_of_flight_instrument}, {MS_maXis_4G, MS_Bruker_Daltonics_maXis_series}, + {MS_compact, MS_quadrupole_time_of_flight_instrument}, {MS_compact, MS_Bruker_Daltonics_micrOTOF_series}, {MS_SRM_feature_level_quantitation, MS_SRM_quantitation_analysis}, {MS_SRM_peptide_level_quantitation, MS_SRM_quantitation_analysis}, @@ -8357,12 +8663,19 @@ CVIDPair relationsIsA_[] = {MS_PTMProphet, MS_Trans_Proteomic_Pipeline_software}, {MS_Bruker_Daltonics_SCION_series, MS_Bruker_Daltonics_instrument_model}, {MS_Bruker_Daltonics_EVOQ_series, MS_Bruker_Daltonics_instrument_model}, + {MS_SCION_SQ, MS_quadrupole_instrument}, {MS_SCION_SQ, MS_Bruker_Daltonics_SCION_series}, + {MS_SCION_TQ, MS_triple_quadrupole_instrument}, {MS_SCION_TQ, MS_Bruker_Daltonics_SCION_series}, + {MS_EVOQ_Elite, MS_triple_quadrupole_instrument}, {MS_EVOQ_Elite, MS_Bruker_Daltonics_EVOQ_series}, + {MS_EVOQ_Qube, MS_triple_quadrupole_instrument}, {MS_EVOQ_Qube, MS_Bruker_Daltonics_EVOQ_series}, + {MS_micrOTOF_Q_III, MS_quadrupole_time_of_flight_instrument}, {MS_micrOTOF_Q_III, MS_Bruker_Daltonics_micrOTOF_series}, + {MS_amaZon_Speed_ETD, MS_ion_trap_instrument}, {MS_amaZon_Speed_ETD, MS_Bruker_Daltonics_amaZon_series}, + {MS_amaZon_Speed, MS_ion_trap_instrument}, {MS_amaZon_Speed, MS_Bruker_Daltonics_amaZon_series}, {MS_Bruker_Container_format, MS_mass_spectrometer_file_format}, {MS_Bruker_Container_nativeID_format, MS_native_spectrum_identifier_format}, @@ -8451,6 +8764,7 @@ CVIDPair relationsIsA_[] = {MS_MALDI_Solutions_LC_MALDI, MS_analysis_software}, {MS_MALDI_Solutions_LC_MALDI, MS_data_processing_software}, {MS_MALDI_Solutions_LC_MALDI, MS_Shimadzu_Corporation_software}, + {MS_Shimadzu_MALDI_7090, MS_tandem_time_of_flight_instrument}, {MS_Shimadzu_MALDI_7090, MS_Shimadzu_MALDI_TOF_instrument_model}, {MS_SCiLS_software, MS_software}, {MS_SCiLS_Lab, MS_SCiLS_software}, @@ -8491,9 +8805,13 @@ CVIDPair relationsIsA_[] = {MS_product_background, MS_quantification_datatype}, {MS_postprocessing_software, MS_data_processing_software}, {MS_protein_group_passes_threshold, MS_protein_group_level_identification_attribute}, + {MS_Orbitrap_Fusion, MS_quadrupole_ion_trap_orbitrap_instrument}, {MS_Orbitrap_Fusion, MS_Thermo_Scientific_instrument_model}, + {MS_Orbitrap_Fusion_ETD, MS_quadrupole_ion_trap_orbitrap_instrument}, {MS_Orbitrap_Fusion_ETD, MS_Thermo_Scientific_instrument_model}, + {MS_TSQ_Quantiva, MS_triple_quadrupole_instrument}, {MS_TSQ_Quantiva, MS_Thermo_Scientific_instrument_model}, + {MS_TSQ_Endura, MS_triple_quadrupole_instrument}, {MS_TSQ_Endura, MS_Thermo_Scientific_instrument_model}, {MS_PASSEL_experiment_URI, MS_external_reference_identifier}, {MS_Paragon_input_parameter, MS_search_engine_specific_input_parameter}, @@ -8518,11 +8836,11 @@ CVIDPair relationsIsA_[] = {MS_Andi_MS_format, MS_mass_spectrometer_file_format}, {MS_chromatograph_file_format, MS_file_format}, {MS_Andi_CHROM_format, MS_chromatograph_file_format}, - {MS_6420_Triple_Quadrupole_LC_MS, MS_triple_quadrupole}, + {MS_6420_Triple_Quadrupole_LC_MS, MS_triple_quadrupole_instrument}, {MS_6420_Triple_Quadrupole_LC_MS, MS_Agilent_instrument_model}, - {MS_6460_Triple_Quadrupole_LC_MS, MS_triple_quadrupole}, + {MS_6460_Triple_Quadrupole_LC_MS, MS_triple_quadrupole_instrument}, {MS_6460_Triple_Quadrupole_LC_MS, MS_Agilent_instrument_model}, - {MS_6490_Triple_Quadrupole_LC_MS, MS_triple_quadrupole}, + {MS_6490_Triple_Quadrupole_LC_MS, MS_triple_quadrupole_instrument}, {MS_6490_Triple_Quadrupole_LC_MS, MS_Agilent_instrument_model}, {MS_Paragon_special_factor, MS_Paragon_input_parameter}, {MS_PEAKS_inChorusPeptideScore, MS_PSM_level_search_engine_specific_statistic}, @@ -8607,9 +8925,13 @@ CVIDPair relationsIsA_[] = {MS_peptide_group_ID, MS_peptide_sequence_level_identification_attribute}, {MS_mass_spectrometry_imaging, MS_run_attribute}, {MS_ProteomeDiscoverer_1__Static_Terminal_Modification, MS_ProteomeDiscoverer_input_parameter}, + {MS_Q_Exactive_HF, MS_quadrupole_orbitrap_instrument}, {MS_Q_Exactive_HF, MS_Thermo_Scientific_instrument_model}, + {MS_PepFinder, MS_Thermo_Scientific_software}, {MS_PepFinder, MS_data_processing_software}, + {MS_TSQ_8000_Evo, MS_triple_quadrupole_instrument}, {MS_TSQ_8000_Evo, MS_Thermo_Scientific_instrument_model}, + {MS_Exactive_Plus, MS_orbitrap_instrument}, {MS_Exactive_Plus, MS_Thermo_Scientific_instrument_model}, {MS_instrument_specific_scan_attribute, MS_scan_attribute}, {MS_synchronous_prefilter_selection, MS_instrument_specific_scan_attribute}, @@ -8617,6 +8939,7 @@ CVIDPair relationsIsA_[] = {MS_baseline_array, MS_binary_data_array}, {MS_UIMF_format, MS_mass_spectrometer_file_format}, {MS_UIMF_nativeID_format, MS_native_spectrum_identifier_format}, + {MS_TripleTOF_6600, MS_quadrupole_time_of_flight_instrument}, {MS_TripleTOF_6600, MS_SCIEX_instrument_model}, {MS_ProLuCID_xcorr, MS_PSM_level_search_engine_specific_statistic}, {MS_ProLuCID_deltacn, MS_PSM_level_search_engine_specific_statistic}, @@ -8662,24 +8985,43 @@ CVIDPair relationsIsA_[] = {MS_ASAPRatio, MS_Trans_Proteomic_Pipeline_software}, {MS_Tide, MS_analysis_software}, {MS_Andromeda_result_format, MS_intermediate_analysis_format}, + {MS_2000_QTRAP, MS_triple_quadrupole_linear_ion_trap_instrument}, {MS_2000_QTRAP, MS_SCIEX_instrument_model}, + {MS_2500_QTRAP, MS_triple_quadrupole_linear_ion_trap_instrument}, {MS_2500_QTRAP, MS_SCIEX_instrument_model}, + {MS_3500_QTRAP, MS_triple_quadrupole_linear_ion_trap_instrument}, {MS_3500_QTRAP, MS_SCIEX_instrument_model}, + {MS_QTRAP_4500, MS_triple_quadrupole_linear_ion_trap_instrument}, {MS_QTRAP_4500, MS_SCIEX_instrument_model}, + {MS_QTRAP_6500, MS_triple_quadrupole_linear_ion_trap_instrument}, {MS_QTRAP_6500, MS_SCIEX_instrument_model}, + {MS_QTRAP_6500_, MS_triple_quadrupole_linear_ion_trap_instrument}, {MS_QTRAP_6500_, MS_SCIEX_instrument_model}, + {MS_TripleTOF_4600, MS_quadrupole_time_of_flight_instrument}, {MS_TripleTOF_4600, MS_SCIEX_instrument_model}, + {MS_TripleTOF_5600_, MS_quadrupole_time_of_flight_instrument}, {MS_TripleTOF_5600_, MS_SCIEX_instrument_model}, + {MS_API_100, MS_quadrupole_instrument}, {MS_API_100, MS_SCIEX_instrument_model}, + {MS_API_100LC, MS_quadrupole_instrument}, {MS_API_100LC, MS_SCIEX_instrument_model}, + {MS_API_165, MS_quadrupole_instrument}, {MS_API_165, MS_SCIEX_instrument_model}, + {MS_API_300, MS_triple_quadrupole_instrument}, {MS_API_300, MS_SCIEX_instrument_model}, + {MS_API_350, MS_triple_quadrupole_instrument}, {MS_API_350, MS_SCIEX_instrument_model}, + {MS_API_365, MS_triple_quadrupole_instrument}, {MS_API_365, MS_SCIEX_instrument_model}, + {MS_Triple_Quad_3500, MS_triple_quadrupole_instrument}, {MS_Triple_Quad_3500, MS_SCIEX_instrument_model}, + {MS_Triple_Quad_4500, MS_triple_quadrupole_instrument}, {MS_Triple_Quad_4500, MS_SCIEX_instrument_model}, + {MS_Triple_Quad_5500, MS_triple_quadrupole_instrument}, {MS_Triple_Quad_5500, MS_SCIEX_instrument_model}, + {MS_Triple_Quad_6500, MS_triple_quadrupole_instrument}, {MS_Triple_Quad_6500, MS_SCIEX_instrument_model}, + {MS_Triple_Quad_6500_, MS_triple_quadrupole_instrument}, {MS_Triple_Quad_6500_, MS_SCIEX_instrument_model}, {MS_ProLuCID, MS_analysis_software}, {MS_MS1_format, MS_mass_spectrometer_file_format}, @@ -8688,6 +9030,7 @@ CVIDPair relationsIsA_[] = {MS_PRIDE_XML, MS_identification_file_format}, {MS_PRIDE_XML, MS_spectrum_identification_result_details}, {MS_mzTab, MS_tab_delimited_text_format}, + {MS_mzTab, MS_identification_file_format}, {MS_sample_label, MS_assay_label_attribute}, {MS_sample_label, MS_sample_attribute}, {MS_ICAT_reagent, MS_sample_label}, @@ -8721,6 +9064,7 @@ CVIDPair relationsIsA_[] = {MS_electron_transfer_higher_energy_collision_dissociation, MS_combined_dissociation_method}, {MS_jPOST_dataset_identifier, MS_external_reference_identifier}, {MS_jPOST_dataset_URI, MS_external_reference_identifier}, + {MS_Q_Exactive_Plus, MS_quadrupole_orbitrap_instrument}, {MS_Q_Exactive_Plus, MS_Thermo_Scientific_instrument_model}, {MS_proteogenomics_search, MS_special_processing}, {MS_proteogenomics_attribute, MS_peptide_sequence_level_identification_attribute}, @@ -8752,7 +9096,9 @@ CVIDPair relationsIsA_[] = {MS_Morpheus_summed_Morpheus_score, MS_search_engine_specific_score_for_protein_groups}, {MS_interaction_score_derived_from_crosslinking, MS_crosslinking_result_details}, {MS_regular_expression_for_interaction_scores_derived_from_crosslinking, MS_regular_expression}, + {MS_impact_II, MS_quadrupole_time_of_flight_instrument}, {MS_impact_II, MS_Bruker_Daltonics_micrOTOF_series}, + {MS_impact_HD, MS_quadrupole_time_of_flight_instrument}, {MS_impact_HD, MS_Bruker_Daltonics_micrOTOF_series}, {MS_frag__iTRAQ_4plex_reporter_ion, MS_fragmentation_ion_type}, {MS_frag__iTRAQ_8plex_reporter_ion, MS_fragmentation_ion_type}, @@ -8760,6 +9106,7 @@ CVIDPair relationsIsA_[] = {MS_frag__TMT_ETD_reporter_ion, MS_fragmentation_ion_type}, {MS_no_modification_threshold, MS_PTM_localization_score_threshold}, {MS_OpenXQuest, MS_TOPP_software}, + {MS_X500R_QTOF, MS_quadrupole_time_of_flight_instrument}, {MS_X500R_QTOF, MS_SCIEX_instrument_model}, {MS_protein_pair_level_global_FDR, MS_interaction_score_derived_from_crosslinking}, {MS_residue_pair_level_global_FDR, MS_interaction_score_derived_from_crosslinking}, @@ -8809,6 +9156,8 @@ CVIDPair relationsIsA_[] = {MS_Waters_DATA_Convert, MS_Waters_software}, {MS_Waters_DATA_Convert, MS_analysis_software}, {MS_Waters_DATA_Convert, MS_data_processing_software}, + {MS_Pegasus_BT, MS_time_of_flight_instrument}, + {MS_Pegasus_BT, MS_gas_chromatography_mass_spectrometry_system}, {MS_Pegasus_BT, MS_LECO_instrument_model}, {MS_MSPathFinder, MS_analysis_software}, {MS_MSPathFinder_SpecEValue, MS_PSM_level_e_value}, @@ -8820,12 +9169,18 @@ CVIDPair relationsIsA_[] = {MS_MSPathFinder_PepQValue, MS_PSM_level_search_engine_specific_statistic}, {MS_MSPathFinder_RawScore, MS_PSM_level_search_engine_specific_statistic}, {MS_SYNAPT_G2_Si, MS_Waters_instrument_model}, - {MS_SYNAPT_G2_Si, MS_quadrupole_ion_mobility_time_of_flight}, + {MS_SYNAPT_G2_Si, MS_quadrupole_ion_mobility_time_of_flight_instrument}, + {MS_MALDI_SYNAPT_G2_Si, MS_quadrupole_ion_mobility_time_of_flight_instrument}, {MS_MALDI_SYNAPT_G2_Si, MS_Waters_instrument_model}, + {MS_Vion_IMS_QTof, MS_quadrupole_ion_mobility_time_of_flight_instrument}, {MS_Vion_IMS_QTof, MS_Waters_instrument_model}, + {MS_Xevo_G2_XS_Tof, MS_time_of_flight_instrument}, {MS_Xevo_G2_XS_Tof, MS_Waters_instrument_model}, + {MS_Xevo_TQ_XS, MS_triple_quadrupole_instrument}, {MS_Xevo_TQ_XS, MS_Waters_instrument_model}, + {MS_Xevo_TQ_S_micro, MS_triple_quadrupole_instrument}, {MS_Xevo_TQ_S_micro, MS_Waters_instrument_model}, + {MS_Orbitrap_Fusion_Lumos, MS_quadrupole_ion_trap_orbitrap_instrument}, {MS_Orbitrap_Fusion_Lumos, MS_Thermo_Scientific_instrument_model}, {MS_peptide_level_spectral_count, MS_peptide_level_quantification_datatype}, {MS_peptide_ion_level_spectral_count, MS_peptide_level_quantification_datatype}, @@ -8877,51 +9232,53 @@ CVIDPair relationsIsA_[] = {MS_DiLeu_reagent_116, MS_DiLeu_reagent}, {MS_DiLeu_reagent_117, MS_DiLeu_reagent}, {MS_DiLeu_reagent_118, MS_DiLeu_reagent}, - {MS_6550_iFunnel_Q_TOF_LC_MS, MS_quadrupole_time_of_flight}, + {MS_6550_iFunnel_Q_TOF_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_6550_iFunnel_Q_TOF_LC_MS, MS_Agilent_instrument_model}, - {MS_6550A_iFunnel_Q_TOF_LC_MS, MS_quadrupole_time_of_flight}, + {MS_6550A_iFunnel_Q_TOF_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_6550A_iFunnel_Q_TOF_LC_MS, MS_Agilent_instrument_model}, - {MS_6520B_Q_TOF_LC_MS, MS_quadrupole_time_of_flight}, + {MS_6520B_Q_TOF_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_6520B_Q_TOF_LC_MS, MS_Agilent_instrument_model}, - {MS_6530A_Q_TOF_LC_MS, MS_quadrupole_time_of_flight}, + {MS_6530A_Q_TOF_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_6530A_Q_TOF_LC_MS, MS_Agilent_instrument_model}, - {MS_6530B_Q_TOF_LC_MS, MS_quadrupole_time_of_flight}, + {MS_6530B_Q_TOF_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_6530B_Q_TOF_LC_MS, MS_Agilent_instrument_model}, - {MS_6538_Q_TOF_LC_MS, MS_quadrupole_time_of_flight}, + {MS_6538_Q_TOF_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_6538_Q_TOF_LC_MS, MS_Agilent_instrument_model}, - {MS_6540_Q_TOF_LC_MS, MS_quadrupole_time_of_flight}, + {MS_6540_Q_TOF_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_6540_Q_TOF_LC_MS, MS_Agilent_instrument_model}, - {MS_6542_Q_TOF_LC_MS, MS_quadrupole_time_of_flight}, + {MS_6542_Q_TOF_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_6542_Q_TOF_LC_MS, MS_Agilent_instrument_model}, - {MS_6545_Q_TOF_LC_MS, MS_quadrupole_time_of_flight}, + {MS_6545_Q_TOF_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_6545_Q_TOF_LC_MS, MS_Agilent_instrument_model}, - {MS_6560_Q_TOF_LC_MS, MS_quadrupole_ion_mobility_time_of_flight}, + {MS_6560_Q_TOF_LC_MS, MS_quadrupole_ion_mobility_time_of_flight_instrument}, {MS_6560_Q_TOF_LC_MS, MS_Agilent_instrument_model}, - {MS_6570_Q_TOF_LC_MS, MS_quadrupole_time_of_flight}, + {MS_6570_Q_TOF_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_6570_Q_TOF_LC_MS, MS_Agilent_instrument_model}, - {MS_6120B_Quadrupole_LC_MS, MS_quadrupole}, + {MS_6120B_Quadrupole_LC_MS, MS_quadrupole_instrument}, {MS_6120B_Quadrupole_LC_MS, MS_Agilent_instrument_model}, - {MS_6150_Quadrupole_LC_MS, MS_quadrupole}, + {MS_6150_Quadrupole_LC_MS, MS_quadrupole_instrument}, {MS_6150_Quadrupole_LC_MS, MS_Agilent_instrument_model}, - {MS_6224_Time_of_Flight_LC_MS, MS_time_of_flight}, + {MS_6224_Time_of_Flight_LC_MS, MS_time_of_flight_instrument}, {MS_6224_Time_of_Flight_LC_MS, MS_Agilent_instrument_model}, - {MS_6230A_Time_of_Flight_LC_MS, MS_time_of_flight}, + {MS_6230A_Time_of_Flight_LC_MS, MS_time_of_flight_instrument}, {MS_6230A_Time_of_Flight_LC_MS, MS_Agilent_instrument_model}, - {MS_6230B_Time_of_Flight_LC_MS, MS_time_of_flight}, + {MS_6230B_Time_of_Flight_LC_MS, MS_time_of_flight_instrument}, {MS_6230B_Time_of_Flight_LC_MS, MS_Agilent_instrument_model}, - {MS_6430_Triple_Quadrupole_LC_MS, MS_triple_quadrupole}, + {MS_6430_Triple_Quadrupole_LC_MS, MS_triple_quadrupole_instrument}, {MS_6430_Triple_Quadrupole_LC_MS, MS_Agilent_instrument_model}, - {MS_6495A_Triple_Quadrupole_LC_MS, MS_triple_quadrupole}, + {MS_6495A_Triple_Quadrupole_LC_MS, MS_triple_quadrupole_instrument}, {MS_6495A_Triple_Quadrupole_LC_MS, MS_Agilent_instrument_model}, - {MS_6495B_Triple_Quadrupole_LC_MS, MS_triple_quadrupole}, + {MS_6495B_Triple_Quadrupole_LC_MS, MS_triple_quadrupole_instrument}, {MS_6495B_Triple_Quadrupole_LC_MS, MS_Agilent_instrument_model}, - {MS_7000A_Triple_Quadrupole_GC_MS, MS_triple_quadrupole}, - {MS_7000A_Triple_Quadrupole_GC_MS, MS_Agilent_gas_chromatography_mass_spectrometry_system_model}, + {MS_7000A_Triple_Quadrupole_GC_MS, MS_triple_quadrupole_instrument}, + {MS_7000A_Triple_Quadrupole_GC_MS, MS_gas_chromatography_mass_spectrometry_system}, {MS_7000A_Triple_Quadrupole_GC_MS, MS_Agilent_instrument_model}, - {MS_7000B_Triple_Quadrupole_GC_MS, MS_triple_quadrupole}, - {MS_7000B_Triple_Quadrupole_GC_MS, MS_Agilent_gas_chromatography_mass_spectrometry_system_model}, + {MS_7000B_Triple_Quadrupole_GC_MS, MS_triple_quadrupole_instrument}, + {MS_7000B_Triple_Quadrupole_GC_MS, MS_gas_chromatography_mass_spectrometry_system}, {MS_7000B_Triple_Quadrupole_GC_MS, MS_Agilent_instrument_model}, + {MS_7800_Quadrupole_ICP_MS, MS_quadrupole_instrument}, {MS_7800_Quadrupole_ICP_MS, MS_Agilent_instrument_model}, + {MS_8800_Triple_Quadrupole_ICP_MS, MS_triple_quadrupole_instrument}, {MS_8800_Triple_Quadrupole_ICP_MS, MS_Agilent_instrument_model}, {MS_ion, MS_molecular_entity}, {MS_positive_mode_adduct_ion, MS_adduct_ion}, @@ -8950,8 +9307,9 @@ CVIDPair relationsIsA_[] = {MS_XCMS_intf, MS_feature_level_quantification_datatype}, {MS_XCMS_maxo, MS_feature_level_quantification_datatype}, {MS_XCMS_area, MS_feature_level_quantification_datatype}, - {MS_alternating_polarity_acquisition, MS_data_file_content}, + {MS_alternating_polarity_acquisition, MS_acquisition_polarity}, {MS_ProteomeDiscoverer_Delta_Score, MS_PSM_level_search_engine_specific_statistic}, + {MS_LTQ_Orbitrap_Classic, MS_ion_trap_orbitrap_instrument}, {MS_LTQ_Orbitrap_Classic, MS_Thermo_Scientific_instrument_model}, {MS_iProX_dataset_identifier, MS_external_reference_identifier}, {MS_iProX_dataset_URI, MS_external_reference_identifier}, @@ -8993,12 +9351,17 @@ CVIDPair relationsIsA_[] = {MS_CAMERA, MS_data_processing_software}, {MS_Panorama_Public_dataset_identifier, MS_external_reference_identifier}, {MS_Panorama_Public_dataset_URI, MS_external_reference_identifier}, + {MS_TSQ_Altis, MS_triple_quadrupole_instrument}, {MS_TSQ_Altis, MS_Thermo_Scientific_instrument_model}, + {MS_TSQ_Quantis, MS_triple_quadrupole_instrument}, {MS_TSQ_Quantis, MS_Thermo_Scientific_instrument_model}, + {MS_TSQ_9000, MS_triple_quadrupole_instrument}, {MS_TSQ_9000, MS_Thermo_Scientific_instrument_model}, + {MS_Q_Exactive_HF_X, MS_quadrupole_orbitrap_instrument}, {MS_Q_Exactive_HF_X, MS_Thermo_Scientific_instrument_model}, {MS_small_molecule_analysis_software, MS_analysis_software}, {MS_Progenesis_QI, MS_small_molecule_analysis_software}, + {MS_Compound_Discoverer, MS_Thermo_Scientific_software}, {MS_Compound_Discoverer, MS_small_molecule_analysis_software}, {MS_MyCompoundID, MS_small_molecule_analysis_software}, {MS_study_variable_average_function, MS_search_statistics}, @@ -9136,19 +9499,30 @@ CVIDPair relationsIsA_[] = {MS_IdentiPy_hyperscore, MS_search_engine_specific_score}, {MS_ms_deisotope, MS_data_processing_software}, {MS_python_psims, MS_conversion_software}, + {MS_Orbitrap_Exploris_GC_MS, MS_quadrupole_orbitrap_instrument}, {MS_Orbitrap_Exploris_GC_MS, MS_Thermo_Scientific_instrument_model}, + {MS_Q_Exactive_Focus, MS_quadrupole_orbitrap_instrument}, {MS_Q_Exactive_Focus, MS_Thermo_Scientific_instrument_model}, + {MS_Orbitrap_Excedion_Pro, MS_quadrupole_orbitrap_instrument}, {MS_Orbitrap_Excedion_Pro, MS_Thermo_Scientific_instrument_model}, {MS_Andromeda_PEP, MS_PSM_level_search_engine_specific_statistic}, {MS_Andromeda_apl_file_format, MS_mass_spectrometer_file_format}, {MS_ProteomeXchange_dataset_identifier_reanalysis_number, MS_external_reference_identifier}, + {MS_LCMS_9030, MS_quadrupole_time_of_flight_instrument}, {MS_LCMS_9030, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_LCMS_8060, MS_triple_quadrupole_instrument}, {MS_LCMS_8060, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_LCMS_8050, MS_triple_quadrupole_instrument}, {MS_LCMS_8050, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_LCMS_8045, MS_triple_quadrupole_instrument}, {MS_LCMS_8045, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_LCMS_8040, MS_triple_quadrupole_instrument}, {MS_LCMS_8040, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_LCMS_2020, MS_quadrupole_instrument}, {MS_LCMS_2020, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_maXis_II, MS_quadrupole_time_of_flight_instrument}, {MS_maXis_II, MS_Bruker_Daltonics_maXis_series}, + {MS_timsTOF_Pro, MS_ion_mobility_quadrupole_time_of_flight_instrument}, {MS_timsTOF_Pro, MS_Bruker_Daltonics_timsTOF_series}, {MS_mean_inverse_reduced_ion_mobility_array, MS_ion_mobility_array}, {MS_raw_ion_mobility_array, MS_ion_mobility_array}, @@ -9177,7 +9551,9 @@ CVIDPair relationsIsA_[] = {MS_OpenPepXL_score, MS_search_engine_specific_score}, {MS_named_element_in_mzIdentML, MS_named_element}, {MS_named_element_in_mzML, MS_named_element}, + {MS_Orbitrap_Exploris_480, MS_quadrupole_orbitrap_instrument}, {MS_Orbitrap_Exploris_480, MS_Thermo_Scientific_instrument_model}, + {MS_Orbitrap_Eclipse, MS_quadrupole_ion_trap_orbitrap_instrument}, {MS_Orbitrap_Eclipse, MS_Thermo_Scientific_instrument_model}, {MS_Mascot_MinNumSigUniqueSeqs, MS_Mascot_input_parameter}, {MS_CPTAC_accession_number, MS_external_reference_identifier}, @@ -9240,8 +9616,11 @@ CVIDPair relationsIsA_[] = {MS_truncation__linear_prediction_and_zlib_compression, MS_binary_data_compression_type}, {MS_number_of_mantissa_bits_truncated, MS_binary_data_compression_parameter}, {MS_Lys_N, MS_cleavage_agent_name}, + {MS_Orbitrap_Exploris_240, MS_quadrupole_orbitrap_instrument}, {MS_Orbitrap_Exploris_240, MS_Thermo_Scientific_instrument_model}, + {MS_Orbitrap_Exploris_120, MS_quadrupole_orbitrap_instrument}, {MS_Orbitrap_Exploris_120, MS_Thermo_Scientific_instrument_model}, + {MS_Orbitrap_Velos_Pro, MS_ion_trap_orbitrap_instrument}, {MS_Orbitrap_Velos_Pro, MS_Thermo_Scientific_instrument_model}, {MS_MaxQuant_protein_group_level_score, MS_search_engine_specific_score_for_protein_groups}, {MS_Andromeda_peptide_PEP, MS_search_engine_specific_peptide_sequence_level_identification_statistic}, @@ -9259,6 +9638,7 @@ CVIDPair relationsIsA_[] = {MS_SIM_XL, MS_analysis_software}, {MS_SIM_XL_score, MS_PSM_level_search_engine_specific_statistic}, {MS_QUIN_XL, MS_quantitation_software_name}, + {MS_Orbitrap_ID_X, MS_quadrupole_ion_trap_orbitrap_instrument}, {MS_Orbitrap_ID_X, MS_Thermo_Scientific_instrument_model}, {MS_OpenMS_ConsensusID_PEP, MS_PSM_level_search_engine_specific_statistic}, {MS_OpenMS_Best_PSM_Score, MS_search_engine_specific_peptide_sequence_level_identification_statistic}, @@ -9270,8 +9650,10 @@ CVIDPair relationsIsA_[] = {MS_EPIFANY_Protein_posterior_probability, MS_search_engine_specific_score_for_proteins}, {MS_OpenMS_LFQ_intensity, MS_quantification_datatype}, {MS_OpenMS_LFQ_spectral_count, MS_quantification_datatype}, + {MS_rapifleX, MS_tandem_time_of_flight_instrument}, {MS_rapifleX, MS_Bruker_Daltonics_flex_series}, {MS_Bruker_Daltonics_timsTOF_series, MS_Bruker_Daltonics_instrument_model}, + {MS_timsTOF_fleX, MS_ion_mobility_quadrupole_time_of_flight_instrument}, {MS_timsTOF_fleX, MS_Bruker_Daltonics_timsTOF_series}, {MS_ProSight_spectral_Q_value, MS_PSM_level_q_value}, {MS_ProSight_spectral_Q_value, MS_PSM_level_search_engine_specific_statistic}, @@ -9294,9 +9676,11 @@ CVIDPair relationsIsA_[] = {MS_ProSight_Run_Subsequence_Search_mode, MS_TDPortal_input_parameter}, {MS_ProSight_Run_Annotated_Proteoform_Search_mode, MS_ProSight_input_parameter}, {MS_ProSight_Run_Annotated_Proteoform_Search_mode, MS_TDPortal_input_parameter}, + {MS_ProSight, MS_Thermo_Scientific_software}, {MS_ProSight, MS_analysis_software}, {MS_TDPortal, MS_analysis_software}, {MS_mass_array, MS_binary_data_array}, + {MS_Triple_Quad_7500, MS_triple_quadrupole_instrument}, {MS_Triple_Quad_7500, MS_SCIEX_instrument_model}, {MS_ThermoRawFileParser, MS_data_processing_software}, {MS_pyteomics, MS_analysis_software}, @@ -9305,6 +9689,7 @@ CVIDPair relationsIsA_[] = {MS_PTMProphet_normalized_information_content, MS_PTM_localization_PSM_level_statistic}, {MS_PTMProphet_information_content, MS_PTM_localization_PSM_level_statistic}, {MS_SHA_256, MS_data_file_checksum_type}, + {MS_GCMS_QP2010SE, MS_quadrupole_instrument}, {MS_GCMS_QP2010SE, MS_Shimadzu_Scientific_Instruments_instrument_model}, {MS_raw_ion_mobility_drift_time_array, MS_ion_mobility_array}, {MS_deconvoluted_ion_mobility_array, MS_ion_mobility_array}, @@ -9326,8 +9711,11 @@ CVIDPair relationsIsA_[] = {MS_numeric_attribute, MS_object_attribute}, {MS_combined_dissociation_method, MS_precursor_activation_attribute}, {MS_electron_transfer_collision_induced_dissociation, MS_combined_dissociation_method}, + {MS_Synapt_XS, MS_quadrupole_ion_mobility_time_of_flight_instrument}, {MS_Synapt_XS, MS_Waters_instrument_model}, + {MS_SELECT_SERIES_Cyclic_IMS, MS_quadrupole_ion_mobility_time_of_flight_instrument}, {MS_SELECT_SERIES_Cyclic_IMS, MS_Waters_instrument_model}, + {MS_SELECT_SERIES_MRT, MS_quadrupole_time_of_flight_instrument}, {MS_SELECT_SERIES_MRT, MS_Waters_instrument_model}, {MS_library_format_version, MS_spectral_library_attribute}, {MS_library_identifier, MS_spectral_library_attribute}, @@ -9390,8 +9778,11 @@ CVIDPair relationsIsA_[] = {MS_data_independent_acquisition_from_dissociation_of_scanning_quadrupole_across_mass_range, MS_data_independent_acquisition}, {MS_data_independent_acquisition_from_dissociation_of_scanning_quadrupole_across_mass_range, MS_dissociation_of_scanning_quadrupole_across_a_specified_mass_range}, {MS_data_independent_acquisition_from_dissociation_of_scanning_quadrupole_across_mass_range, MS_mass_spectrometry_acquisition_method}, + {MS_timsTOF, MS_ion_mobility_quadrupole_time_of_flight_instrument}, {MS_timsTOF, MS_Bruker_Daltonics_timsTOF_series}, + {MS_timsTOF_Pro_2, MS_ion_mobility_quadrupole_time_of_flight_instrument}, {MS_timsTOF_Pro_2, MS_Bruker_Daltonics_timsTOF_series}, + {MS_timsTOF_SCP, MS_ion_mobility_quadrupole_time_of_flight_instrument}, {MS_timsTOF_SCP, MS_Bruker_Daltonics_timsTOF_series}, {MS_PeakForest, MS_analysis_software}, {MS_PeakForest, MS_library_creation_software}, @@ -9405,6 +9796,7 @@ CVIDPair relationsIsA_[] = {MS_rank_transform, MS_peak_intensity_transform}, {MS_adduct_ion_mass, MS_adduct_ion_property}, {MS_peptide_accession_number, MS_peptidoform_attribute}, + {MS_Q_Exactive_UHMR, MS_quadrupole_orbitrap_instrument}, {MS_Q_Exactive_UHMR, MS_Thermo_Scientific_instrument_model}, {MS_ultraviolet_photodissociation, MS_photodissociation}, {MS_negative_electron_transfer_dissociation, MS_dissociation_method}, @@ -9414,6 +9806,7 @@ CVIDPair relationsIsA_[] = {MS_count_of_identified_peptidoforms, MS_single_value}, {MS_count_of_identified_spectra, MS_PSM_level_result_list_attribute}, {MS_count_of_identified_spectra, MS_single_value}, + {MS_Xevo_G2_XS_QTof, MS_quadrupole_time_of_flight_instrument}, {MS_Xevo_G2_XS_QTof, MS_Waters_instrument_model}, {MS_DIA_NN, MS_quantitation_software_name}, {MS_DIA_NN, MS_analysis_software}, @@ -9448,7 +9841,9 @@ CVIDPair relationsIsA_[] = {MS_intensity_of_highest_unassigned_peak, MS_interpreted_spectrum_attribute}, {MS_number_of_unassigned_peaks_among_top_20_peaks, MS_interpreted_spectrum_attribute}, {MS_Luciphor_deltaScore, MS_PTM_localization_PSM_level_statistic}, + {MS_TSQ_Altis_Plus, MS_triple_quadrupole_instrument}, {MS_TSQ_Altis_Plus, MS_Thermo_Scientific_instrument_model}, + {MS_ZenoTOF_7600, MS_quadrupole_time_of_flight_instrument}, {MS_ZenoTOF_7600, MS_SCIEX_instrument_model}, {MS_electron_activated_dissociation, MS_electron_capture_dissociation}, {MS_summary_statistics_of_replicates, MS_spectrum_aggregation_attribute}, @@ -9518,6 +9913,7 @@ CVIDPair relationsIsA_[] = {MS_non_native_top_down_proteomics, MS_top_down_proteomics}, {MS_middle_down_proteomics, MS_mass_spectrometry_proteomics}, {MS_bottom_up_proteomics, MS_mass_spectrometry_proteomics}, + {MS_Orbitrap_Ascend, MS_quadrupole_ion_trap_orbitrap_instrument}, {MS_Orbitrap_Ascend, MS_Thermo_Scientific_instrument_model}, {MS_ANN_SoLo, MS_analysis_software}, {MS_XCorr_rank, MS_PSM_level_search_engine_specific_statistic}, @@ -9543,14 +9939,18 @@ CVIDPair relationsIsA_[] = {MS_ChemClipse, MS_data_processing_software}, {MS_OpenChrom, MS_analysis_software}, {MS_OpenChrom, MS_data_processing_software}, + {MS_Orbitrap_Astral, MS_quadrupole_orbitrap_astral_instrument}, {MS_Orbitrap_Astral, MS_Thermo_Scientific_instrument_model}, {MS_asymmetric_track_lossless_time_of_flight_analyzer, MS_time_of_flight}, + {MS_Xevo_G3_QTof, MS_quadrupole_time_of_flight_instrument}, {MS_Xevo_G3_QTof, MS_Waters_instrument_model}, + {MS_ACQUITY_RDa_Detector, MS_time_of_flight_instrument}, {MS_ACQUITY_RDa_Detector, MS_Waters_instrument_model}, {MS_waters_connect, MS_Waters_software}, {MS_waters_connect, MS_acquisition_software}, {MS_waters_connect, MS_analysis_software}, {MS_waters_connect, MS_data_processing_software}, + {MS_timsTOF_Ultra, MS_ion_mobility_quadrupole_time_of_flight_instrument}, {MS_timsTOF_Ultra, MS_Bruker_Daltonics_timsTOF_series}, {MS_semantic_version_regexp, MS_regular_expression}, {MS_mzIdentML_crosslinking_extension_document_version, MS_mzIdentML_extension_version}, @@ -9569,8 +9969,10 @@ CVIDPair relationsIsA_[] = {MS_SelexION_separation_voltage, MS_ion_mobility_attribute}, {MS_SelexION_separation_voltage, MS_ion_selection_attribute}, {MS_SelexION_separation_voltage, MS_peak_attribute}, + {MS_Q_Exactive_GC_Orbitrap, MS_quadrupole_orbitrap_instrument}, {MS_Q_Exactive_GC_Orbitrap, MS_Thermo_Scientific_instrument_model}, {MS_8890, MS_Agilent_gas_chromatography_system_model}, + {MS_timsTOF_fleX_MALDI_2, MS_ion_mobility_quadrupole_time_of_flight_instrument}, {MS_timsTOF_fleX_MALDI_2, MS_Bruker_Daltonics_timsTOF_series}, {MS_deconvoluted_data, MS_data_file_content}, {MS_quality_control_software, MS_data_processing_software}, @@ -9579,14 +9981,18 @@ CVIDPair relationsIsA_[] = {MS_pymzqc, MS_quality_control_software}, {MS_InChI, MS_spectrum_identification_result_details}, {MS_InChI, MS_structural_formula}, + {MS_timsTOF_HT, MS_ion_mobility_quadrupole_time_of_flight_instrument}, {MS_timsTOF_HT, MS_Bruker_Daltonics_timsTOF_series}, {MS_mzRecal, MS_data_processing_software}, {MS_spectrum_clustering_software, MS_software}, {MS_Scout, MS_analysis_software}, {MS_Scout_score, MS_PSM_level_search_engine_specific_statistic}, + {MS_Stellar, MS_quadrupole_ion_trap_instrument}, {MS_Stellar, MS_Thermo_Scientific_instrument_model}, {MS_electron_beam_energy, MS_precursor_activation_attribute}, + {MS_Orbitrap_IQ_X, MS_quadrupole_ion_trap_orbitrap_instrument}, {MS_Orbitrap_IQ_X, MS_Thermo_Scientific_instrument_model}, + {MS_timsTOF_Ultra_2, MS_ion_mobility_quadrupole_time_of_flight_instrument}, {MS_timsTOF_Ultra_2, MS_Bruker_Daltonics_timsTOF_series}, {MS_Kojak, MS_analysis_software}, {MS_Kojak_score, MS_PSM_level_search_engine_specific_statistic}, @@ -9600,6 +10006,7 @@ CVIDPair relationsIsA_[] = {MS_Kojak_expectation_value_xlink, MS_search_engine_specific_score}, {MS_Kojak_expectation_value_xlink, MS_PSM_level_search_engine_specific_statistic}, {MS_Kojak_matched_ions_xlink, MS_PSM_level_search_engine_specific_statistic}, + {MS_Orbitrap_Exploris_GC_240, MS_quadrupole_orbitrap_instrument}, {MS_Orbitrap_Exploris_GC_240, MS_Thermo_Scientific_instrument_model}, {MS_selected_fragment_theoretical_m_z_observed_intensity_spectrum, MS_spectrum_origin_type}, {MS_quantms, MS_analysis_software}, @@ -9629,9 +10036,13 @@ CVIDPair relationsIsA_[] = {MS_ion_mobility_frame_representation, MS_spectrum_attribute}, {MS_ion_mobility_profile_frame, MS_ion_mobility_frame_representation}, {MS_ion_mobility_centroid_frame, MS_ion_mobility_frame_representation}, + {MS_Orbitrap_Astral_Zoom, MS_quadrupole_orbitrap_astral_instrument}, {MS_Orbitrap_Astral_Zoom, MS_Thermo_Scientific_instrument_model}, + {MS_ZenoTOF_8600, MS_quadrupole_time_of_flight_instrument}, {MS_ZenoTOF_8600, MS_SCIEX_instrument_model}, + {MS_ZenoTOF_7600_, MS_quadrupole_time_of_flight_instrument}, {MS_ZenoTOF_7600_, MS_SCIEX_instrument_model}, + {MS_SCIEX_7500_, MS_triple_quadrupole_instrument}, {MS_SCIEX_7500_, MS_SCIEX_instrument_model}, {MS_SCIEX_OS, MS_SCIEX_software}, {MS_SCIEX_OS, MS_acquisition_software}, @@ -9640,6 +10051,7 @@ CVIDPair relationsIsA_[] = {MS_SCIEX_MS_Data_Converter, MS_SCIEX_software}, {MS_SCIEX_MS_Data_Converter, MS_data_processing_software}, {MS_SCIEX_WIFF2_format, MS_mass_spectrometer_file_format}, + {MS_ISQ_7000, MS_quadrupole_instrument}, {MS_ISQ_7000, MS_Thermo_Scientific_instrument_model}, {MS_FAIMS_compensation_voltage_ramp_start, MS_ion_mobility_attribute}, {MS_FAIMS_compensation_voltage_ramp_start, MS_ion_selection_attribute}, @@ -9651,176 +10063,270 @@ CVIDPair relationsIsA_[] = {MS_JEOL_instrument_model, MS_instrument_model}, {MS_IONTOF_instrument_model, MS_instrument_model}, {MS_PerkinElmer_instrument_model, MS_instrument_model}, + {MS_TripleTOF_6600_, MS_quadrupole_time_of_flight_instrument}, {MS_TripleTOF_6600_, MS_SCIEX_instrument_model}, + {MS_Triple_Quad_5500_, MS_triple_quadrupole_instrument}, {MS_Triple_Quad_5500_, MS_SCIEX_instrument_model}, + {MS_Triple_Quad_5500__QTRAP_Ready, MS_triple_quadrupole_linear_ion_trap_instrument}, {MS_Triple_Quad_5500__QTRAP_Ready, MS_SCIEX_instrument_model}, + {MS_APEX_Qe, MS_quadrupole_fourier_transform_ion_cyclotron_resonance_instrument}, {MS_APEX_Qe, MS_Bruker_Daltonics_apex_series}, + {MS_autoflex_speed_TOF_TOF, MS_tandem_time_of_flight_instrument}, {MS_autoflex_speed_TOF_TOF, MS_Bruker_Daltonics_flex_series}, + {MS_esquire_3000, MS_ion_trap_instrument}, {MS_esquire_3000, MS_Bruker_Daltonics_esquire_series}, + {MS_maXis_impact, MS_quadrupole_time_of_flight_instrument}, {MS_maXis_impact, MS_Bruker_Daltonics_maXis_series}, + {MS_maXis_impact_HD, MS_quadrupole_time_of_flight_instrument}, {MS_maXis_impact_HD, MS_Bruker_Daltonics_maXis_series}, + {MS_maXis_3G, MS_quadrupole_time_of_flight_instrument}, {MS_maXis_3G, MS_Bruker_Daltonics_maXis_series}, + {MS_solariX_XR, MS_quadrupole_fourier_transform_ion_cyclotron_resonance_instrument}, {MS_solariX_XR, MS_Bruker_Daltonics_solarix_series}, + {MS_amaZon_SL, MS_ion_trap_instrument}, {MS_amaZon_SL, MS_Bruker_Daltonics_amaZon_series}, + {MS_EVOQ_DART_TQ_, MS_triple_quadrupole_instrument}, {MS_EVOQ_DART_TQ_, MS_Bruker_Daltonics_EVOQ_series}, + {MS_EVOQ_LC_TQ, MS_triple_quadrupole_instrument}, {MS_EVOQ_LC_TQ, MS_Bruker_Daltonics_EVOQ_series}, + {MS_EVOQ_GC_TQ, MS_triple_quadrupole_instrument}, {MS_EVOQ_GC_TQ, MS_Bruker_Daltonics_EVOQ_series}, + {MS_Toxtyper, MS_ion_trap_instrument}, {MS_Toxtyper, MS_Bruker_Daltonics_instrument_model}, + {MS_impact_II_VIP, MS_quadrupole_time_of_flight_instrument}, {MS_impact_II_VIP, MS_Bruker_Daltonics_micrOTOF_series}, + {MS_ecTOF, MS_time_of_flight_instrument}, {MS_ecTOF, MS_Bruker_Daltonics_instrument_model}, + {MS_autoflex_maX, MS_time_of_flight_instrument}, {MS_autoflex_maX, MS_Bruker_Daltonics_flex_series}, + {MS_rapifleX_MALDI_PharmaPulse, MS_tandem_time_of_flight_instrument}, {MS_rapifleX_MALDI_PharmaPulse, MS_Bruker_Daltonics_flex_series}, + {MS_smartfleX, MS_time_of_flight_instrument}, {MS_smartfleX, MS_Bruker_Daltonics_flex_series}, + {MS_neofleX, MS_tandem_time_of_flight_instrument}, {MS_neofleX, MS_Bruker_Daltonics_flex_series}, + {MS_MALDI_Biotyper, MS_time_of_flight_instrument}, {MS_MALDI_Biotyper, MS_Bruker_Daltonics_instrument_model}, + {MS_scimaX, MS_quadrupole_fourier_transform_ion_cyclotron_resonance_instrument}, {MS_scimaX, MS_Bruker_Daltonics_instrument_model}, + {MS_timsMetabo, MS_ion_mobility_quadrupole_time_of_flight_instrument}, {MS_timsMetabo, MS_Bruker_Daltonics_timsTOF_series}, + {MS_timsUltra_AIP, MS_ion_mobility_quadrupole_time_of_flight_instrument}, {MS_timsUltra_AIP, MS_Bruker_Daltonics_timsTOF_series}, + {MS_timsOmni, MS_ion_mobility_quadrupole_time_of_flight_instrument}, {MS_timsOmni, MS_Bruker_Daltonics_timsTOF_series}, + {MS_timsTOF_MALDI_PharmaPulse, MS_ion_mobility_quadrupole_time_of_flight_instrument}, {MS_timsTOF_MALDI_PharmaPulse, MS_Bruker_Daltonics_timsTOF_series}, + {MS_4000_GC_MS, MS_ion_trap_instrument}, + {MS_4000_GC_MS, MS_gas_chromatography_mass_spectrometry_system}, {MS_4000_GC_MS, MS_Varian_instrument_model}, + {MS_210_MS_GC_MS_Ion_Trap, MS_ion_trap_instrument}, + {MS_210_MS_GC_MS_Ion_Trap, MS_gas_chromatography_mass_spectrometry_system}, {MS_210_MS_GC_MS_Ion_Trap, MS_Varian_instrument_model}, + {MS_LCMS_8030, MS_triple_quadrupole_instrument}, {MS_LCMS_8030, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_LCMS_8030_Plus, MS_triple_quadrupole_instrument}, {MS_LCMS_8030_Plus, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_GCMS_QP2010_Plus, MS_quadrupole_instrument}, {MS_GCMS_QP2010_Plus, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_LCMS_8060NX, MS_triple_quadrupole_instrument}, {MS_LCMS_8060NX, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_GCMS_TQ8050NX, MS_triple_quadrupole_instrument}, {MS_GCMS_TQ8050NX, MS_Shimadzu_Scientific_Instruments_instrument_model}, - {MS_GCMS_TQ8050NX, MS_Shimadzu_gas_chromatography_mass_spectrometry_system_model}, + {MS_GCMS_TQ8050NX, MS_gas_chromatography_mass_spectrometry_system}, + {MS_GCMS_TQ8040NX, MS_triple_quadrupole_instrument}, {MS_GCMS_TQ8040NX, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_GCMS_TQ8040, MS_triple_quadrupole_instrument}, {MS_GCMS_TQ8040, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_GCMS_QP5000, MS_quadrupole_instrument}, {MS_GCMS_QP5000, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_GCMS_QP2020, MS_quadrupole_instrument}, {MS_GCMS_QP2020, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_GCMS_QP2010_Ultra, MS_quadrupole_instrument}, {MS_GCMS_QP2010_Ultra, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_Velos_Pro, MS_ion_trap_instrument}, {MS_Velos_Pro, MS_Thermo_Scientific_instrument_model}, + {MS_MALDI_LTQ_Orbitrap_XL, MS_ion_trap_orbitrap_instrument}, {MS_MALDI_LTQ_Orbitrap_XL, MS_Thermo_Scientific_instrument_model}, + {MS_MALDI_LTQ_Orbitrap_Discovery, MS_ion_trap_orbitrap_instrument}, {MS_MALDI_LTQ_Orbitrap_Discovery, MS_Thermo_Scientific_instrument_model}, + {MS_TSQ_Quantum_Access_MAX, MS_triple_quadrupole_instrument}, {MS_TSQ_Quantum_Access_MAX, MS_Thermo_Scientific_instrument_model}, + {MS_LTQ_Orbitrap_Velos_ETD, MS_ion_trap_orbitrap_instrument}, {MS_LTQ_Orbitrap_Velos_ETD, MS_Thermo_Scientific_instrument_model}, + {MS_ISQ_LT, MS_quadrupole_instrument}, {MS_ISQ_LT, MS_Thermo_Scientific_instrument_model}, + {MS_ITQ, MS_ion_trap_instrument}, {MS_ITQ, MS_Thermo_Scientific_instrument_model}, + {MS_TSQ_Quantum_XLS, MS_triple_quadrupole_instrument}, {MS_TSQ_Quantum_XLS, MS_Thermo_Scientific_instrument_model}, + {MS_TSQ_8000, MS_triple_quadrupole_instrument}, {MS_TSQ_8000, MS_Thermo_Scientific_instrument_model}, + {MS_DeltaPlus_IRMS, MS_magnetic_sector_instrument}, {MS_DeltaPlus_IRMS, MS_Thermo_Scientific_instrument_model}, + {MS_ACQUITY_QDa, MS_quadrupole_instrument}, {MS_ACQUITY_QDa, MS_Waters_instrument_model}, + {MS_LCT_Premier, MS_time_of_flight_instrument}, {MS_LCT_Premier, MS_Waters_instrument_model}, + {MS_Quattro_Premier_XE, MS_triple_quadrupole_instrument}, {MS_Quattro_Premier_XE, MS_Waters_instrument_model}, + {MS_Synapt_G1_HDMS, MS_quadrupole_ion_mobility_time_of_flight_instrument}, {MS_Synapt_G1_HDMS, MS_Waters_instrument_model}, + {MS_Synapt_G2_Si_HDMS, MS_quadrupole_ion_mobility_time_of_flight_instrument}, {MS_Synapt_G2_Si_HDMS, MS_Waters_instrument_model}, + {MS_Synapt_G1, MS_quadrupole_time_of_flight_instrument}, {MS_Synapt_G1, MS_Waters_instrument_model}, + {MS_Synapt_G2_XS_QTOF, MS_quadrupole_ion_mobility_time_of_flight_instrument}, {MS_Synapt_G2_XS_QTOF, MS_Waters_instrument_model}, + {MS_Xevo_TQ_Absolute, MS_triple_quadrupole_instrument}, {MS_Xevo_TQ_Absolute, MS_Waters_instrument_model}, + {MS_Xevo_TQ_Absolute_XR, MS_triple_quadrupole_instrument}, {MS_Xevo_TQ_Absolute_XR, MS_Waters_instrument_model}, - {MS_5973_MSD, MS_quadrupole}, - {MS_5973_MSD, MS_Agilent_gas_chromatography_mass_spectrometry_system_model}, + {MS_5973_MSD, MS_quadrupole_instrument}, + {MS_5973_MSD, MS_gas_chromatography_mass_spectrometry_system}, {MS_5973_MSD, MS_Agilent_instrument_model}, - {MS_5973N_MSD, MS_quadrupole}, - {MS_5973N_MSD, MS_Agilent_gas_chromatography_mass_spectrometry_system_model}, + {MS_5973N_MSD, MS_quadrupole_instrument}, + {MS_5973N_MSD, MS_gas_chromatography_mass_spectrometry_system}, {MS_5973N_MSD, MS_Agilent_instrument_model}, - {MS_5975_MSD, MS_quadrupole}, - {MS_5975_MSD, MS_Agilent_gas_chromatography_mass_spectrometry_system_model}, + {MS_5975_MSD, MS_quadrupole_instrument}, + {MS_5975_MSD, MS_gas_chromatography_mass_spectrometry_system}, {MS_5975_MSD, MS_Agilent_instrument_model}, - {MS_5975B_MSD, MS_quadrupole}, - {MS_5975B_MSD, MS_Agilent_gas_chromatography_mass_spectrometry_system_model}, + {MS_5975B_MSD, MS_quadrupole_instrument}, + {MS_5975B_MSD, MS_gas_chromatography_mass_spectrometry_system}, {MS_5975B_MSD, MS_Agilent_instrument_model}, - {MS_5975C_inert_XL_MSD, MS_quadrupole}, - {MS_5975C_inert_XL_MSD, MS_Agilent_gas_chromatography_mass_spectrometry_system_model}, + {MS_5975C_inert_XL_MSD, MS_quadrupole_instrument}, + {MS_5975C_inert_XL_MSD, MS_gas_chromatography_mass_spectrometry_system}, {MS_5975C_inert_XL_MSD, MS_Agilent_instrument_model}, - {MS_5975C_MSD, MS_quadrupole}, - {MS_5975C_MSD, MS_Agilent_gas_chromatography_mass_spectrometry_system_model}, + {MS_5975C_MSD, MS_quadrupole_instrument}, + {MS_5975C_MSD, MS_gas_chromatography_mass_spectrometry_system}, {MS_5975C_MSD, MS_Agilent_instrument_model}, - {MS_5975T_MSD, MS_quadrupole}, - {MS_5975T_MSD, MS_Agilent_gas_chromatography_mass_spectrometry_system_model}, + {MS_5975T_MSD, MS_quadrupole_instrument}, + {MS_5975T_MSD, MS_gas_chromatography_mass_spectrometry_system}, {MS_5975T_MSD, MS_Agilent_instrument_model}, - {MS_5977_MSD, MS_quadrupole}, - {MS_5977_MSD, MS_Agilent_gas_chromatography_mass_spectrometry_system_model}, + {MS_5977_MSD, MS_quadrupole_instrument}, + {MS_5977_MSD, MS_gas_chromatography_mass_spectrometry_system}, {MS_5977_MSD, MS_Agilent_instrument_model}, - {MS_5977A_MSD, MS_quadrupole}, - {MS_5977A_MSD, MS_Agilent_gas_chromatography_mass_spectrometry_system_model}, + {MS_5977A_MSD, MS_quadrupole_instrument}, + {MS_5977A_MSD, MS_gas_chromatography_mass_spectrometry_system}, {MS_5977A_MSD, MS_Agilent_instrument_model}, - {MS_5977B_MSD, MS_quadrupole}, - {MS_5977B_MSD, MS_Agilent_gas_chromatography_mass_spectrometry_system_model}, + {MS_5977B_MSD, MS_quadrupole_instrument}, + {MS_5977B_MSD, MS_gas_chromatography_mass_spectrometry_system}, {MS_5977B_MSD, MS_Agilent_instrument_model}, - {MS_5977C_MSD, MS_quadrupole}, - {MS_5977C_MSD, MS_Agilent_gas_chromatography_mass_spectrometry_system_model}, + {MS_5977C_MSD, MS_quadrupole_instrument}, + {MS_5977C_MSD, MS_gas_chromatography_mass_spectrometry_system}, {MS_5977C_MSD, MS_Agilent_instrument_model}, - {MS_6230_Time_of_Flight_LC_MS, MS_time_of_flight}, + {MS_6230_Time_of_Flight_LC_MS, MS_time_of_flight_instrument}, {MS_6230_Time_of_Flight_LC_MS, MS_Agilent_instrument_model}, - {MS_6410A_Triple_Quadrupole_LC_MS, MS_triple_quadrupole}, + {MS_6410A_Triple_Quadrupole_LC_MS, MS_triple_quadrupole_instrument}, {MS_6410A_Triple_Quadrupole_LC_MS, MS_Agilent_instrument_model}, - {MS_6445_Q_TOF_LC_MS, MS_quadrupole_time_of_flight}, + {MS_6445_Q_TOF_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_6445_Q_TOF_LC_MS, MS_Agilent_instrument_model}, - {MS_6456_Q_TOF_LC_MS, MS_quadrupole_time_of_flight}, + {MS_6456_Q_TOF_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_6456_Q_TOF_LC_MS, MS_Agilent_instrument_model}, - {MS_6470_Triple_Quadrupole_LC_MS, MS_triple_quadrupole}, + {MS_6470_Triple_Quadrupole_LC_MS, MS_triple_quadrupole_instrument}, {MS_6470_Triple_Quadrupole_LC_MS, MS_Agilent_instrument_model}, - {MS_6490A_Triple_Quadrupole_LC_MS, MS_triple_quadrupole}, + {MS_6490A_Triple_Quadrupole_LC_MS, MS_triple_quadrupole_instrument}, {MS_6490A_Triple_Quadrupole_LC_MS, MS_Agilent_instrument_model}, - {MS_6495_Triple_Quadrupole_LC_MS, MS_triple_quadrupole}, + {MS_6495_Triple_Quadrupole_LC_MS, MS_triple_quadrupole_instrument}, {MS_6495_Triple_Quadrupole_LC_MS, MS_Agilent_instrument_model}, - {MS_6520_Q_TOF_LC_MS, MS_quadrupole_time_of_flight}, + {MS_6520_Q_TOF_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_6520_Q_TOF_LC_MS, MS_Agilent_instrument_model}, - {MS_6530_Q_TOF_LC_MS, MS_quadrupole_time_of_flight}, + {MS_6530_Q_TOF_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_6530_Q_TOF_LC_MS, MS_Agilent_instrument_model}, - {MS_6543_Q_TOF_LC_MS, MS_quadrupole_time_of_flight}, + {MS_6543_Q_TOF_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_6543_Q_TOF_LC_MS, MS_Agilent_instrument_model}, - {MS_6545XT_Q_TOF_LC_MS, MS_quadrupole_time_of_flight}, + {MS_6545XT_Q_TOF_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_6545XT_Q_TOF_LC_MS, MS_Agilent_instrument_model}, - {MS_6546_Q_TOF_LC_MS, MS_quadrupole_time_of_flight}, + {MS_6546_Q_TOF_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_6546_Q_TOF_LC_MS, MS_Agilent_instrument_model}, - {MS_6600_Q_TOF_LC_MS, MS_quadrupole_time_of_flight}, + {MS_6600_Q_TOF_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_6600_Q_TOF_LC_MS, MS_Agilent_instrument_model}, - {MS_7000C_Triple_Quadrupole_GC_MS, MS_triple_quadrupole}, - {MS_7000C_Triple_Quadrupole_GC_MS, MS_Agilent_gas_chromatography_mass_spectrometry_system_model}, + {MS_7000C_Triple_Quadrupole_GC_MS, MS_triple_quadrupole_instrument}, + {MS_7000C_Triple_Quadrupole_GC_MS, MS_gas_chromatography_mass_spectrometry_system}, {MS_7000C_Triple_Quadrupole_GC_MS, MS_Agilent_instrument_model}, - {MS_7000D_Triple_Quadrupole_GC_MS, MS_triple_quadrupole}, - {MS_7000D_Triple_Quadrupole_GC_MS, MS_Agilent_gas_chromatography_mass_spectrometry_system_model}, + {MS_7000D_Triple_Quadrupole_GC_MS, MS_triple_quadrupole_instrument}, + {MS_7000D_Triple_Quadrupole_GC_MS, MS_gas_chromatography_mass_spectrometry_system}, {MS_7000D_Triple_Quadrupole_GC_MS, MS_Agilent_instrument_model}, - {MS_7010_Triple_Quadrupole_GC_MS, MS_triple_quadrupole}, - {MS_7010_Triple_Quadrupole_GC_MS, MS_Agilent_gas_chromatography_mass_spectrometry_system_model}, + {MS_7010_Triple_Quadrupole_GC_MS, MS_triple_quadrupole_instrument}, + {MS_7010_Triple_Quadrupole_GC_MS, MS_gas_chromatography_mass_spectrometry_system}, {MS_7010_Triple_Quadrupole_GC_MS, MS_Agilent_instrument_model}, - {MS_7010B_Triple_Quadrupole_GC_MS, MS_triple_quadrupole}, - {MS_7010B_Triple_Quadrupole_GC_MS, MS_Agilent_gas_chromatography_mass_spectrometry_system_model}, + {MS_7010B_Triple_Quadrupole_GC_MS, MS_triple_quadrupole_instrument}, + {MS_7010B_Triple_Quadrupole_GC_MS, MS_gas_chromatography_mass_spectrometry_system}, {MS_7010B_Triple_Quadrupole_GC_MS, MS_Agilent_instrument_model}, - {MS_7200_Q_TOF_GC_MS, MS_quadrupole_time_of_flight}, - {MS_7200_Q_TOF_GC_MS, MS_Agilent_gas_chromatography_mass_spectrometry_system_model}, + {MS_7200_Q_TOF_GC_MS, MS_quadrupole_time_of_flight_instrument}, + {MS_7200_Q_TOF_GC_MS, MS_gas_chromatography_mass_spectrometry_system}, {MS_7200_Q_TOF_GC_MS, MS_Agilent_instrument_model}, - {MS_7250_Q_TOF_GC_MS, MS_quadrupole_time_of_flight}, - {MS_7250_Q_TOF_GC_MS, MS_Agilent_gas_chromatography_mass_spectrometry_system_model}, + {MS_7250_Q_TOF_GC_MS, MS_quadrupole_time_of_flight_instrument}, + {MS_7250_Q_TOF_GC_MS, MS_gas_chromatography_mass_spectrometry_system}, {MS_7250_Q_TOF_GC_MS, MS_Agilent_instrument_model}, - {MS_CE_TOFMS, MS_time_of_flight}, + {MS_CE_TOFMS, MS_time_of_flight_instrument}, {MS_CE_TOFMS, MS_Agilent_instrument_model}, - {MS_G3250AA_Time_of_Flight_LC_MS, MS_time_of_flight}, + {MS_G3250AA_Time_of_Flight_LC_MS, MS_time_of_flight_instrument}, {MS_G3250AA_Time_of_Flight_LC_MS, MS_Agilent_instrument_model}, - {MS_Revident_Q_TOF_LC_MS, MS_quadrupole_time_of_flight}, + {MS_Revident_Q_TOF_LC_MS, MS_quadrupole_time_of_flight_instrument}, {MS_Revident_Q_TOF_LC_MS, MS_Agilent_instrument_model}, + {MS_Pegasus_BT_4D, MS_time_of_flight_instrument}, + {MS_Pegasus_BT_4D, MS_gas_chromatography_mass_spectrometry_system}, {MS_Pegasus_BT_4D, MS_LECO_instrument_model}, + {MS_Pegasus_HT, MS_time_of_flight_instrument}, + {MS_Pegasus_HT, MS_gas_chromatography_mass_spectrometry_system}, {MS_Pegasus_HT, MS_LECO_instrument_model}, + {MS_Pegasus_IV, MS_time_of_flight_instrument}, + {MS_Pegasus_IV, MS_gas_chromatography_mass_spectrometry_system}, {MS_Pegasus_IV, MS_LECO_instrument_model}, + {MS_PTR_TOF_8000, MS_time_of_flight_instrument}, {MS_PTR_TOF_8000, MS_Ionicon_Analytik_instrument_model}, + {MS_AccuTOF_GCv, MS_time_of_flight_instrument}, + {MS_AccuTOF_GCv, MS_gas_chromatography_mass_spectrometry_system}, {MS_AccuTOF_GCv, MS_JEOL_instrument_model}, + {MS_TOF_SIMS_5, MS_time_of_flight_instrument}, {MS_TOF_SIMS_5, MS_IONTOF_instrument_model}, + {MS_TurboMass_GC_MS, MS_quadrupole_instrument}, + {MS_TurboMass_GC_MS, MS_gas_chromatography_mass_spectrometry_system}, {MS_TurboMass_GC_MS, MS_PerkinElmer_instrument_model}, + {MS_ThermoQuest_Voyager, MS_quadrupole_instrument}, {MS_ThermoQuest_Voyager, MS_Thermo_Finnigan_instrument_model}, + {MS_AXIMA_LNR, MS_time_of_flight_instrument}, {MS_AXIMA_LNR, MS_Shimadzu_MALDI_TOF_instrument_model}, + {MS_AXIMA_TOF__sq__, MS_tandem_time_of_flight_instrument}, {MS_AXIMA_TOF__sq__, MS_Shimadzu_MALDI_TOF_instrument_model}, + {MS_AXIMA_Resonance, MS_ion_trap_time_of_flight_instrument}, {MS_AXIMA_Resonance, MS_Shimadzu_MALDI_TOF_instrument_model}, + {MS_MALDI_8020, MS_time_of_flight_instrument}, {MS_MALDI_8020, MS_Shimadzu_MALDI_TOF_instrument_model}, + {MS_MALDI_8030, MS_time_of_flight_instrument}, {MS_MALDI_8030, MS_Shimadzu_MALDI_TOF_instrument_model}, + {MS_MALDI_8020_EasyCare, MS_time_of_flight_instrument}, {MS_MALDI_8020_EasyCare, MS_Shimadzu_MALDI_TOF_instrument_model}, + {MS_MALDI_8030_EasyCare, MS_time_of_flight_instrument}, {MS_MALDI_8030_EasyCare, MS_Shimadzu_MALDI_TOF_instrument_model}, + {MS_LCMS_2010, MS_quadrupole_instrument}, {MS_LCMS_2010, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_LCMS_2050, MS_quadrupole_instrument}, {MS_LCMS_2050, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_LCMS_8045RX, MS_triple_quadrupole_instrument}, {MS_LCMS_8045RX, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_LCMS_8050RX, MS_triple_quadrupole_instrument}, {MS_LCMS_8050RX, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_LCMS_8060RX, MS_triple_quadrupole_instrument}, {MS_LCMS_8060RX, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_LCMS_8065XE, MS_triple_quadrupole_instrument}, {MS_LCMS_8065XE, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_LCMS_9050, MS_quadrupole_time_of_flight_instrument}, {MS_LCMS_9050, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_GCMS_QP5050A, MS_quadrupole_instrument}, {MS_GCMS_QP5050A, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_GCMS_QP2010S, MS_quadrupole_instrument}, {MS_GCMS_QP2010S, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_GCMS_QP2010, MS_quadrupole_instrument}, {MS_GCMS_QP2010, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_GCMS_QP2020NX, MS_quadrupole_instrument}, {MS_GCMS_QP2020NX, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_GCMS_QP2050, MS_quadrupole_instrument}, {MS_GCMS_QP2050, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_GCMS_TQ_8030, MS_triple_quadrupole_instrument}, {MS_GCMS_TQ_8030, MS_Shimadzu_Scientific_Instruments_instrument_model}, + {MS_GCMS_TQ_8050, MS_triple_quadrupole_instrument}, {MS_GCMS_TQ_8050, MS_Shimadzu_Scientific_Instruments_instrument_model}, {MS_all_ions_fragmentation_DIA_alignment, MS_data_processing_action}, {MS_hyphenated_separation, MS_run_attribute}, @@ -9839,7 +10345,7 @@ CVIDPair relationsIsA_[] = {MS_ultra_high_performance_liquid_chromatography_system, MS_liquid_chromatography_system}, {MS_fast_protein_liquid_chromatography_system, MS_liquid_chromatography_system}, {MS_three_dimensional_liquid_chromatography_system, MS_liquid_chromatography_system}, - {MS_planar_chomatography_system, MS_liquid_chromatography_system}, + {MS_planar_chromatography_system, MS_liquid_chromatography_system}, {MS_thin_layer_chromatography_system, MS_liquid_chromatography_system}, {MS_high_performance_thin_layer_chromatography_system, MS_liquid_chromatography_system}, {MS_two_dimensional_liquid_chromatography_system, MS_liquid_chromatography_system}, @@ -10065,8 +10571,6 @@ CVIDPair relationsIsA_[] = {MS_Agilent_gas_chromatography_system_model, MS_gas_chromatography_system_model}, {MS_6890N, MS_Agilent_gas_chromatography_system_model}, {MS_gas_chromatography_mass_spectrometry_system, MS_hyphenated_separation_system}, - {MS_gas_chromatography_mass_spectrometry_system_model, MS_gas_chromatography_mass_spectrometry_system}, - {MS_Shimadzu_gas_chromatography_mass_spectrometry_system_model, MS_gas_chromatography_mass_spectrometry_system_model}, {MS_5975C, MS_Agilent_gas_chromatography_system_model}, {MS_5975T, MS_Agilent_gas_chromatography_system_model}, {MS_6890, MS_Agilent_gas_chromatography_system_model}, @@ -10090,26 +10594,59 @@ CVIDPair relationsIsA_[] = {MS_TRACE_GC, MS_Thermo_Scientific_gas_chromatography_system_model}, {MS_TRACE_GC_Ultra, MS_Thermo_Scientific_gas_chromatography_system_model}, {MS_FOCUS_GC, MS_Thermo_Scientific_gas_chromatography_system_model}, - {MS_triple_quadrupole, MS_instrument_class}, - {MS_quadrupole_time_of_flight, MS_instrument_class}, - {MS_ion_trap_time_of_flight, MS_instrument_class}, - {MS_triple_quadrupole_linear_ion_trap, MS_instrument_class}, - {MS_quadrupole_fourier_transform_ion_cyclotron_resonance, MS_instrument_class}, - {MS_quadrupole_ion_mobility_time_of_flight, MS_instrument_class}, - {MS_ion_trap_orbitrap, MS_instrument_class}, - {MS_quadrupole_orbitrap, MS_instrument_class}, - {MS_quadrupole_ion_trap_orbitrap, MS_instrument_class}, - {MS_quadrupole_orbitrap_astral, MS_instrument_class}, - {MS_mixed_polarity_acquisition, MS_data_file_content}, + {MS_triple_quadrupole_instrument, MS_instrument_class}, + {MS_quadrupole_time_of_flight_instrument, MS_instrument_class}, + {MS_ion_trap_time_of_flight_instrument, MS_instrument_class}, + {MS_triple_quadrupole_linear_ion_trap_instrument, MS_instrument_class}, + {MS_quadrupole_fourier_transform_ion_cyclotron_resonance_instrument, MS_instrument_class}, + {MS_quadrupole_ion_mobility_time_of_flight_instrument, MS_instrument_class}, + {MS_ion_trap_orbitrap_instrument, MS_instrument_class}, + {MS_quadrupole_orbitrap_instrument, MS_instrument_class}, + {MS_quadrupole_ion_trap_orbitrap_instrument, MS_instrument_class}, + {MS_quadrupole_orbitrap_astral_instrument, MS_instrument_class}, + {MS_mixed_polarity_acquisition, MS_acquisition_polarity}, {MS_secondary_electrospray_ionization, MS_atmospheric_pressure_ionization}, + {MS_acquisition_polarity, MS_data_file_content}, {MS_zstd_compression, MS_binary_data_compression_type}, {MS_byte_shuffled_zstd_compression, MS_binary_data_compression_type}, {MS_dictionary_encoded_zstd_compression, MS_binary_data_compression_type}, {MS_MS_Numpress_linear_prediction_compression_followed_by_zstd_compression, MS_binary_data_compression_type}, {MS_MS_Numpress_positive_integer_compression_followed_by_zstd_compression, MS_binary_data_compression_type}, {MS_MS_Numpress_short_logged_float_compression_followed_by_zstd_compression, MS_binary_data_compression_type}, + {MS_electrophoretic_separation, MS_run_attribute}, + {MS_capillary_electrophoresis, MS_electrophoretic_separation}, + {MS_electrochromatography, MS_liquid_chromatography_separation}, + {MS_ion_pair_reversed_phase_chromatography, MS_reversed_phase_chromatography}, + {MS_supercritical_fluid_chromatography, MS_chromatography_separation}, + {MS_TSQ_Certis, MS_triple_quadrupole_instrument}, {MS_TSQ_Certis, MS_Thermo_Scientific_instrument_model}, {MS_AccurateMassSearch, MS_TOPP_software}, + {MS_Ionoptika_instrument_model, MS_instrument_model}, + {MS_Ionoptika_software, MS_software}, + {MS_Ionoptika_J105, MS_time_of_flight_instrument}, + {MS_Ionoptika_J105, MS_Ionoptika_instrument_model}, + {MS_J_Series_III, MS_time_of_flight_instrument}, + {MS_J_Series_III, MS_Ionoptika_instrument_model}, + {MS_NeoSIMS, MS_acquisition_software}, + {MS_NeoSIMS, MS_Ionoptika_software}, + {MS_Ionoptika_Image_Analyser, MS_analysis_software}, + {MS_Ionoptika_Image_Analyser, MS_data_processing_software}, + {MS_Ionoptika_Image_Analyser, MS_Ionoptika_software}, + {MS_J105_Ionoptika_Mass_Imager, MS_analysis_software}, + {MS_J105_Ionoptika_Mass_Imager, MS_data_processing_software}, + {MS_J105_Ionoptika_Mass_Imager, MS_Ionoptika_software}, + {MS_IoDataConverter, MS_data_processing_software}, + {MS_IoDataConverter, MS_Ionoptika_software}, + {MS_Ionoptika_V1_format, MS_mass_spectrometer_file_format}, + {MS_Ionoptika_V3_format, MS_mass_spectrometer_file_format}, + {MS_lambda_max, MS_spectrum_property}, + {MS_list_of_doubles, MS_list_of_type}, + {MS_coordinate_spacing_model, MS_spectrum_attribute}, + {MS_polynomial_delta_coordinate_interpolation, MS_coordinate_spacing_model}, + {MS_grid_coordinate_interpolation, MS_coordinate_spacing_model}, + {MS_linear_grid_interpolation, MS_grid_coordinate_interpolation}, + {MS_square_root_grid_interpolation, MS_grid_coordinate_interpolation}, + {MS_coordinate_grid_encoding, MS_binary_data_compression_type}, {MS_zero_intensity_point_trimming, MS_data_processing_action}, {MS_zero_intensity_point_trimming_interpolation, MS_zero_intensity_point_trimming}, {MS_untargeted_analysis, MS_analysis}, @@ -10117,7 +10654,132 @@ CVIDPair relationsIsA_[] = {MS_semi_targeted_analysis, MS_analysis}, {MS_parallel_reaction_monitoring, MS_mass_spectrometry_acquisition_method_aspect}, {MS_parallel_reaction_monitoring, MS_mass_spectrometry_acquisition_method}, - {MS_Agilent_gas_chromatography_mass_spectrometry_system_model, MS_gas_chromatography_mass_spectrometry_system_model}, + {MS_centroid_peak, MS_peak}, + {MS_two_dimensional_gas_chromatography, MS_gas_chromatography_separation}, + {MS_SpectroSwiss_software, MS_software}, + {MS_Peak_by_Peak, MS_SpectroSwiss_software}, + {MS_Peak_by_Peak, MS_analysis_software}, + {MS_Peak_by_Peak, MS_data_processing_software}, + {MS_chromatographic_column, MS_run_attribute}, + {MS_liquid_chromatographic_column, MS_chromatographic_column_type}, + {MS_chromatographic_stationary_phase, MS_run_attribute}, + {MS_chromatographic_stationary_phase_attribute, MS_run_attribute}, + {MS_pore_size, MS_chromatographic_stationary_phase_attribute}, + {MS_particle_diameter, MS_chromatographic_stationary_phase_attribute}, + {MS_chromatographic_column_attribute, MS_run_attribute}, + {MS_column_length, MS_chromatographic_column_attribute}, + {MS_column_internal_diameter, MS_chromatographic_column_attribute}, + {MS_particle_porosity, MS_chromatographic_stationary_phase_attribute}, + {MS_fully_porous, MS_particle_porosity}, + {MS_superficially_porous, MS_particle_porosity}, + {MS_non_porous, MS_particle_porosity}, + {MS_support_material, MS_chromatographic_stationary_phase_attribute}, + {MS_silica_based, MS_support_material}, + {MS_hybrid_particle, MS_support_material}, + {MS_polymer_based, MS_support_material}, + {MS_monolithic, MS_support_material}, + {MS_porous_graphitic_carbon, MS_support_material}, + {MS_trap_column, MS_chromatographic_column_role}, + {MS_guard_column, MS_chromatographic_column_role}, + {MS_analytical_column, MS_chromatographic_column_role}, + {MS_gas_chromatographic_column, MS_chromatographic_column_type}, + {MS_chromatographic_column_role, MS_run_attribute}, + {MS_chromatographic_column_type, MS_run_attribute}, + {MS_tandem_time_of_flight_instrument, MS_instrument_class}, + {MS_magnetic_sector_ion_trap_instrument, MS_instrument_class}, + {MS_fourier_transform_ion_cyclotron_resonance_instrument, MS_instrument_class}, + {MS_magnetic_sector_instrument, MS_instrument_class}, + {MS_quadrupole_instrument, MS_instrument_class}, + {MS_time_of_flight_instrument, MS_instrument_class}, + {MS_ion_trap_instrument, MS_instrument_class}, + {MS_orbitrap_instrument, MS_instrument_class}, + {MS_argon_gas_cluster_ion_beam, MS_gas_cluster_ion_beam}, + {MS_singly_charged_bismuth_trimer_liquid_metal_ion_gun, MS_bismuth_liquid_metal_ion_gun}, + {MS_doubly_charged_bismuth_trimer_liquid_metal_ion_gun, MS_bismuth_liquid_metal_ion_gun}, + {MS_two_dimensional_liquid_chromatography, MS_liquid_chromatography_separation}, + {MS_bismuth_liquid_metal_ion_gun, MS_liquid_metal_ion_gun}, + {MS_gas_cluster_ion_beam, MS_fast_ion_bombardment}, + {MS_liquid_metal_ion_gun, MS_fast_ion_bombardment}, + {MS_Thermo_Scientific_software, MS_software}, + {MS_TraceFinder, MS_Thermo_Scientific_software}, + {MS_TraceFinder, MS_acquisition_software}, + {MS_TraceFinder, MS_analysis_software}, + {MS_TraceFinder, MS_data_processing_software}, + {MS_FreeStyle, MS_Thermo_Scientific_software}, + {MS_FreeStyle, MS_analysis_software}, + {MS_FreeStyle, MS_data_processing_software}, + {MS_Chromeleon_CDS, MS_Thermo_Scientific_software}, + {MS_Chromeleon_CDS, MS_acquisition_software}, + {MS_Chromeleon_CDS, MS_analysis_software}, + {MS_Chromeleon_CDS, MS_data_processing_software}, + {MS_Mass_Frontier, MS_Thermo_Scientific_software}, + {MS_Mass_Frontier, MS_analysis_software}, + {MS_Mass_Frontier, MS_data_processing_software}, + {MS_LipidSearch, MS_Thermo_Scientific_software}, + {MS_LipidSearch, MS_analysis_software}, + {MS_LipidSearch, MS_data_processing_software}, + {MS_mzVault, MS_Thermo_Scientific_software}, + {MS_mzVault, MS_analysis_software}, + {MS_mzVault, MS_data_processing_software}, + {MS_SIEVE, MS_Thermo_Scientific_software}, + {MS_SIEVE, MS_analysis_software}, + {MS_SIEVE, MS_data_processing_software}, + {MS_BioPharma_Finder, MS_Thermo_Scientific_software}, + {MS_BioPharma_Finder, MS_analysis_software}, + {MS_BioPharma_Finder, MS_data_processing_software}, + {MS_ion_mobility_quadrupole_time_of_flight_instrument, MS_instrument_class}, + {MS_ion_trap_fourier_transform_ion_cyclotron_resonance_instrument, MS_instrument_class}, + {MS_quadrupole_ion_trap_instrument, MS_instrument_class}, + {MS_LECO_PEG_format, MS_mass_spectrometer_file_format}, + {MS_JEOL_JPF_format, MS_mass_spectrometer_file_format}, + {MS_retention_time_window_target, MS_retention_time_window_attribute}, + {MS_Monocle, MS_data_processing_software}, + {MS_______DE______AFILMV___P__, MS_Cleavage_agent_regular_expression}, + {MS_Thermolysin, MS_cleavage_agent_name}, + {MS_____AEFILTVWY__, MS_Cleavage_agent_regular_expression}, + {MS_peptidase_K, MS_cleavage_agent_name}, + {MS_____N____G_, MS_Cleavage_agent_regular_expression}, + {MS_hydroxylamine, MS_cleavage_agent_name}, + {MS_amino_acid_confidence_level, MS_PSM_level_identification_statistic}, + {MS_peptidoform_token_confidence_level, MS_PSM_level_identification_statistic}, + {MS_protein_sequence, MS_protein_attribute}, + {MS_Orbitrap_Tribrid_Apex, MS_quadrupole_ion_trap_orbitrap_instrument}, + {MS_Orbitrap_Tribrid_Apex, MS_Thermo_Scientific_instrument_model}, + {MS_Xevo_MRT_P10, MS_Waters_instrument_model}, + {MS_Xevo_MRT_P10, MS_quadrupole_time_of_flight_instrument}, + {MS_Cyclic_IMS_P20, MS_Waters_instrument_model}, + {MS_Cyclic_IMS_P20, MS_quadrupole_ion_mobility_time_of_flight_instrument}, + {MS_Orbitrap_Excedion, MS_Thermo_Scientific_instrument_model}, + {MS_Orbitrap_Excedion, MS_quadrupole_orbitrap_instrument}, + {MS_novus_V55, MS_SCIEX_instrument_model}, + {MS_novus_V55, MS_triple_quadrupole_instrument}, + {MS_9500_Triple_Quadrupole_ICP_MS, MS_Agilent_instrument_model}, + {MS_9500_Triple_Quadrupole_ICP_MS, MS_triple_quadrupole_instrument}, + {MS_InfinityLab_Pro_iQ, MS_Agilent_instrument_model}, + {MS_InfinityLab_Pro_iQ, MS_quadrupole_instrument}, + {MS_ion_mobility_quadrupole_FT_ICR_instrument, MS_instrument_class}, + {MS_timsMRMS, MS_Bruker_Daltonics_instrument_model}, + {MS_timsMRMS, MS_ion_mobility_quadrupole_FT_ICR_instrument}, + {MS_DeepNovo, MS_analysis_software}, + {MS_DeepNovo, MS_BSI_software}, + {MS_DeepNovo_DIA, MS_analysis_software}, + {MS_DeepNovo_DIA, MS_BSI_software}, + {MS_PointNovo, MS_analysis_software}, + {MS_PGPointNovo, MS_analysis_software}, + {MS_BiATNovo, MS_analysis_software}, + {MS_NovoB, MS_analysis_software}, + {MS_PepNet, MS_analysis_software}, + {MS__xCF__x80__HelixNovo, MS_analysis_software}, + {MS__xCF__x80__PrimeNovo, MS_analysis_software}, + {MS_PowerNovo, MS_analysis_software}, + {MS_pUniFind, MS_analysis_software}, + {MS_Sage, MS_analysis_software}, + {MS_Sage, MS_quantitation_software_name}, + {MS_BiblioSpec_Spectrum_Sequence_List, MS_tab_delimited_text_format}, + {MS_BiblioSpec_Spectrum_Sequence_List, MS_identification_file_format}, + {MS_ProteoScape, MS_analysis_software}, + {MS_ProteoScape, MS_Bruker_software}, + {MS_Stitch, MS_analysis_software}, {NCIT_Number_of_Occurrences, NCIT_Number}, {MS_single_value, MS_QC_metric_value_type}, {MS_n_tuple, MS_QC_metric_value_type}, @@ -11865,6 +12527,15 @@ CVIDPair relationsIsA_[] = {UNIMOD_b_type_ion, UNIMOD_unimod_root_node}, {UNIMOD_PnTAG, UNIMOD_unimod_root_node}, {UNIMOD_DMA_PEG3, UNIMOD_unimod_root_node}, + {UNIMOD_HCCA_Lys, UNIMOD_unimod_root_node}, + {UNIMOD_Phosphocholine, UNIMOD_unimod_root_node}, + {UNIMOD_Methyl_13C_1_2H_2_, UNIMOD_unimod_root_node}, + {UNIMOD_c_type_ion, UNIMOD_unimod_root_node}, + {UNIMOD_x_type_ion, UNIMOD_unimod_root_node}, + {UNIMOD_z_type_ion, UNIMOD_unimod_root_node}, + {UNIMOD_Dehydromethionine, UNIMOD_unimod_root_node}, + {UNIMOD_Label_2H_8_, UNIMOD_unimod_root_node}, + {UNIMOD_imidazolone, UNIMOD_unimod_root_node}, {UO_length_unit, UO_unit}, {UO_mass_unit, UO_unit}, {UO_time_unit, UO_unit}, @@ -12631,6 +13302,13 @@ CVIDPair relationsPartOf_[] = {MS_instrument_class, MS_instrument}, {MS_analysis, MS_Proteomics_Standards_Initiative_Mass_Spectrometry_Vocabularies}, {MS_parallel_reaction_monitoring, MS_targeted_analysis}, + {MS_chromatographic_column, MS_chromatography_separation}, + {MS_chromatographic_stationary_phase, MS_chromatographic_column}, + {MS_chromatographic_stationary_phase_attribute, MS_chromatographic_stationary_phase}, + {MS_chromatographic_column_attribute, MS_chromatographic_column}, + {MS_chromatographic_column_role, MS_chromatographic_column}, + {MS_chromatographic_column_type, MS_chromatographic_column}, + {MS_peak_group, MS_Proteomics_Standards_Initiative_Mass_Spectrometry_Vocabularies}, {MS_PSI_MS_CV_Quality_Control_Vocabulary, MS_Proteomics_Standards_Initiative_Mass_Spectrometry_Vocabularies}, {MS_QC_metric, MS_PSI_MS_CV_Quality_Control_Vocabulary}, {MS_QC_metric_value_type, MS_PSI_MS_CV_Quality_Control_Vocabulary}, @@ -13093,6 +13771,22 @@ OtherRelationPair relationsOther_[] = {MS_adduct_ion_average_mass, "has_units", UO_dalton}, {MS_theoretical_neutral_monoisotopic_mass, "has_units", UO_dalton}, {MS_theoretical_neutral_average_mass, "has_units", UO_dalton}, + {MS_lambda_max, "has_units", UO_nanometer}, + {MS_coordinate_spacing_model, "has_value_type", MS_list_of_doubles}, + {MS_pore_size, "has_units", UO_angstrom}, + {MS_particle_diameter, "has_units", UO_micrometer}, + {MS_column_length, "has_units", UO_millimeter}, + {MS_column_internal_diameter, "has_units", UO_millimeter}, + {MS_retention_time_window_target, "has_units", UO_second}, + {MS_retention_time_window_target, "has_units", UO_minute}, + {MS_Thermolysin, "has_regexp", MS_______DE______AFILMV___P__}, + {MS_peptidase_K, "has_regexp", MS_____AEFILTVWY__}, + {MS_hydroxylamine, "has_regexp", MS_____N____G_}, + {MS_amino_acid_confidence_level, "has_domain", MS_value_between_0_and_1_inclusive}, + {MS_amino_acid_confidence_level, "has_value_type", MS_list_of_floats}, + {MS_peptidoform_token_confidence_level, "has_domain", MS_value_between_0_and_1_inclusive}, + {MS_peptidoform_token_confidence_level, "has_value_type", MS_list_of_floats}, + {MS_protein_sequence, "has_value_type", MS_AA_sequence}, {MS_precursor_ion_current_chromatogram, "has_metric_category", MS_ID_free_metric}, {MS_precursor_ion_current_chromatogram, "has_metric_category", MS_single_run_based_metric}, {MS_precursor_ion_current_chromatogram, "has_metric_category", MS_chromatogram_metric}, @@ -13853,6 +14547,7 @@ CVIDStringPair relationsExactSynonym_[] = {MS_low_intensity_data_point_removal, "thresholding"}, {MS_electron_transfer_dissociation, "ETD"}, {MS_pulsed_q_dissociation, "PQD"}, + {MS_ProteinLynx_Global_Server, "PLGS"}, {MS_ProteoWizard_software, "pwiz"}, {MS_photodiode_array_detector, "PDA"}, {MS_inductive_detector, "image current detector"}, @@ -13924,6 +14619,7 @@ CVIDStringPair relationsExactSynonym_[] = {MS_Orbitrap_Velos_Pro, "LTQ Orbitrap Velos Pro"}, {MS_mzPAF_peptide_ion_annotation_format, "peptide ion annotation format"}, {MS_crosslinked_peptide_ion_annotation_format, "cross-linked peptide ion annotation format"}, + {MS_ProSight, "ProSightPD"}, {MS_no_isolation, "isolation window full range"}, {MS_PTX_QC, "PTXQC"}, {MS_QuaMeter_IDFree, "QuaMeter"}, @@ -13944,13 +14640,41 @@ CVIDStringPair relationsExactSynonym_[] = {MS_asymmetric_track_lossless_time_of_flight_analyzer, "Astral"}, {MS_AlphaLP, "alpha-lytic endopeptidase"}, {MS_AlphaLP, "alpha-lytic protease"}, - {MS_triple_quadrupole, "QqQ"}, - {MS_quadrupole_time_of_flight, "Q-TOF"}, - {MS_ion_trap_time_of_flight, "IT-TOF"}, - {MS_triple_quadrupole_linear_ion_trap, "QqLIT"}, - {MS_quadrupole_fourier_transform_ion_cyclotron_resonance, "Q-FT-ICR"}, - {MS_quadrupole_ion_mobility_time_of_flight, "Q-IMS-TOF"}, + {MS_triple_quadrupole_instrument, "QqQ"}, + {MS_quadrupole_time_of_flight_instrument, "Q-TOF"}, + {MS_ion_trap_time_of_flight_instrument, "IT-TOF"}, + {MS_triple_quadrupole_linear_ion_trap_instrument, "QqLIT"}, + {MS_quadrupole_fourier_transform_ion_cyclotron_resonance_instrument, "Q-FT-ICR"}, + {MS_quadrupole_ion_mobility_time_of_flight_instrument, "Q-IMS-TOF"}, + {MS_capillary_electrophoresis, "capilliary zone electrophoresis"}, + {MS_capillary_electrophoresis, "CE"}, + {MS_supercritical_fluid_chromatography, "SFC"}, + {MS_lambda_max, "λ-max"}, {MS_parallel_reaction_monitoring, "PRM"}, + {MS_two_dimensional_gas_chromatography, "GCxGC"}, + {MS_Peak_by_Peak, "PeakByPeak"}, + {MS_column_internal_diameter, "column I.D."}, + {MS_superficially_porous, "core-shell particle"}, + {MS_porous_graphitic_carbon, "PGC stationary phase"}, + {MS_tandem_time_of_flight_instrument, "TOF/TOF"}, + {MS_tandem_time_of_flight_instrument, "TOF-TOF"}, + {MS_argon_gas_cluster_ion_beam, "Ar GCIB"}, + {MS_singly_charged_bismuth_trimer_liquid_metal_ion_gun, "[Bi3]+ LMIG"}, + {MS_doubly_charged_bismuth_trimer_liquid_metal_ion_gun, "[Bi3]2+ LMIG"}, + {MS_two_dimensional_liquid_chromatography, "2D-LC"}, + {MS_two_dimensional_liquid_chromatography, "LCxLC"}, + {MS_bismuth_liquid_metal_ion_gun, "Bi LMIG"}, + {MS_gas_cluster_ion_beam, "GCIB"}, + {MS_liquid_metal_ion_gun, "LMIG"}, + {MS_Chromeleon_CDS, "Chromeleon Chromatography Data System"}, + {MS_ion_mobility_quadrupole_time_of_flight_instrument, "IMS-Q-TOF"}, + {MS_Thermolysin, "Bacillus thermoproteolyticus neutral proteinase"}, + {MS_peptidase_K, "endopeptidase K"}, + {MS_peptidase_K, "proteinase K"}, + {MS_peptidase_K, "Tritirachium album proteinase K"}, + {MS_peptidase_K, "Tritirachium alkaline proteinase"}, + {MS__xCF__x80__HelixNovo, "pi-HelixNovo"}, + {MS__xCF__x80__PrimeNovo, "pi-PrimeNovo"}, {MS_precursor_ion_current_chromatogram, "precursor ion chromatogram"}, {MS_XIC50_fraction, "XIC-WideFrac"}, {MS_number_of_MS1_spectra, "MS1-Count"}, @@ -28758,6 +29482,72 @@ PropertyValuePair propertyValue_[] = {UNIMOD_DMA_PEG3, "spec_6_hidden", "1"}, {UNIMOD_DMA_PEG3, "spec_6_position", "Anywhere"}, {UNIMOD_DMA_PEG3, "spec_6_site", "Y"}, + {UNIMOD_HCCA_Lys, "approved", "0"}, + {UNIMOD_HCCA_Lys, "delta_composition", "H(28) C(22) N(4) O(4)"}, + {UNIMOD_HCCA_Lys, "spec_1_classification", "Chemical derivative"}, + {UNIMOD_HCCA_Lys, "spec_1_hidden", "1"}, + {UNIMOD_HCCA_Lys, "spec_1_position", "Anywhere"}, + {UNIMOD_HCCA_Lys, "spec_1_site", "K"}, + {UNIMOD_Phosphocholine, "approved", "0"}, + {UNIMOD_Phosphocholine, "delta_composition", "H(12) C(5) N O(3) P"}, + {UNIMOD_Phosphocholine, "spec_1_classification", "Post-translational"}, + {UNIMOD_Phosphocholine, "spec_1_hidden", "1"}, + {UNIMOD_Phosphocholine, "spec_1_position", "Anywhere"}, + {UNIMOD_Phosphocholine, "spec_1_site", "S"}, + {UNIMOD_Phosphocholine, "spec_2_classification", "Post-translational"}, + {UNIMOD_Phosphocholine, "spec_2_hidden", "1"}, + {UNIMOD_Phosphocholine, "spec_2_position", "Anywhere"}, + {UNIMOD_Phosphocholine, "spec_2_site", "T"}, + {UNIMOD_Phosphocholine, "spec_3_classification", "Post-translational"}, + {UNIMOD_Phosphocholine, "spec_3_hidden", "1"}, + {UNIMOD_Phosphocholine, "spec_3_position", "Anywhere"}, + {UNIMOD_Phosphocholine, "spec_3_site", "Y"}, + {UNIMOD_Methyl_13C_1_2H_2_, "approved", "0"}, + {UNIMOD_Methyl_13C_1_2H_2_, "delta_composition", "2H(2) 13C"}, + {UNIMOD_Methyl_13C_1_2H_2_, "spec_1_classification", "Isotopic label"}, + {UNIMOD_Methyl_13C_1_2H_2_, "spec_1_hidden", "1"}, + {UNIMOD_Methyl_13C_1_2H_2_, "spec_1_position", "Anywhere"}, + {UNIMOD_Methyl_13C_1_2H_2_, "spec_1_site", "K"}, + {UNIMOD_Methyl_13C_1_2H_2_, "spec_2_classification", "Isotopic label"}, + {UNIMOD_Methyl_13C_1_2H_2_, "spec_2_hidden", "1"}, + {UNIMOD_Methyl_13C_1_2H_2_, "spec_2_position", "Anywhere"}, + {UNIMOD_Methyl_13C_1_2H_2_, "spec_2_site", "N-term"}, + {UNIMOD_c_type_ion, "approved", "0"}, + {UNIMOD_c_type_ion, "delta_composition", "H N O(-1)"}, + {UNIMOD_c_type_ion, "spec_1_classification", "Other"}, + {UNIMOD_c_type_ion, "spec_1_hidden", "1"}, + {UNIMOD_c_type_ion, "spec_1_position", "Any C-term"}, + {UNIMOD_c_type_ion, "spec_1_site", "C-term"}, + {UNIMOD_x_type_ion, "approved", "0"}, + {UNIMOD_x_type_ion, "delta_composition", "H(-2) C O"}, + {UNIMOD_x_type_ion, "spec_1_classification", "Other"}, + {UNIMOD_x_type_ion, "spec_1_hidden", "1"}, + {UNIMOD_x_type_ion, "spec_1_position", "Any N-term"}, + {UNIMOD_x_type_ion, "spec_1_site", "N-term"}, + {UNIMOD_z_type_ion, "approved", "0"}, + {UNIMOD_z_type_ion, "delta_composition", "H(-3) N(-1)"}, + {UNIMOD_z_type_ion, "spec_1_classification", "Other"}, + {UNIMOD_z_type_ion, "spec_1_hidden", "1"}, + {UNIMOD_z_type_ion, "spec_1_position", "Any N-term"}, + {UNIMOD_z_type_ion, "spec_1_site", "N-term"}, + {UNIMOD_Dehydromethionine, "approved", "0"}, + {UNIMOD_Dehydromethionine, "delta_composition", "H(-2)"}, + {UNIMOD_Dehydromethionine, "spec_1_classification", "Post-translational"}, + {UNIMOD_Dehydromethionine, "spec_1_hidden", "1"}, + {UNIMOD_Dehydromethionine, "spec_1_position", "Protein N-term"}, + {UNIMOD_Dehydromethionine, "spec_1_site", "M"}, + {UNIMOD_Label_2H_8_, "approved", "0"}, + {UNIMOD_Label_2H_8_, "delta_composition", "H(-8) 2H(8)"}, + {UNIMOD_Label_2H_8_, "spec_1_classification", "Isotopic label"}, + {UNIMOD_Label_2H_8_, "spec_1_hidden", "1"}, + {UNIMOD_Label_2H_8_, "spec_1_position", "Anywhere"}, + {UNIMOD_Label_2H_8_, "spec_1_site", "K"}, + {UNIMOD_imidazolone, "approved", "0"}, + {UNIMOD_imidazolone, "delta_composition", "H(8) C(6) O(4)"}, + {UNIMOD_imidazolone, "spec_1_classification", "Non-standard residue"}, + {UNIMOD_imidazolone, "spec_1_hidden", "1"}, + {UNIMOD_imidazolone, "spec_1_position", "Anywhere"}, + {UNIMOD_imidazolone, "spec_1_site", "R"}, }; // propertyValue_ @@ -28809,16 +29599,16 @@ class CVTermData : public boost::singleton cvMap_["PEFF"].URI = cvMap_["MS"].URI; cvMap_["MS"].id = "MS"; - cvMap_["MS"].version = "4.1.232"; + cvMap_["MS"].version = "4.1.257"; cvMap_["NCIT"].id = "NCIT"; - cvMap_["NCIT"].version = "4.1.232"; + cvMap_["NCIT"].version = "4.1.257"; cvMap_["PEFF"].id = "PEFF"; - cvMap_["PEFF"].version = "4.1.232"; + cvMap_["PEFF"].version = "4.1.257"; cvMap_["UNIMOD"].id = "UNIMOD"; - cvMap_["UNIMOD"].version = "2025-06-17"; + cvMap_["UNIMOD"].version = "2026-02-17"; cvMap_["UO"].id = "UO"; cvMap_["UO"].version = "releases/2026-01-16"; diff --git a/pwiz/data/common/cv.hpp b/pwiz/data/common/cv.hpp index 9e4a852cbee..9a17374edd1 100644 --- a/pwiz/data/common/cv.hpp +++ b/pwiz/data/common/cv.hpp @@ -41,9 +41,9 @@ // [psi-ms.obo] #define _PSI_MS_OBO_ // format-version: 1.2 -// data-version: 4.1.232 -// date: 16:01:2026 12:00 -// saved-by: Jonathan Hunter +// data-version: 4.1.257 +// date: 23:06:2026 22:00 +// saved-by: Douwe Schulte // default-namespace: MS // namespace-id-rule: * MS:$sequence(7,0,9999999)$ // namespace-id-rule: * PEFF:$sequence(7,0,9999999)$ @@ -70,6 +70,7 @@ // remark: creator: Jonathan Hunter ebi.ac.uk> // remark: creator: Samuel Wein openms.de> // remark: creator: Jeroen Van Goey instadeep.com> +// remark: creator: Jannick Kappelmann gmail.com> // remark: publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics Working Group // remark: When appropriate the definition and synonyms of a term are reported exactly as in the chapter 12 of IUPAC orange book. See http://www.iupac.org/projects/2003/2003-056-2-500.html and http://mass-spec.lsu.edu/msterms/index.php/Main_Page // remark: For any queries contact psidev-ms-vocab@lists.sourceforge.net @@ -81,7 +82,7 @@ // [unimod.obo] #define _UNIMOD_OBO_ // format-version: 1.4 -// date: 17:06:2025 11:31 +// date: 17:02:2026 11:36 // // [unit.obo] #define _UNIT_OBO_ @@ -136,7 +137,7 @@ enum PWIZ_API_DECL CVID /// DbDate: PEFF keyword for the database date (release or file date of the source) according to database provider. PEFF_DbDate_OBSOLETE = 200000014, - /// NumberOfEntries: PEFF keyword for the sumber of sequence entries in the database. + /// NumberOfEntries: PEFF keyword for the number of sequence entries in the database. PEFF_NumberOfEntries = 200000015, /// Conversion: PEFF keyword for the description of the conversion from original format to this current one. @@ -202,7 +203,7 @@ enum PWIZ_API_DECL CVID /// ModResPsi: PEFF keyword for the modified residue with PSI-MOD identifier. PEFF_ModResPsi = 200001012, - /// ModRes: PEFF keyword for the modified residue without aPSI-MOD or UniMod identifier. + /// ModRes: PEFF keyword for the modified residue without a PSI-MOD or Unimod identifier. PEFF_ModRes = 200001013, /// AltAC: PEFF keyword for the Alternative Accession Code. @@ -244,7 +245,7 @@ enum PWIZ_API_DECL CVID /// ID: PEFF keyword for the UniProtKB specific Protein identifier ID; a UniProtKB term. PEFF_ID = 200001026, - /// ModResUnimod: PEFF keyword for the modified residue with UniMod identifier. + /// ModResUnimod: PEFF keyword for the modified residue with Unimod identifier. PEFF_ModResUnimod = 200001027, /// VariantSimple: PEFF keyword for the simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term. @@ -781,19 +782,19 @@ enum PWIZ_API_DECL CVID /// Waters instrument model: Waters Corporation instrument model. MS_Waters_instrument_model = 1000126, - /// centroid spectrum: Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset. + /// centroid spectrum: A spectrum representation in which each peak is recorded as a single discrete data point at a distinct coordinate value (e.g. m/z; wavelength; drift time) with a corresponding intensity. MS_centroid_spectrum = 1000127, - /// Discrete Mass Spectrum (centroid spectrum): Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset. + /// Discrete Mass Spectrum (centroid spectrum): A spectrum representation in which each peak is recorded as a single discrete data point at a distinct coordinate value (e.g. m/z; wavelength; drift time) with a corresponding intensity. MS_Discrete_Mass_Spectrum = MS_centroid_spectrum, - /// profile spectrum: A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis. + /// profile spectrum: A spectrum representation in which ion signal for each peak is recorded as a distribution of intensity values across the coordinate range (e.g. m/z; wavelength; drift time). MS_profile_spectrum = 1000128, - /// continuous mass spectrum (profile spectrum): A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis. + /// continuous mass spectrum (profile spectrum): A spectrum representation in which ion signal for each peak is recorded as a distribution of intensity values across the coordinate range (e.g. m/z; wavelength; drift time). MS_continuous_mass_spectrum = MS_profile_spectrum, - /// Continuum Mass Spectrum (profile spectrum): A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis. + /// Continuum Mass Spectrum (profile spectrum): A spectrum representation in which ion signal for each peak is recorded as a distribution of intensity values across the coordinate range (e.g. m/z; wavelength; drift time). MS_Continuum_Mass_Spectrum = MS_profile_spectrum, /// negative scan: Polarity of the scan is negative. @@ -2527,6 +2528,9 @@ enum PWIZ_API_DECL CVID /// ProteinLynx Global Server: Waters software for data analysis. MS_ProteinLynx_Global_Server = 1000601, + /// PLGS (ProteinLynx Global Server): Waters software for data analysis. + MS_PLGS = MS_ProteinLynx_Global_Server, + /// Shimadzu MALDI-TOF instrument model: Shimadzu MALDI-TOF instrument model. MS_Shimadzu_MALDI_TOF_instrument_model = 1000602, @@ -7237,7 +7241,7 @@ enum PWIZ_API_DECL CVID /// ProteomeDiscoverer:Mascot:Significance High: Calculated relaxed significance when performing a decoy search for medium-confidence peptides. MS_ProteomeDiscoverer_Mascot_Significance_High = 1002230, - /// regular expressions for a GUID: ([A-Fa-f0-9]\{8\}-([A-Fa-f0-9]\{4\}-)\{3\}[A-Fa-f0-9]\{12\}). + /// regular expressions for a GUID: ([A-Fa-f0-9]\\{8\\}-([A-Fa-f0-9]\\{4\\}-)\\{3\\}[A-Fa-f0-9]\\{12\\}). MS_regular_expressions_for_a_GUID = 1002231, /// ProteomeDiscoverer:Default FDR calculator: The default FDR calculator as globally unique identifier (GUID). @@ -7993,7 +7997,7 @@ enum PWIZ_API_DECL CVID /// regular expression: Regular expression. MS_regular_expression = 1002479, - /// regular expression for a digital object identifier (DOI): (10[.][0-9]\{4,\}(?:[.][0-9]+)*/(?:(?![\"&\'<>])[^ \t\\r\n\\v\\f])+). + /// regular expression for a digital object identifier (DOI): (10[.][0-9]\\{4,\\}(?:[.][0-9]+)*/(?:(?![\\\"&\\'<>])[^ \\t\\r\\n\\v\\f])+). MS_regular_expression_for_a_digital_object_identifier__DOI_ = 1002480, /// higher energy beam-type collision-induced dissociation: A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV. @@ -8071,7 +8075,7 @@ enum PWIZ_API_DECL CVID /// modification index: The order of modifications to be referenced elsewhere in the document. MS_modification_index = 1002504, - /// regular expression for modification localization scoring: (?[0-9]+):(?[01][.][0-9]+(?:[Ee][+\-]?[0-9]+)?):(?[0-9]+(?:[|][0-9]+)*):(?true|false) + /// regular expression for modification localization scoring: (?[0-9]+):(?[01][.][0-9]+(?:[Ee][+\\-]?[0-9]+)?):(?[0-9]+(?:[|][0-9]+)*):(?true|false) MS_regular_expression_for_modification_localization_scoring = 1002505, /// modification position score: Modification position score. @@ -9022,7 +9026,7 @@ enum PWIZ_API_DECL CVID /// adduct ion isotope: Isotope of the matrix molecule M of an adduct formation. MS_adduct_ion_isotope = 1002811, - /// Regular expression for adduct ion formula: (\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-]). + /// Regular expression for adduct ion formula: (\\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\\][:digit:]{0,1}[+-]). MS_Regular_expression_for_adduct_ion_formula = 1002812, /// adduct ion formula: Adduct formation formula of the form M+X or M-X, as constrained by the provided regular expression. @@ -10030,6 +10034,9 @@ enum PWIZ_API_DECL CVID /// ProSight: ProSight: Database search engine for top-down proteomics. MS_ProSight = 1003141, + /// ProSightPD (ProSight): ProSight: Database search engine for top-down proteomics. + MS_ProSightPD = MS_ProSight, + /// TDPortal: TDPortal: Database search engine for top-down proteomics. MS_TDPortal = 1003142, @@ -10234,7 +10241,7 @@ enum PWIZ_API_DECL CVID /// constituent library file: Source library URI which(at least) a subset of spectra were extracted from. MS_constituent_library_file = 1003205, - /// library creation log: String of logging information generated when the library was constructed from its constituent files. Multiple lines should be separated with escaped \n + /// library creation log: String of logging information generated when the library was constructed from its constituent files. Multiple lines should be separated with escaped \\n MS_library_creation_log = 1003206, /// library creation software: Library creation software @@ -10822,7 +10829,7 @@ enum PWIZ_API_DECL CVID /// crosslinker cleavage characteristics: Signifies that the crosslinker is cleavable and on cleavage can leave a given stub. The pattern specifies three slots ::. MS_crosslinker_cleavage_characteristics = 1003390, - /// crosslinker cleavage regular expression: ^(?[A-Za-z]):(?[+-]?[0-9]+(\.[0-9]+)?([eE][+-]?[0-9]+(\.[0-9]+)?)?):(?[A-Za-z]+)$ + /// crosslinker cleavage regular expression: ^(?[A-Za-z]):(?[+-]?[0-9]+(\\.[0-9]+)?([eE][+-]?[0-9]+(\\.[0-9]+)?)?):(?[A-Za-z]+)$ MS_crosslinker_cleavage_regular_expression = 1003391, /// search modification id: A unique identifier within an in mzIdentML document denoting a search modification rule. The same modification may be present multiple times with different id values to reflect different specificities or neutral losses. @@ -11437,8 +11444,8 @@ enum PWIZ_API_DECL CVID /// three-dimensional liquid chromatography system: A system for Three-dimensional liquid chromatography (3D-LC), an advanced separation technique that combines three distinct liquid chromatography (LC) methods to achieve significantly enhanced separation power for complex mixtures, particularly in fields like proteomics. MS_three_dimensional_liquid_chromatography_system = 1003594, - /// planar chomatography system: A system for on-line planar chomatography. - MS_planar_chomatography_system = 1003595, + /// planar chromatography system: A system for on-line planar chromatography. + MS_planar_chromatography_system = 1003595, /// thin layer chromatography system: A system for on-line Thin Layer Chromatography (TLC), based upon a widely used, simple, and cost-effective analytical technique for separating and identifying components in a mixture. MS_thin_layer_chromatography_system = 1003596, @@ -11848,12 +11855,6 @@ enum PWIZ_API_DECL CVID /// gas chromatography mass spectrometry system: A gas chromatography mass spectrometry system (GC–MS) integrates a gas chromatograph for volatile analyte separation with a mass spectrometer for ionization and detection, enabling sensitive qualitative or quantitative analysis. MS_gas_chromatography_mass_spectrometry_system = 1003733, - /// gas chromatography mass spectrometry system model: Gas chromatography mass spectrometry system model name not including the vendor's name. - MS_gas_chromatography_mass_spectrometry_system_model = 1003734, - - /// Shimadzu gas chromatography mass spectrometry system model: Shimadzu Corporation gas chromatography mass spectrometry system model. - MS_Shimadzu_gas_chromatography_mass_spectrometry_system_model = 1003735, - /// separation system: A system to effect separation of compounds. MS_separation_system = 1003737, @@ -11929,53 +11930,53 @@ enum PWIZ_API_DECL CVID /// instrument class: Instruments classified based on their architecture with respect to mass analyzers. MS_instrument_class = 1003761, - /// triple quadrupole: A triple quadrupole mass spectrometer (TQMS; QqQ) is a tandem mass spectrometry (MS/MS) system that employs three linear quadrupoles in series to achieve highly selective and sensitive targeted quantification of specific compounds. The first quadrupole (Q1) may select a precursor ion, the second (Q2) induces fragmentation via collision-induced dissociation (CID), and the third (Q3) monitors specific product ions, typically through Multiple Reaction Monitoring (MRM). - MS_triple_quadrupole = 1003762, + /// triple quadrupole instrument: A tandem instrument that employs three quadrupoles in series, where the first (Q1) acts as a mass filter for precursor ion selection, the second (q2) serves as a collision cell for fragmentation, and the third (Q3) as a mass filter for product ion detection. + MS_triple_quadrupole_instrument = 1003762, - /// QqQ (triple quadrupole): A triple quadrupole mass spectrometer (TQMS; QqQ) is a tandem mass spectrometry (MS/MS) system that employs three linear quadrupoles in series to achieve highly selective and sensitive targeted quantification of specific compounds. The first quadrupole (Q1) may select a precursor ion, the second (Q2) induces fragmentation via collision-induced dissociation (CID), and the third (Q3) monitors specific product ions, typically through Multiple Reaction Monitoring (MRM). - MS_QqQ = MS_triple_quadrupole, + /// QqQ (triple quadrupole instrument): A tandem instrument that employs three quadrupoles in series, where the first (Q1) acts as a mass filter for precursor ion selection, the second (q2) serves as a collision cell for fragmentation, and the third (Q3) as a mass filter for product ion detection. + MS_QqQ = MS_triple_quadrupole_instrument, - /// quadrupole time-of-flight: A quadrupole time-of-flight (Q-TOF) mass spectrometer is a hybrid instrument that combines a quadrupole mass filter with a time-of-flight (TOF) mass analyzer to provide both highly accurate mass measurements and fragmentation data. The quadrupole may be used to select a specific precursor ion which is then fragmented, and the resulting product ions are measured by the TOF analyzer, providing high resolution and mass accuracy for structural elucidation and quantification. - MS_quadrupole_time_of_flight = 1003763, + /// quadrupole time-of-flight instrument: A hybrid instrument that combines a quadrupole mass filter for precursor ion selection with a time-of-flight mass analyzer for high-resolution, accurate-mass detection of product ions. + MS_quadrupole_time_of_flight_instrument = 1003763, - /// Q-TOF (quadrupole time-of-flight): A quadrupole time-of-flight (Q-TOF) mass spectrometer is a hybrid instrument that combines a quadrupole mass filter with a time-of-flight (TOF) mass analyzer to provide both highly accurate mass measurements and fragmentation data. The quadrupole may be used to select a specific precursor ion which is then fragmented, and the resulting product ions are measured by the TOF analyzer, providing high resolution and mass accuracy for structural elucidation and quantification. - MS_Q_TOF = MS_quadrupole_time_of_flight, + /// Q-TOF (quadrupole time-of-flight instrument): A hybrid instrument that combines a quadrupole mass filter for precursor ion selection with a time-of-flight mass analyzer for high-resolution, accurate-mass detection of product ions. + MS_Q_TOF = MS_quadrupole_time_of_flight_instrument, - /// ion trap time-of-flight: An ion trap time-of-flight (IT-TOF) mass spectrometer is a hybrid instrument that uses an ion trap to accumulate, store, and often fragment ions, which are then periodically injected into a time-of-flight (TOF) mass analyzer for high-resolution mass analysis. This combination allows for sensitive MSn experiments (multiple stages of mass spectrometry) within the ion trap for structural elucidation and provides high mass accuracy and resolution via the TOF component. - MS_ion_trap_time_of_flight = 1003764, + /// ion trap time-of-flight instrument: A hybrid instrument that combines an ion trap for ion accumulation, storage, and fragmentation with a time-of-flight mass analyzer for high-resolution, accurate-mass detection. + MS_ion_trap_time_of_flight_instrument = 1003764, - /// IT-TOF (ion trap time-of-flight): An ion trap time-of-flight (IT-TOF) mass spectrometer is a hybrid instrument that uses an ion trap to accumulate, store, and often fragment ions, which are then periodically injected into a time-of-flight (TOF) mass analyzer for high-resolution mass analysis. This combination allows for sensitive MSn experiments (multiple stages of mass spectrometry) within the ion trap for structural elucidation and provides high mass accuracy and resolution via the TOF component. - MS_IT_TOF = MS_ion_trap_time_of_flight, + /// IT-TOF (ion trap time-of-flight instrument): A hybrid instrument that combines an ion trap for ion accumulation, storage, and fragmentation with a time-of-flight mass analyzer for high-resolution, accurate-mass detection. + MS_IT_TOF = MS_ion_trap_time_of_flight_instrument, - /// triple quadrupole linear ion trap: A triple quadrupole linear ion trap (QqLIT) mass spectrometer is a hybrid instrument that can operate as a conventional triple quadrupole for high-sensitivity quantification (e.g., in Multiple Reaction Monitoring mode) or as a linear ion trap for qualitative analysis, such as MSn experiments and structural elucidation. The final quadrupole (Q3) of the system can be rapidly switched between functioning as a mass-resolving filter and a high-capacity linear ion trap, allowing for both precise quantification and comprehensive structural information to be acquired in a single analytical run. - MS_triple_quadrupole_linear_ion_trap = 1003765, + /// triple quadrupole linear ion trap instrument: A hybrid instrument that combines a triple quadrupole configuration with a linear ion trap, where the third quadrupole can function either as a conventional mass filter or as a linear ion trap for MSn analysis. + MS_triple_quadrupole_linear_ion_trap_instrument = 1003765, - /// QqLIT (triple quadrupole linear ion trap): A triple quadrupole linear ion trap (QqLIT) mass spectrometer is a hybrid instrument that can operate as a conventional triple quadrupole for high-sensitivity quantification (e.g., in Multiple Reaction Monitoring mode) or as a linear ion trap for qualitative analysis, such as MSn experiments and structural elucidation. The final quadrupole (Q3) of the system can be rapidly switched between functioning as a mass-resolving filter and a high-capacity linear ion trap, allowing for both precise quantification and comprehensive structural information to be acquired in a single analytical run. - MS_QqLIT = MS_triple_quadrupole_linear_ion_trap, + /// QqLIT (triple quadrupole linear ion trap instrument): A hybrid instrument that combines a triple quadrupole configuration with a linear ion trap, where the third quadrupole can function either as a conventional mass filter or as a linear ion trap for MSn analysis. + MS_QqLIT = MS_triple_quadrupole_linear_ion_trap_instrument, - /// quadrupole fourier transform ion cyclotron resonance: A quadrupole Fourier-transform ion cyclotron resonance (Q-FT-ICR) mass spectrometer is a hybrid instrument that uses an initial quadrupole for ion guiding or mass filtering before the ions are introduced into a Penning trap, where the mass analysis occurs. Once in the Penning trap, the ions' mass-to-charge ratios (m/z) are determined with ultra-high resolution and mass accuracy by measuring their unique cyclotron frequencies in a strong magnetic field and converting the resulting image current signal into a mass spectrum via a Fourier transform. - MS_quadrupole_fourier_transform_ion_cyclotron_resonance = 1003766, + /// quadrupole fourier transform ion cyclotron resonance instrument: A hybrid instrument that combines a quadrupole for ion guiding or mass filtering with a Fourier transform ion cyclotron resonance mass analyzer for ultra-high resolution and mass accuracy. + MS_quadrupole_fourier_transform_ion_cyclotron_resonance_instrument = 1003766, - /// Q-FT-ICR (quadrupole fourier transform ion cyclotron resonance): A quadrupole Fourier-transform ion cyclotron resonance (Q-FT-ICR) mass spectrometer is a hybrid instrument that uses an initial quadrupole for ion guiding or mass filtering before the ions are introduced into a Penning trap, where the mass analysis occurs. Once in the Penning trap, the ions' mass-to-charge ratios (m/z) are determined with ultra-high resolution and mass accuracy by measuring their unique cyclotron frequencies in a strong magnetic field and converting the resulting image current signal into a mass spectrum via a Fourier transform. - MS_Q_FT_ICR = MS_quadrupole_fourier_transform_ion_cyclotron_resonance, + /// Q-FT-ICR (quadrupole fourier transform ion cyclotron resonance instrument): A hybrid instrument that combines a quadrupole for ion guiding or mass filtering with a Fourier transform ion cyclotron resonance mass analyzer for ultra-high resolution and mass accuracy. + MS_Q_FT_ICR = MS_quadrupole_fourier_transform_ion_cyclotron_resonance_instrument, - /// quadrupole ion mobility time-of-flight: A quadrupole ion mobility time-of-flight (Q-IMS-TOF) mass spectrometer is a hybrid instrument that adds an ion mobility spectrometry (IMS) cell between the quadrupole and the time-of-flight (TOF) analyzer, providing an additional dimension of separation based on ion size, shape, and charge in a buffer gas. This configuration allows for the separation of isobars and isomers that have the same mass-to-charge ratio (m/z) but different three-dimensional structures, which significantly enhances analytical confidence for complex samples such as in proteomics, environmental analysis, and drug screening. - MS_quadrupole_ion_mobility_time_of_flight = 1003767, + /// quadrupole ion mobility time-of-flight instrument: A hybrid instrument that combines a quadrupole mass filter, an ion mobility spectrometry separation cell, and a time-of-flight mass analyzer, enabling separation of ions by size and shape in addition to mass-to-charge ratio. + MS_quadrupole_ion_mobility_time_of_flight_instrument = 1003767, - /// Q-IMS-TOF (quadrupole ion mobility time-of-flight): A quadrupole ion mobility time-of-flight (Q-IMS-TOF) mass spectrometer is a hybrid instrument that adds an ion mobility spectrometry (IMS) cell between the quadrupole and the time-of-flight (TOF) analyzer, providing an additional dimension of separation based on ion size, shape, and charge in a buffer gas. This configuration allows for the separation of isobars and isomers that have the same mass-to-charge ratio (m/z) but different three-dimensional structures, which significantly enhances analytical confidence for complex samples such as in proteomics, environmental analysis, and drug screening. - MS_Q_IMS_TOF = MS_quadrupole_ion_mobility_time_of_flight, + /// Q-IMS-TOF (quadrupole ion mobility time-of-flight instrument): A hybrid instrument that combines a quadrupole mass filter, an ion mobility spectrometry separation cell, and a time-of-flight mass analyzer, enabling separation of ions by size and shape in addition to mass-to-charge ratio. + MS_Q_IMS_TOF = MS_quadrupole_ion_mobility_time_of_flight_instrument, - /// ion trap orbitrap: A hybrid instrument that combines an ion trap for ion storage and fragmentation with an Orbitrap mass analyzer for high-resolution, accurate-mass (HRAM) detection. - MS_ion_trap_orbitrap = 1003768, + /// ion trap orbitrap instrument: A hybrid instrument that combines an ion trap for ion storage and fragmentation with an Orbitrap mass analyzer for high-resolution, accurate-mass detection. + MS_ion_trap_orbitrap_instrument = 1003768, - /// quadrupole orbitrap: A quadrupole Orbitrap mass spectrometer is a hybrid instrument that uses a quadrupole mass filter for precursor ion selection, a collision cell for fragmentation, followed by an Orbitrap mass analyzer which determines the precise mass-to-charge ratios of ions with high resolution and mass accuracy via Fourier transform. - MS_quadrupole_orbitrap = 1003769, + /// quadrupole orbitrap instrument: A hybrid instrument that combines a quadrupole mass filter for precursor ion selection with an Orbitrap mass analyzer for high-resolution, accurate-mass detection. + MS_quadrupole_orbitrap_instrument = 1003769, - /// quadrupole ion trap orbitrap: A mass spectrometer that integrates a quadrupole mass filter, a linear ion trap, and an Orbitrap mass analyzer to provide precursor ion selection, multiple-stage fragmentation (MSn), and ultra-high resolution mass analysis. - MS_quadrupole_ion_trap_orbitrap = 1003770, + /// quadrupole ion trap orbitrap instrument: A hybrid instrument that combines a quadrupole mass filter, a linear ion trap for MSn fragmentation, and an Orbitrap mass analyzer for high-resolution, accurate-mass detection. + MS_quadrupole_ion_trap_orbitrap_instrument = 1003770, - /// quadrupole orbitrap astral: A instrument that integrates a quadrupole mass filter, an Orbitrap mass analyzer, and the ASTRAL analyzer for high performance in ion selection, high-resolution analysis, and high-speed, high-sensitivity MS2 measurements. - MS_quadrupole_orbitrap_astral = 1003771, + /// quadrupole orbitrap astral instrument: A hybrid instrument that combines a quadrupole mass filter, an Orbitrap mass analyzer, and an asymmetric track lossless (ASTRAL) analyzer for high-resolution analysis and high-speed MS/MS measurements. + MS_quadrupole_orbitrap_astral_instrument = 1003771, /// mixed polarity acquisition: The scans of a run include both positive and negative polarity acquisitions in a pattern that is not strictly alternating, such as discrete blocks of each polarity, irregular switching sequences, or other non-alternating arrangements. MS_mixed_polarity_acquisition = 1003774, @@ -11983,6 +11984,9 @@ enum PWIZ_API_DECL CVID /// secondary electrospray ionization: Secondary electrospray ionization (SESI) is an atmospheric pressure ionization (API) technique that uses a primary nano-electrospray plume of solvent ions to ionize neutral gaseous molecules in the gas phase via efficient proton transfer reactions. Operating at atmospheric pressure, SESI allows for the sensitive and real-time detection of volatile organic compounds (VOCs) and vapors with minimal sample preparation, making it ideal for applications like breath analysis and environmental monitoring. MS_secondary_electrospray_ionization = 1003775, + /// acquisition polarity: The ion polarity configuration used during data acquisition of a sample run. + MS_acquisition_polarity = 1003776, + /// zstd compression: Zstandard compression, a fast, modern, general purpose lossless compression algorithm. MS_zstd_compression = 1003780, @@ -12001,12 +12005,93 @@ enum PWIZ_API_DECL CVID /// MS-Numpress short logged float compression followed by zstd compression: Compression using MS-Numpress short logged float compression and Zstandard. MS_MS_Numpress_short_logged_float_compression_followed_by_zstd_compression = 1003785, + /// electrophoretic separation: Electrophoretic separation is a technique in which charged analytes are separated by differential migration in an applied electric field. + MS_electrophoretic_separation = 1003786, + + /// capillary electrophoresis: Capillary electrophoresis (CE) is an electrophoretic separation technique performed in narrow-bore capillaries, in which analytes migrate through an electrolyte solution under the influence of an electric field and separate according to their electrophoretic mobility. + MS_capillary_electrophoresis = 1003787, + + /// capilliary zone electrophoresis (capillary electrophoresis): Capillary electrophoresis (CE) is an electrophoretic separation technique performed in narrow-bore capillaries, in which analytes migrate through an electrolyte solution under the influence of an electric field and separate according to their electrophoretic mobility. + MS_capilliary_zone_electrophoresis = MS_capillary_electrophoresis, + + /// CE (capillary electrophoresis): Capillary electrophoresis (CE) is an electrophoretic separation technique performed in narrow-bore capillaries, in which analytes migrate through an electrolyte solution under the influence of an electric field and separate according to their electrophoretic mobility. + MS_CE = MS_capillary_electrophoresis, + + /// electrochromatography: Electrochromatography is a liquid chromatography technique in which the mobile phase is driven through a stationary phase by electroosmotic flow generated by an applied electric field, combining electrophoretic migration with chromatographic retention. + MS_electrochromatography = 1003788, + + /// ion-pair reversed phase chromatography: Ion-pair reversed-phase chromatography is a reversed-phase chromatography technique in which an ion-pairing reagent is added to the mobile phase to enable retention and separation of charged or ionizable analytes on a nonpolar stationary phase. + MS_ion_pair_reversed_phase_chromatography = 1003789, + + /// supercritical fluid chromatography: Supercritical fluid chromatography (SFC) is a separation technique in which the mobile phase is a fluid above and relatively close to its critical temperature and pressure. + MS_supercritical_fluid_chromatography = 1003790, + + /// SFC (supercritical fluid chromatography): Supercritical fluid chromatography (SFC) is a separation technique in which the mobile phase is a fluid above and relatively close to its critical temperature and pressure. + MS_SFC = MS_supercritical_fluid_chromatography, + /// TSQ Certis: Thermo Scientific TSQ Certis Triple Quadrupole MS. MS_TSQ_Certis = 1003800, /// AccurateMassSearch: OpenMS TOPP tool to assemble metabolite features from singleton mass traces. MS_AccurateMassSearch = 1003801, + /// Ionoptika instrument model: Ionoptika Ltd. instrument model. + MS_Ionoptika_instrument_model = 1003802, + + /// Ionoptika software: Ionoptika software for data acquisition and analysis. + MS_Ionoptika_software = 1003803, + + /// Ionoptika J105: Ionoptika J105 time-of-flight secondary ion mass spectrometer. + MS_Ionoptika_J105 = 1003804, + + /// J Series III: Ionoptika J Series III time-of-flight secondary ion mass spectrometer. + MS_J_Series_III = 1003805, + + /// NeoSIMS: Ionoptika software for data acquisition. + MS_NeoSIMS = 1003806, + + /// Ionoptika Image Analyser: Ionoptika software for image data analysis. + MS_Ionoptika_Image_Analyser = 1003807, + + /// J105 Ionoptika Mass Imager: Ionoptika J105 software for mass spectrometry imaging data analysis. + MS_J105_Ionoptika_Mass_Imager = 1003808, + + /// IoDataConverter: Ionoptika software for converting Ionoptika data formats to imzML or HDF5. + MS_IoDataConverter = 1003809, + + /// Ionoptika V1 format: Ionoptika data format generated by J105 TOF-SIMS instrument. + MS_Ionoptika_V1_format = 1003810, + + /// Ionoptika V3 format: Ionoptika data format generated by J105 TOF-SIMS instrument. + MS_Ionoptika_V3_format = 1003811, + + /// lambda max: The wavelength of maximum absorbance for a substance. This is analogous to the base peak m/z for UV-Vis spectroscopy. + MS_lambda_max = 1003812, + + /// λ-max (lambda max): The wavelength of maximum absorbance for a substance. This is analogous to the base peak m/z for UV-Vis spectroscopy. + MS__xCE__xBB__max = MS_lambda_max, + + /// list of doubles: A list of xsd:double. + MS_list_of_doubles = 1003813, + + /// coordinate spacing model: Defines a model for calculating or correcting the spacing between points along a continuous dimension. + MS_coordinate_spacing_model = 1003820, + + /// polynomial delta coordinate interpolation: A coordinate spacing model that predicts the next coordinate as a function of a low degree polynomial on the current coordinate, for instance a 2nd degree $x_{i + 1} = (a*x_i^2 + b*x_i + c) + x_i$. It is assumed that the parameters are inferred from the value list and the number implies the polynomial degree. + MS_polynomial_delta_coordinate_interpolation = 1003821, + + /// grid coordinate interpolation: A coordinate spacing model that uses some form of interpolation to calculate coordinate values between a fixed minimum and maximum value. This includes formula for (potentially lossily) converting a coordinate to an integer index and vice-versa. The grid model and recalibration function parameters are given by the value list. The recalibration function may be the identity function, or a more complex model defined in a child term. + MS_grid_coordinate_interpolation = 1003822, + + /// linear grid interpolation: A coordinate spacing model that uses linear interpolation to map grid indices to coordinates $x_i = f_x(b + i * a)$ where $f$ is some recalibration function. + MS_linear_grid_interpolation = 1003824, + + /// square root grid interpolation: A coordinate spacing model that maps grid indices to coordinates $x_i = f_x((b + i * a)^2)$ where $f$ is some recalibration function. The square root of the coordinate is linear with respect to the index. This mirrors the formula relating time-of-flight to m/z, $t = k\\sqrt{m/z}$ + MS_square_root_grid_interpolation = 1003825, + + /// coordinate grid encoding: This array stores indices or spans into some form of coordinate space model rather than the coordinates themselves, and that grid is stored externally from this data array. The objective being that these coordinates are more compact to store than the raw coordinates themselves. The value of this parameter is the grid identifier, if there are multiple to choose from. A separate coordinate spacing model parameter will signify what form of coordinate space model is used. + MS_coordinate_grid_encoding = 1003826, + /// zero intensity point trimming: Apply an algorithm to remove excess zero intensity value data points from a spectrum. Data may be retained for interperatbility such as retaining only zeros that flank non-zero intensity value data points from a profile spectrum.. MS_zero_intensity_point_trimming = 1003901, @@ -12031,8 +12116,356 @@ enum PWIZ_API_DECL CVID /// PRM (parallel reaction monitoring): Parallel Reaction Monitoring (PRM) utilizes high-resolution, accurate-mass mass spectrometry, typically a quadrupole orbitrap or quadrupole time-of-flight instrument, to isolate specific precursor ions and detect all resulting product ions in parallel. Unlike Selected Reaction Monitoring (SRM), which filters for pre-selected transitions, PRM acquires full MS/MS spectra for each target, thereby eliminating the need for transition optimization and providing high specificity through high-resolution interference rejection. MS_PRM = MS_parallel_reaction_monitoring, - /// Agilent gas chromatography mass spectrometry system model: Agilent Technologies gas chromatography mass spectrometry system model. - MS_Agilent_gas_chromatography_mass_spectrometry_system_model = 1003914, + /// centroid peak: A peak represented as a single discrete data point defined by a distinct coordinate value (e.g. m/z; wavelength; drift time) and a corresponding intensity value. + MS_centroid_peak = 1003908, + + /// two-dimensional gas chromatography: Comprehensive two-dimensional gas chromatography (GCxGC) is a multidimensional separation technique that utilizes two columns with different stationary phases connected by a modulator, which traps, focuses and reinjects fractions from the first column to the second. This approach leads to a 2D chromatogram offering higher peak capacity and separation power. + MS_two_dimensional_gas_chromatography = 1003915, + + /// GCxGC (two-dimensional gas chromatography): Comprehensive two-dimensional gas chromatography (GCxGC) is a multidimensional separation technique that utilizes two columns with different stationary phases connected by a modulator, which traps, focuses and reinjects fractions from the first column to the second. This approach leads to a 2D chromatogram offering higher peak capacity and separation power. + MS_GCxGC = MS_two_dimensional_gas_chromatography, + + /// SpectroSwiss software: SpectroSwiss software for mass spectrometry data processing and analysis. + MS_SpectroSwiss_software = 1003916, + + /// Peak-by-Peak: SpectroSwiss software for Fourier transform mass spectrometry (FTMS) data processing and analysis, providing advanced workflows including the processing of unreduced, transient data. + MS_Peak_by_Peak = 1003917, + + /// PeakByPeak (Peak-by-Peak): SpectroSwiss software for Fourier transform mass spectrometry (FTMS) data processing and analysis, providing advanced workflows including the processing of unreduced, transient data. + MS_PeakByPeak = MS_Peak_by_Peak, + + /// chromatographic column: A tube or housing containing a stationary phase, through which a mobile phase flows to achieve chromatographic separation of analytes. + MS_chromatographic_column = 1003920, + + /// liquid chromatographic column: A chromatographic column designed for use with a liquid mobile phase, housing a stationary phase for analyte separation. + MS_liquid_chromatographic_column = 1003921, + + /// chromatographic stationary phase: The immobile phase in a chromatographic system with which analytes interact differentially, enabling separation based on chemical or physical properties. + MS_chromatographic_stationary_phase = 1003922, + + /// chromatographic stationary phase attribute: Chromatographic stationary phase properties that are associated with a value. + MS_chromatographic_stationary_phase_attribute = 1003923, + + /// pore size: The average diameter of the pores within the particles of the stationary phase, typically represented in angstroms (Å) + MS_pore_size = 1003924, + + /// particle diameter: The average diameter of the solid particles that constitute the stationary phase. + MS_particle_diameter = 1003925, + + /// chromatographic column attribute: Properties of the chromatographic column hardware that are associated with a value. + MS_chromatographic_column_attribute = 1003926, + + /// column length: The length of the chromatographic column, representing the path length available for separation. + MS_column_length = 1003927, + + /// column internal diameter: The inner diameter of the chromatographic column. + MS_column_internal_diameter = 1003928, + + /// column I.D. (column internal diameter): The inner diameter of the chromatographic column. + MS_column_I_D_ = MS_column_internal_diameter, + + /// particle porosity: The porosity of the particles composing the chromatographic stationary phase. + MS_particle_porosity = 1003929, + + /// fully porous: A chromatographic stationary phase particle with pores distributed throughout its entire volume. + MS_fully_porous = 1003930, + + /// superficially porous: A chromatographic stationary phase particle consisting of a solid, non-porous core surrounded by a porous shell. + MS_superficially_porous = 1003931, + + /// core-shell particle (superficially porous): A chromatographic stationary phase particle consisting of a solid, non-porous core surrounded by a porous shell. + MS_core_shell_particle = MS_superficially_porous, + + /// non-porous: A solid chromatographic stationary phase particle without internal pores. + MS_non_porous = 1003932, + + /// support material: The base material from which the chromatographic stationary phase is constructed. + MS_support_material = 1003933, + + /// silica-based: A chromatographic stationary phase constructed from silica particles, optionally with surface chemical modification. + MS_silica_based = 1003934, + + /// hybrid particle: A chromatographic stationary phase constructed from organic-inorganic hybrid particles, such as ethylene-bridged hybrid (BEH), providing enhanced chemical stability and pH range. + MS_hybrid_particle = 1003935, + + /// polymer-based: A chromatographic stationary phase constructed from organic polymer particles such as polystyrene-divinylbenzene or methacrylate-based polymers. + MS_polymer_based = 1003936, + + /// monolithic: A chromatographic stationary phase consisting of a single continuous porous rod rather than packed discrete particles. + MS_monolithic = 1003937, + + /// porous graphitic carbon: A chromatographic stationary phase composed of porous graphitic carbon, providing strong retention of polar compounds and chemical robustness across a wide pH range. + MS_porous_graphitic_carbon = 1003938, + + /// PGC stationary phase (porous graphitic carbon): A chromatographic stationary phase composed of porous graphitic carbon, providing strong retention of polar compounds and chemical robustness across a wide pH range. + MS_PGC_stationary_phase = MS_porous_graphitic_carbon, + + /// trap column: A short chromatographic column used for on-line sample loading, concentration, and desalting prior to separation on the analytical column. + MS_trap_column = 1003939, + + /// guard column: A short protective chromatographic column placed upstream of the analytical column to capture contaminants and extend analytical column lifetime. + MS_guard_column = 1003940, + + /// analytical column: The primary chromatographic column in which analyte separation occurs. + MS_analytical_column = 1003941, + + /// gas chromatographic column: A chromatographic column designed for use with a gaseous mobile phase. + MS_gas_chromatographic_column = 1003943, + + /// chromatographic column role: The functional role of a chromatographic column within the separation workflow. + MS_chromatographic_column_role = 1003944, + + /// chromatographic column type: The type of chromatographic column classified by the mobile phase it is designed to operate with. + MS_chromatographic_column_type = 1003945, + + /// tandem time-of-flight instrument: A tandem instrument that combines two time-of-flight mass analyzers in series, where the first selects precursor ions and the second analyzes fragment ions produced by collision-induced dissociation or post-source decay. + MS_tandem_time_of_flight_instrument = 1003946, + + /// TOF/TOF (tandem time-of-flight instrument): A tandem instrument that combines two time-of-flight mass analyzers in series, where the first selects precursor ions and the second analyzes fragment ions produced by collision-induced dissociation or post-source decay. + MS_TOF_TOF = MS_tandem_time_of_flight_instrument, + + /// magnetic sector ion trap instrument: A hybrid instrument that combines a double-focusing magnetic sector analyzer for high-resolution precursor ion selection with an ion trap for MSn fragmentation analysis. + MS_magnetic_sector_ion_trap_instrument = 1003947, + + /// fourier transform ion cyclotron resonance instrument: An instrument that uses a Fourier transform ion cyclotron resonance mass analyzer as its primary means of mass analysis. + MS_fourier_transform_ion_cyclotron_resonance_instrument = 1003948, + + /// magnetic sector instrument: An instrument that uses a magnetic sector mass analyzer as its primary means of mass analysis. + MS_magnetic_sector_instrument = 1003949, + + /// quadrupole instrument: An instrument that uses a single quadrupole mass analyzer as its primary means of mass analysis. + MS_quadrupole_instrument = 1003950, + + /// time-of-flight instrument: An instrument that uses a time-of-flight mass analyzer as its primary means of mass analysis. + MS_time_of_flight_instrument = 1003951, + + /// ion trap instrument: An instrument that uses an ion trap mass analyzer as its primary means of mass analysis. + MS_ion_trap_instrument = 1003952, + + /// orbitrap instrument: An instrument that uses an Orbitrap mass analyzer as its primary means of mass analysis. + MS_orbitrap_instrument = 1003953, + + /// argon gas cluster ion beam: Argon gas cluster ion beam (Ar GCIB) bombardment uses a focused beam of large argon cluster ions, typically [Ar500]+ to [Ar10000]+, accelerated to high energies to sputter and generate secondary ions from a surface, enabling molecular depth profiling and imaging of organic and biological materials with reduced subsurface damage compared to monatomic ion beams. + MS_argon_gas_cluster_ion_beam = 1003954, + + /// Ar GCIB (argon gas cluster ion beam): Argon gas cluster ion beam (Ar GCIB) bombardment uses a focused beam of large argon cluster ions, typically [Ar500]+ to [Ar10000]+, accelerated to high energies to sputter and generate secondary ions from a surface, enabling molecular depth profiling and imaging of organic and biological materials with reduced subsurface damage compared to monatomic ion beams. + MS_Ar_GCIB = MS_argon_gas_cluster_ion_beam, + + /// singly charged bismuth trimer liquid metal ion gun: A beam of singly charged bismuth trimer ([Bi3]+) ions for desorption and ionisation from a surface, providing high spatial resolution imaging and enhanced molecular secondary ion yields compared to monatomic primary ion beams. + MS_singly_charged_bismuth_trimer_liquid_metal_ion_gun = 1003955, + + /// [Bi3]+ LMIG (singly charged bismuth trimer liquid metal ion gun): A beam of singly charged bismuth trimer ([Bi3]+) ions for desorption and ionisation from a surface, providing high spatial resolution imaging and enhanced molecular secondary ion yields compared to monatomic primary ion beams. + MS__Bi3___LMIG = MS_singly_charged_bismuth_trimer_liquid_metal_ion_gun, + + /// doubly charged bismuth trimer liquid metal ion gun: A beam of doubly charged bismuth trimer ([Bi3]2+) ions for desorption and ionisation from a surface. Ions achieve a higher velocity at a given acceleration voltage compared to singly charged [Bi3]+, resulting in enhanced secondary ion yields for surface analysis. + MS_doubly_charged_bismuth_trimer_liquid_metal_ion_gun = 1003956, + + /// [Bi3]2+ LMIG (doubly charged bismuth trimer liquid metal ion gun): A beam of doubly charged bismuth trimer ([Bi3]2+) ions for desorption and ionisation from a surface. Ions achieve a higher velocity at a given acceleration voltage compared to singly charged [Bi3]+, resulting in enhanced secondary ion yields for surface analysis. + MS__Bi3_2__LMIG = MS_doubly_charged_bismuth_trimer_liquid_metal_ion_gun, + + /// two-dimensional liquid chromatography: Two-dimensional liquid chromatography (2D-LC) is a multidimensional separation technique that couples two liquid chromatography columns with different selectivities, such as strong cation exchange and reversed phase, connected by a switching valve or modulator to provide significantly higher peak capacity and resolving power for complex mixtures than one-dimensional liquid chromatography. + MS_two_dimensional_liquid_chromatography = 1003957, + + /// 2D-LC (two-dimensional liquid chromatography): Two-dimensional liquid chromatography (2D-LC) is a multidimensional separation technique that couples two liquid chromatography columns with different selectivities, such as strong cation exchange and reversed phase, connected by a switching valve or modulator to provide significantly higher peak capacity and resolving power for complex mixtures than one-dimensional liquid chromatography. + MS_2D_LC = MS_two_dimensional_liquid_chromatography, + + /// LCxLC (two-dimensional liquid chromatography): Two-dimensional liquid chromatography (2D-LC) is a multidimensional separation technique that couples two liquid chromatography columns with different selectivities, such as strong cation exchange and reversed phase, connected by a switching valve or modulator to provide significantly higher peak capacity and resolving power for complex mixtures than one-dimensional liquid chromatography. + MS_LCxLC = MS_two_dimensional_liquid_chromatography, + + /// bismuth liquid metal ion gun: Bismuth liquid metal ion gun (Bi LMIG) bombardment uses a focused beam of bismuth ions emitted from a liquid metal ion source to desorb and ionize molecules from a surface. The LMIG source generates a diversity of monomers and clusters, which are filtered prior to the sample in order to select the specific ionisation characteristics. + MS_bismuth_liquid_metal_ion_gun = 1003958, + + /// Bi LMIG (bismuth liquid metal ion gun): Bismuth liquid metal ion gun (Bi LMIG) bombardment uses a focused beam of bismuth ions emitted from a liquid metal ion source to desorb and ionize molecules from a surface. The LMIG source generates a diversity of monomers and clusters, which are filtered prior to the sample in order to select the specific ionisation characteristics. + MS_Bi_LMIG = MS_bismuth_liquid_metal_ion_gun, + + /// gas cluster ion beam: A gas cluster ion beam (GCIB) is an ion source that generates and accelerates large aggregates of gas atoms or molecules to high energies. The low energy per constituent atom minimizes surface damage and molecular fragmentation, making it highly effective for molecular depth profiling and the analysis of fragile organic and biological materials. + MS_gas_cluster_ion_beam = 1003959, + + /// GCIB (gas cluster ion beam): A gas cluster ion beam (GCIB) is an ion source that generates and accelerates large aggregates of gas atoms or molecules to high energies. The low energy per constituent atom minimizes surface damage and molecular fragmentation, making it highly effective for molecular depth profiling and the analysis of fragile organic and biological materials. + MS_GCIB = MS_gas_cluster_ion_beam, + + /// liquid metal ion gun: A liquid metal ion gun (LMIG) is an ion source that extracts and ionizes a thin layer of liquid metal from a fine heated needle using a high-voltage electric field. It produces a high-brightness, tightly focused beam of metal ions or clusters, enabling high-resolution imaging and analysis in Secondary Ion Mass Spectrometry (SIMS). + MS_liquid_metal_ion_gun = 1003960, + + /// LMIG (liquid metal ion gun): A liquid metal ion gun (LMIG) is an ion source that extracts and ionizes a thin layer of liquid metal from a fine heated needle using a high-voltage electric field. It produces a high-brightness, tightly focused beam of metal ions or clusters, enabling high-resolution imaging and analysis in Secondary Ion Mass Spectrometry (SIMS). + MS_LMIG = MS_liquid_metal_ion_gun, + + /// Thermo Scientific software: Thermo Scientific software for data acquisition and analysis. + MS_Thermo_Scientific_software = 1003961, + + /// TraceFinder: Thermo Scientific software for targeted quantitative and screening analysis of LC-MS, GC-MS, and IC-MS data, supporting automated data acquisition, processing, and reporting for diverse workflows. + MS_TraceFinder = 1003962, + + /// FreeStyle: Thermo Scientific software for interactive qualitative visualization and review of mass spectrometry data, including chromatographic peak detection, spectral library searching, and high-resolution deconvolution. + MS_FreeStyle = 1003963, + + /// Chromeleon CDS: Thermo Scientific enterprise chromatography data system with integrated mass spectrometry instrument control and data processing, supporting GC-MS, LC-MS, and IC-MS platforms with GxP/21 CFR Part 11 compliance. + MS_Chromeleon_CDS = 1003964, + + /// Chromeleon Chromatography Data System (Chromeleon CDS): Thermo Scientific enterprise chromatography data system with integrated mass spectrometry instrument control and data processing, supporting GC-MS, LC-MS, and IC-MS platforms with GxP/21 CFR Part 11 compliance. + MS_Chromeleon_Chromatography_Data_System = MS_Chromeleon_CDS, + + /// Mass Frontier: Thermo Scientific software for mass spectral interpretation and structural elucidation of small molecules, featuring the HighChem fragmentation library, fragmentation prediction, and spectral tree searching. + MS_Mass_Frontier = 1003965, + + /// LipidSearch: Thermo Scientific software for automated identification of lipid molecular species from LC-MS and LC-MS/MS data using a comprehensive database of predicted lipid ion fragments. + MS_LipidSearch = 1003966, + + /// mzVault: Thermo Scientific software for offline storage, searching, and management of high-resolution accurate-mass spectral libraries, including curated mzCloud content and user-generated in-house libraries. + MS_mzVault = 1003967, + + /// SIEVE: Thermo Scientific software for label-free differential expression analysis of LC-MS and GC-MS data, providing chromatographic alignment, feature detection, and statistical comparison for proteomics and metabolomics. + MS_SIEVE = 1003968, + + /// BioPharma Finder: Thermo Scientific software for complex biotherapeutic characterization by LC-MS, supporting intact protein analysis, peptide mapping, oligonucleotide analysis, multi-attribute method workflows, and top-down or middle-down approaches. + MS_BioPharma_Finder = 1003969, + + /// ion mobility quadrupole time-of-flight instrument: An instrument that uses an ion mobility analyzer followed by a quadrupole mass filter and a time-of-flight mass analyzer as its primary means of mass analysis. + MS_ion_mobility_quadrupole_time_of_flight_instrument = 1003970, + + /// IMS-Q-TOF (ion mobility quadrupole time-of-flight instrument): An instrument that uses an ion mobility analyzer followed by a quadrupole mass filter and a time-of-flight mass analyzer as its primary means of mass analysis. + MS_IMS_Q_TOF = MS_ion_mobility_quadrupole_time_of_flight_instrument, + + /// ion trap fourier transform ion cyclotron resonance instrument: An instrument that uses a linear ion trap coupled to a fourier transform ion cyclotron resonance mass analyzer as its primary means of mass analysis. + MS_ion_trap_fourier_transform_ion_cyclotron_resonance_instrument = 1003971, + + /// quadrupole ion trap instrument: An instrument that uses a quadrupole mass filter followed by an ion trap mass analyzer as its primary means of mass analysis. + MS_quadrupole_ion_trap_instrument = 1003972, + + /// LECO PEG format: Proprietary binary data format with extension '.peg', used by LECO ChromaTOF software to store raw and processed data from LECO Pegasus series mass spectrometers. + MS_LECO_PEG_format = 1003973, + + /// JEOL JPF format: Proprietary binary data format with extension '.jpf', used by JEOL mass spectrometry systems and associated data processing software to store mass spectral data. + MS_JEOL_JPF_format = 1003974, + + /// peak group: A collection of co-eluting chromatographic peaks with matching profiles, derived from a single source analyte. Examples include: related product ion peaks of a single precursor; related peaks derived from different adducts, multimers or isotopologues of a given analyte; and related peaks derived from in-source fragmentation of a given analyte. + MS_peak_group = 1003975, + + /// retention time window target: The reference retention time from which a retention time window is defined. The target may be derived from a predicted, expected, observed, or user-specified retention time. + MS_retention_time_window_target = 1003976, + + /// Monocle: A software program for converting Thermo Scientific RAW file format to mzXML, mzML, or CSV with improved monoisotopic mass estimation. Monocle was originally developed at the Gygi Lab at Harvard Medical School. + MS_Monocle = 1003977, + + /// (?<=[^DE])(?=[AFILMV][^P]): Regular expression for Thermolysin. + MS_______DE______AFILMV___P__ = 1003978, + + /// Thermolysin: Thermostable extracellular metalloendopeptidase containing four calcium ions + MS_Thermolysin = 1003979, + + /// Bacillus thermoproteolyticus neutral proteinase (Thermolysin): Thermostable extracellular metalloendopeptidase containing four calcium ions + MS_Bacillus_thermoproteolyticus_neutral_proteinase = MS_Thermolysin, + + /// (?=[AEFILTVWY]): Regular expression for peptidase K. + MS_____AEFILTVWY__ = 1003980, + + /// peptidase K: Peptidase from the mold Tritirachium album Limber + MS_peptidase_K = 1003981, + + /// endopeptidase K (peptidase K): Peptidase from the mold Tritirachium album Limber + MS_endopeptidase_K = MS_peptidase_K, + + /// proteinase K (peptidase K): Peptidase from the mold Tritirachium album Limber + MS_proteinase_K = MS_peptidase_K, + + /// Tritirachium album proteinase K (peptidase K): Peptidase from the mold Tritirachium album Limber + MS_Tritirachium_album_proteinase_K = MS_peptidase_K, + + /// Tritirachium alkaline proteinase (peptidase K): Peptidase from the mold Tritirachium album Limber + MS_Tritirachium_alkaline_proteinase = MS_peptidase_K, + + /// (?<=N)(?=G): Regular expression for hydroxylamine. + MS_____N____G_ = 1003982, + + /// hydroxylamine: NH2OH + MS_hydroxylamine = 1003983, + + /// amino acid confidence level: The confidence level of the PSM assignment per amino acid, where 0 is not confident and 1 is maximally confident. + MS_amino_acid_confidence_level = 1003984, + + /// peptidoform token confidence level: The confidence level of the PSM assignment per peptidoform token, so separately for each amino acid and modification, where 0 is not confident and 1 is maximally confident. + MS_peptidoform_token_confidence_level = 1003985, + + /// protein sequence: The protein sequence of a protein in a database. + MS_protein_sequence = 1003986, + + /// Orbitrap Tribrid Apex: Thermo Scientific Orbitrap Tribrid Apex mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. + MS_Orbitrap_Tribrid_Apex = 1003987, + + /// Xevo MRT P10: Waters Xevo MRT P10 quadrupole - multi-reflecting time-of-flight mass spectrometer. + MS_Xevo_MRT_P10 = 1003988, + + /// Cyclic IMS P20: Waters Cyclic IMS P20 multipass cyclic ion mobility quadrupole time-of-flight mass spectrometer. + MS_Cyclic_IMS_P20 = 1003989, + + /// Orbitrap Excedion: Thermo Scientific Orbitrap Excedion mass spectrometer. + MS_Orbitrap_Excedion = 1003990, + + /// novus V55: SCIEX novus V55 triple quadrupole mass spectrometer. + MS_novus_V55 = 1003991, + + /// 9500 Triple Quadrupole ICP-MS: Agilent 9500 Triple Quadrupole ICP-MS inductively coupled plasma triple quadrupole mass spectrometer. + MS_9500_Triple_Quadrupole_ICP_MS = 1003992, + + /// InfinityLab Pro iQ: Agilent InfinityLab Pro iQ single quadrupole LC mass detector. + MS_InfinityLab_Pro_iQ = 1003993, + + /// ion mobility quadrupole FT-ICR instrument: Instrument class combining trapped ion mobility spectrometry (TIMS) with a quadrupole mass filter and fourier transform ion cyclotron resonance (magnetic resonance) mass analysis. + MS_ion_mobility_quadrupole_FT_ICR_instrument = 1003994, + + /// timsMRMS: Bruker timsMRMS instrument combining trapped ion mobility spectrometry with magnetic resonance (FT-ICR) mass spectrometry. + MS_timsMRMS = 1003995, + + /// DeepNovo: DeepNovo is a deep-learning based de novo peptide sequencer for DDA. + MS_DeepNovo = 1003996, + + /// DeepNovo-DIA: DeepNovo is a deep-learning based de novo peptide sequencer for DDA and DIA. + MS_DeepNovo_DIA = 1003997, + + /// PointNovo: PointNovo is neural network based de novo peptide sequencing model. + MS_PointNovo = 1003998, + + /// PGPointNovo: PGPointNovo is a modification of PointNovo that allows parallel processing and a better optimization strategy. + MS_PGPointNovo = 1003999, + + /// BiATNovo: BiATNovo an attention based bidirectional de novo peptide sequencing software. + MS_BiATNovo = 1004000, + + /// NovoB: NovoB a transformer based bidirectional de novo peptide sequencing software. + MS_NovoB = 1004001, + + /// PepNet: PepNet a convolutional neural network de novo peptide sequencing software. + MS_PepNet = 1004002, + + /// π-HelixNovo: π-HelixNovo a transformer based de novo peptide sequencing software. + MS__xCF__x80__HelixNovo = 1004003, + + /// pi-HelixNovo (π-HelixNovo): π-HelixNovo a transformer based de novo peptide sequencing software. + MS_pi_HelixNovo = MS__xCF__x80__HelixNovo, + + /// π-PrimeNovo: π-PrimeNovo a non-autoregressive de novo peptide sequencing software. + MS__xCF__x80__PrimeNovo = 1004004, + + /// pi-PrimeNovo (π-PrimeNovo): π-PrimeNovo a non-autoregressive de novo peptide sequencing software. + MS_pi_PrimeNovo = MS__xCF__x80__PrimeNovo, + + /// PowerNovo: PowerNovo a BERT and transformer ensemble de novo peptide sequencing software. + MS_PowerNovo = 1004005, + + /// pUniFind: pUniFind a open modification de novo peptide sequencing and rescoring software. + MS_pUniFind = 1004006, + + /// Sage: A database search based peptide identification software with retention time prediction, quantification, rescoring, and false discovery rate control. + MS_Sage = 1004007, + + /// BiblioSpec Spectrum Sequence List: Tabular result format for proteomics and small molecule experiments, saved with extension '.ssl'. + MS_BiblioSpec_Spectrum_Sequence_List = 1004008, + + /// ProteoScape: Bruker ProteoScape is a GPU-powered platform delivering parallel computing capabilities and real-time database search results for bottom-up proteomics. + MS_ProteoScape = 1004009, + + /// Stitch: Template-based assembly of PSMs for de novo protein sequencing. + MS_Stitch = 1004010, /// Number of Occurrences: The number of times something happened. NCIT_Number_of_Occurrences = 103150827, @@ -17323,6 +17756,33 @@ enum PWIZ_API_DECL CVID /// DMA-PEG3: DimethylaminoPEG3ylation. UNIMOD_DMA_PEG3 = 300002136, + /// HCCA-Lys: Lysine labelled with HCCA tag. + UNIMOD_HCCA_Lys = 300002138, + + /// Phosphocholine: Serine/Threonine/Tyrosine of a protein becomes posttranslationally modified with a phosphocholine moiety.. + UNIMOD_Phosphocholine = 300002139, + + /// Methyl:13C(1)2H(2): Heavy-Methyl:13C(1)2H(2). + UNIMOD_Methyl_13C_1_2H_2_ = 300002140, + + /// c-type-ion: Cleavage at the N atom from the N+1 residue as reaction inside the mass spectrometer. + UNIMOD_c_type_ion = 300002141, + + /// x-type-ion: Cleavage at the carbonyl from the N-1 residue as reaction inside the mass spectrometer. + UNIMOD_x_type_ion = 300002142, + + /// z-type-ion: Ammonia loss from N-terminus as reaction inside the mass spectrometer. + UNIMOD_z_type_ion = 300002143, + + /// Dehydromethionine: Intramolecular cyclization product of N-terminal methionine, forming a five-membered azasulfonium ion where the sulfur atom bonds to the amine group. + UNIMOD_Dehydromethionine = 300002144, + + /// Label:2H(8): SILAC: Lysine_D8. + UNIMOD_Label_2H_8_ = 300002146, + + /// imidazolone: Imidazolone from 3-DG. + UNIMOD_imidazolone = 300002147, + /// unit: A unit of measurement is a standardized quantity of a physical quality. UO_unit = 400000000, diff --git a/pwiz/data/common/cvgen.cpp b/pwiz/data/common/cvgen.cpp index 5e93eded97d..cdd6740b1dd 100644 --- a/pwiz/data/common/cvgen.cpp +++ b/pwiz/data/common/cvgen.cpp @@ -168,6 +168,7 @@ void writeHpp(const vector& obos, const string& basename, const bfs::path& os << "/// enumeration of controlled vocabulary (CV) terms, generated from OBO file(s)\n" "enum PWIZ_API_DECL CVID\n{\n" " CVID_Unknown = -1"; + set emittedEnumNames; // track emitted enum names to avoid redefinitions (e.g. synonyms that escape to the same name) for (vector::const_iterator obo=obos.begin(); obo!=obos.end(); ++obo) for(const Term& term : obo->terms) { @@ -176,14 +177,20 @@ void writeHpp(const vector& obos, const string& basename, const bfs::path& os << ",\n\n" << " /// " << term.name << ": " << term.def << "\n" << " " << eName << " = " << enumValue(term, enumMultiplierByPrefix[term.prefix]); + emittedEnumNames.insert(eName); if (term.prefix == "MS") // add synonyms for PSI-MS only { for(const string& synonym : term.exactSynonyms) { auto synonym_enum_name = enumName(term.prefix, synonym, term.isObsolete); - if (eName == synonym_enum_name) // Should not happen, but just in case - cerr << "Warning: synonym enum name collision for term id " << term.id << ": " << synonym << ": " << eName << endl; + // skip synonyms whose escaped enum name collides with an already-emitted name + // (e.g. a term with both "TOF/TOF" and "TOF-TOF" synonyms both escape to MS_TOF_TOF) + if (!emittedEnumNames.insert(synonym_enum_name).second) + { + cerr << "Warning: skipping duplicate synonym enum name for term id " << term.id << ": " << synonym << ": " << synonym_enum_name << endl; + continue; + } os << ",\n\n" << " /// " << synonym << " (" << term.name << "): " << term.def << "\n" << " " << synonym_enum_name << " = " << eName; diff --git a/pwiz/data/common/cvtest.cpp b/pwiz/data/common/cvtest.cpp index d1093e152d9..e8b39ccab8d 100644 --- a/pwiz/data/common/cvtest.cpp +++ b/pwiz/data/common/cvtest.cpp @@ -61,7 +61,7 @@ void test() unit_assert(cvTermInfo(MS_None____OBSOLETE).isObsolete); - unit_assert(cvTermInfo(MS_regular_expressions_for_a_GUID).def == "([A-Fa-f0-9]\\{8\\}-([A-Fa-f0-9]\\{4\\}-)\\{3\\}[A-Fa-f0-9]\\{12\\})."); + unit_assert(cvTermInfo(MS_regular_expressions_for_a_GUID).def == "([A-Fa-f0-9]\\\\{8\\\\}-([A-Fa-f0-9]\\\\{4\\\\}-)\\\\{3\\\\}[A-Fa-f0-9]\\\\{12\\\\})."); } diff --git a/pwiz/data/common/psi-ms.obo b/pwiz/data/common/psi-ms.obo index e03850ce2a7..46bd44c0134 100644 --- a/pwiz/data/common/psi-ms.obo +++ b/pwiz/data/common/psi-ms.obo @@ -1,7 +1,7 @@ format-version: 1.2 -data-version: 4.1.232 -date: 16:01:2026 12:00 -saved-by: Jonathan Hunter +data-version: 4.1.257 +date: 23:06:2026 22:00 +saved-by: Douwe Schulte default-namespace: MS namespace-id-rule: * MS:$sequence(7,0,9999999)$ namespace-id-rule: * PEFF:$sequence(7,0,9999999)$ @@ -28,6 +28,7 @@ remark: creator: David Cox sciex.com> remark: creator: Jonathan Hunter ebi.ac.uk> remark: creator: Samuel Wein openms.de> remark: creator: Jeroen Van Goey instadeep.com> +remark: creator: Jannick Kappelmann gmail.com> remark: publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics Working Group remark: When appropriate the definition and synonyms of a term are reported exactly as in the chapter 12 of IUPAC orange book. See http://www.iupac.org/projects/2003/2003-056-2-500.html and http://mass-spec.lsu.edu/msterms/index.php/Main_Page remark: For any queries contact psidev-ms-vocab@lists.sourceforge.net @@ -733,13 +734,13 @@ is_a: MS:1000247 ! desorption ionization id: MS:1000076 name: negative polarity acquisition def: "Polarities of the scans of a run are all negative." [PSI:MS] -is_a: MS:1000524 ! data file content +is_a: MS:1003776 ! acquisition polarity [Term] id: MS:1000077 name: positive polarity acquisition def: "Polarities of the scans of a run are all positive." [PSI:MS] -is_a: MS:1000524 ! data file content +is_a: MS:1003776 ! acquisition polarity [Term] id: MS:1000078 @@ -753,21 +754,18 @@ name: fourier transform ion cyclotron resonance def: "A device based on the principle of ion cyclotron resonance in which an ion in a magnetic field moves in a circular orbit at a frequency characteristic of its m/z value. Ions are coherently excited to a larger radius orbit using a pulse of radio frequency energy and their image charge is detected on receiver plates as a time domain signal. Fourier transformation of the time domain signal results in a frequency domain signal which is converted to a mass spectrum based in the inverse relationship between frequency and m/z." [PSI:MS] synonym: "FT_ICR" EXACT [] is_a: MS:1000443 ! mass analyzer type -is_a: MS:1003761 ! instrument class [Term] id: MS:1000080 name: magnetic sector def: "A device that produces a magnetic field perpendicular to a charged particle beam that deflects the beam to an extent that is proportional to the particle momentum per unit charge. For a monoenergetic beam, the deflection is proportional to m/z." [PSI:MS] is_a: MS:1000443 ! mass analyzer type -is_a: MS:1003761 ! instrument class [Term] id: MS:1000081 name: quadrupole def: "A device that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis." [PSI:MS] is_a: MS:1000443 ! mass analyzer type -is_a: MS:1003761 ! instrument class [Term] id: MS:1000082 @@ -790,7 +788,6 @@ name: time-of-flight def: "Instrument that separates ions by m/z in a field-free region after acceleration to a fixed acceleration energy." [PSI:MS] synonym: "TOF" EXACT [] is_a: MS:1000443 ! mass analyzer type -is_a: MS:1003761 ! instrument class [Term] id: MS:1000085 @@ -1072,14 +1069,14 @@ is_a: MS:1000031 ! instrument model [Term] id: MS:1000127 name: centroid spectrum -def: "Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset." [PSI:MS] +def: "A spectrum representation in which each peak is recorded as a single discrete data point at a distinct coordinate value (e.g. m/z; wavelength; drift time) with a corresponding intensity." [PSI:MS] synonym: "Discrete Mass Spectrum" EXACT [] is_a: MS:1000525 ! spectrum representation [Term] id: MS:1000128 name: profile spectrum -def: "A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis." [PSI:MS] +def: "A spectrum representation in which ion signal for each peak is recorded as a distribution of intensity values across the coordinate range (e.g. m/z; wavelength; drift time)." [PSI:MS] synonym: "continuous mass spectrum" EXACT [] synonym: "Continuum Mass Spectrum" EXACT [] is_a: MS:1000525 ! spectrum representation @@ -1160,96 +1157,112 @@ relationship: has_value_type xsd:float ! The allowed value-type for this CV term id: MS:1000139 name: 4000 QTRAP def: "Applied Biosystems/MDS SCIEX Q 4000 TRAP MS." [PSI:MS] +is_a: MS:1003765 ! triple quadrupole linear ion trap instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000140 name: 4700 Proteomics Analyzer def: "Applied Biosystems/MDS SCIEX 4700 Proteomics Analyzer MS." [PSI:MS] +is_a: MS:1003946 ! tandem time-of-flight instrument is_a: MS:1000495 ! Applied Biosystems instrument model [Term] id: MS:1000141 name: apex IV def: "Bruker Daltonics' apex IV: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR." [PSI:MS] +is_a: MS:1003948 ! fourier transform ion cyclotron resonance instrument is_a: MS:1001556 ! Bruker Daltonics apex series [Term] id: MS:1000142 name: apex Q def: "Bruker Daltonics' apex Q: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR." [PSI:MS] +is_a: MS:1003766 ! quadrupole fourier transform ion cyclotron resonance instrument is_a: MS:1001556 ! Bruker Daltonics apex series [Term] id: MS:1000143 name: API 150EX def: "Applied Biosystems/MDS SCIEX API 150EX MS." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000144 name: API 150EX Prep def: "Applied Biosystems/MDS SCIEX API 150EX Prep MS." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000145 name: API 2000 def: "Applied Biosystems/MDS SCIEX API 2000 MS." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000146 name: API 3000 def: "Applied Biosystems/MDS SCIEX API 3000 MS." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000147 name: API 4000 def: "Applied Biosystems/MDS SCIEX API 4000 MS." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000148 name: autoflex II def: "Bruker Daltonics' autoflex II: MALDI TOF." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1000149 name: autoflex TOF/TOF def: "Bruker Daltonics' autoflex TOF/TOF MS: MALDI TOF." [PSI:MS] +is_a: MS:1003946 ! tandem time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1000150 name: Auto Spec Ultima NT def: "Waters magnetic sector based AutoSpec Ultima NT MS." [PSI:MS] +is_a: MS:1003949 ! magnetic sector instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000151 name: BioTOF II def: "Bruker Daltonics' BioTOF II: ESI TOF." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1001535 ! Bruker Daltonics BioTOF series [Term] id: MS:1000152 name: BioTOF-Q def: "Bruker Daltonics' BioTOF-Q: ESI Q-TOF." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1001535 ! Bruker Daltonics BioTOF series [Term] id: MS:1000153 name: DELTA plusAdvantage def: "ThermoFinnigan DELTA plusAdvantage MS." [PSI:MS] +is_a: MS:1003949 ! magnetic sector instrument is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000154 name: DELTAplusXP def: "ThermoFinnigan DELTAplusXP MS." [PSI:MS] +is_a: MS:1003949 ! magnetic sector instrument is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] @@ -1263,144 +1276,168 @@ is_obsolete: true id: MS:1000156 name: esquire 4000 def: "Bruker Daltonics' esquire 4000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1001533 ! Bruker Daltonics esquire series [Term] id: MS:1000157 name: esquire 6000 def: "Bruker Daltonics' esquire 6000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1001533 ! Bruker Daltonics esquire series [Term] id: MS:1000158 name: explorer def: "IonSpec Explorer MS." [PSI:MS] +is_a: MS:1003948 ! fourier transform ion cyclotron resonance instrument is_a: MS:1000123 ! IonSpec instrument model [Term] id: MS:1000159 name: GCT def: "Waters oa-ToF based GCT." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000160 name: HCT def: "Bruker Daltonics' HCT: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000697 ! Bruker Daltonics HCT Series [Term] id: MS:1000161 name: HCTplus def: "Bruker Daltonics' HCTplus: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000697 ! Bruker Daltonics HCT Series [Term] id: MS:1000162 name: HiRes ESI def: "IonSpec HiResESI MS." [PSI:MS] +is_a: MS:1003948 ! fourier transform ion cyclotron resonance instrument is_a: MS:1000123 ! IonSpec instrument model [Term] id: MS:1000163 name: HiRes MALDI def: "IonSpec HiResMALDI MS." [PSI:MS] +is_a: MS:1003948 ! fourier transform ion cyclotron resonance instrument is_a: MS:1000123 ! IonSpec instrument model [Term] id: MS:1000164 name: IsoPrime def: "Waters IsoPrime MS." [PSI:MS] +is_a: MS:1003949 ! magnetic sector instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000165 name: IsoProbe def: "Waters IsoProbe MS." [PSI:MS] +is_a: MS:1003949 ! magnetic sector instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000166 name: IsoProbe T def: "Waters IsoProbe T MS." [PSI:MS] +is_a: MS:1003949 ! magnetic sector instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000167 name: LCQ Advantage def: "ThermoFinnigan LCQ Advantage MS." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000168 name: LCQ Classic def: "ThermoFinnigan LCQ Classic MS." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000169 name: LCQ Deca XP Plus def: "ThermoFinnigan LCQ Deca XP Plus MS." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000170 name: M@LDI L def: "Waters oa-ToF based MALDI L." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000171 name: M@LDI LR def: "Waters oa-ToF based MALDI LR." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000172 name: MAT253 def: "ThermoFinnigan MAT253 MS." [PSI:MS] +is_a: MS:1003949 ! magnetic sector instrument is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000173 name: MAT900XP def: "ThermoFinnigan MAT900XP MS." [PSI:MS] +is_a: MS:1003949 ! magnetic sector instrument is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000174 name: MAT900XP Trap def: "ThermoFinnigan MAT900XP Trap MS." [PSI:MS] +is_a: MS:1003947 ! magnetic sector ion trap instrument is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000175 name: MAT95XP def: "ThermoFinnigan MAT95XP MS." [PSI:MS] +is_a: MS:1003949 ! magnetic sector instrument is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000176 name: MAT95XP Trap def: "ThermoFinnigan MAT95XP Trap MS." [PSI:MS] +is_a: MS:1003947 ! magnetic sector ion trap instrument is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000177 name: microflex def: "Bruker Daltonics' microflex: MALDI TOF." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1000178 name: microTOF LC def: "Bruker Daltonics' microTOF LC: ESI TOF, Nanospray, APCI, APPI." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1000179 name: neptune def: "ThermoFinnigan NEPTUNE MS." [PSI:MS] +is_a: MS:1003949 ! magnetic sector instrument is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] @@ -1413,18 +1450,21 @@ is_a: MS:1000126 ! Waters instrument model id: MS:1000181 name: OMEGA def: "IonSpec OMEGA MS." [PSI:MS] +is_a: MS:1003948 ! fourier transform ion cyclotron resonance instrument is_a: MS:1000123 ! IonSpec instrument model [Term] id: MS:1000182 name: OMEGA-2001 def: "IonSpec OMEGA-2001 MS." [PSI:MS] +is_a: MS:1003948 ! fourier transform ion cyclotron resonance instrument is_a: MS:1000123 ! IonSpec instrument model [Term] id: MS:1000183 name: OmniFlex def: "Bruker Daltonics' OmniFlex: MALDI TOF." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] @@ -1437,6 +1477,7 @@ is_a: MS:1000126 ! Waters instrument model id: MS:1000185 name: PolarisQ def: "ThermoFinnigan PolarisQ MS." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] @@ -1449,42 +1490,49 @@ is_a: MS:1000121 ! SCIEX instrument model id: MS:1000187 name: Q TRAP def: "Applied Biosystems/MDS SCIEX Q TRAP MS." [PSI:MS] +is_a: MS:1003765 ! triple quadrupole linear ion trap instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000188 name: Q-Tof micro def: "Waters oa-ToF based Q-Tof micro." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000189 name: Q-Tof Ultima def: "Waters oa-ToF based Q-Tof Ultima." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000190 name: QSTAR def: "Applied Biosystems/MDS SCIEX QSTAR MS." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000191 name: quattro micro def: "Waters (triple) quadrupole based micro." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000192 name: Quattro Ultima def: "Waters (triple) quadrupole based Ultima." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000193 name: Surveyor MSQ def: "ThermoFinnigan Surveyor MSQ MS." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] @@ -1503,54 +1551,63 @@ is_a: MS:1000121 ! SCIEX instrument model id: MS:1000196 name: TEMPUS TOF def: "ThermoFinnigan TEMPUS TOF MS." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000197 name: TRACE DSQ def: "ThermoFinnigan TRACE DSQ MS." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000198 name: TRITON def: "ThermoFinnigan TRITON MS." [PSI:MS] +is_a: MS:1003949 ! magnetic sector instrument is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000199 name: TSQ Quantum def: "ThermoFinnigan TSQ Quantum MS." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000200 name: ultima def: "IonSpec Ultima MS." [PSI:MS] +is_a: MS:1003948 ! fourier transform ion cyclotron resonance instrument is_a: MS:1000123 ! IonSpec instrument model [Term] id: MS:1000201 name: ultraflex def: "Bruker Daltonics' ultraflex: MALDI TOF." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1000202 name: ultraflex TOF/TOF def: "Bruker Daltonics' ultraflex TOF/TOF: MALDI TOF." [PSI:MS] +is_a: MS:1003946 ! tandem time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1000203 name: Voyager-DE PRO def: "Applied Biosystems/MDS SCIEX Voyager-DE PRO MS." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000495 ! Applied Biosystems instrument model [Term] id: MS:1000204 name: Voyager-DE STR def: "Applied Biosystems/MDS SCIEX Voyager-DE STR MS." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000495 ! Applied Biosystems instrument model [Term] @@ -2017,7 +2074,6 @@ name: ion trap def: "A device for spatially confining ions using electric and magnetic fields alone or in combination." [PSI:MS] synonym: "IT" EXACT [] is_a: MS:1000443 ! mass analyzer type -is_a: MS:1003761 ! instrument class [Term] id: MS:1000265 @@ -3276,24 +3332,28 @@ is_a: MS:1000008 ! ionization type id: MS:1000447 name: LTQ def: "Finnigan LTQ MS." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000448 name: LTQ FT def: "Finnigan LTQ FT MS." [PSI:MS] +is_a: MS:1003971 ! ion trap fourier transform ion cyclotron resonance instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000449 name: LTQ Orbitrap def: "Finnigan LTQ Orbitrap MS." [PSI:MS] +is_a: MS:1003768 ! ion trap orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000450 name: LXQ def: "Finnigan LXQ MS." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -3408,70 +3468,70 @@ is_obsolete: true id: MS:1000467 name: 1200 series LC/MSD SL def: "The 1200 Series LC/MSD SL ion trap belongs to the Agilent LC/MSD ion trap family. It provides fast polarity switching and multisignal data acquisition capabilities in a single run while also providing 5 stages of automated data dependent MS2 and 11 stages of manual MS2." [PSI:MS] -is_a: MS:1000264 ! ion trap +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000468 name: 6110 Quadrupole LC/MS def: "The 6110 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with an entry level single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6110 Quadrupole mass spectrometer has m/z range of 10-1500 and 2500 u/s scan speed. It proves useful for wide range of SIM quantitative applications." [PSI:MS] -is_a: MS:1000081 ! quadrupole +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000469 name: 6120A Quadrupole LC/MS def: "The 6120A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. 6120 quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan speed and utilizes multiple signal acquisition." [PSI:MS] -is_a: MS:1000081 ! quadrupole +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000470 name: 6130 Quadrupole LC/MS def: "The 6130 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 series of Agilent mass spectrometers. The 6130 quadrupole mass spectrometer has m/z range of 2-3000, 2500 u/s scan speed in standard mode and 5250 u/s speed in fast-scan mode. It also uses multiple signal acquisition." [PSI:MS] -is_a: MS:1000081 ! quadrupole +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000471 name: 6140 Quadrupole LC/MS def: "The 6140 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6140 Quadrupole mass spectrometer has m/z range of 10-1350, 2500 u/s scan speed in standard mode and 10000 u/s speed in fast-scan mode. It also uses multiple signal acquisition." [PSI:MS] -is_a: MS:1000081 ! quadrupole +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000472 name: 6210 Time-of-Flight LC/MS def: "The 6210 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS] -is_a: MS:1000084 ! time-of-flight +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000473 name: 6310 Ion Trap LC/MS def: "The 6310 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.35 resolution and mass range of 200-4000 with resolution of 3-4. The scan speed varies from 1650-27000 for the respective mass ranges." [PSI:MS] -is_a: MS:1000264 ! ion trap +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000474 name: 6320 Ion Trap LC/MS def: "The 6320 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges." [PSI:MS] -is_a: MS:1000264 ! ion trap +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000475 name: 6330 Ion Trap LC/MS def: "The 6330 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges." [PSI:MS] -is_a: MS:1000264 ! ion trap +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000476 name: 6340 Ion Trap LC/MS def: "The 6340 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges." [PSI:MS] -is_a: MS:1000264 ! ion trap +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000490 ! Agilent instrument model [Term] @@ -3479,14 +3539,14 @@ id: MS:1000477 name: 6410 Triple Quadrupole LC/MS def: "The 6410 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. Mass range of the mass spectrometer is 15-1650 m/z, resolution is at three settings of 0.7 u (unit), 1.2 u (wide) and 2.5 u (widest). The mass accuracy for 6410 mass spectrometer is 0.1 across the mass range. The collision cell is a hexapole with linear acceleration." [PSI:MS] synonym: "6410 Triple Quad LC/MS" EXACT [] -is_a: MS:1003762 ! triple quadrupole +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000478 name: 1200 series LC/MSD VL def: "The LC/MSD VL ion trap is part of the family of Agilent ion trap mass spectrometers. It has ESI, APCI and APPI ion sources and is a useful ion trap when the amount of sample is not the limiting factor." [PSI:MS] -is_a: MS:1000264 ! ion trap +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000490 ! Agilent instrument model [Term] @@ -3526,7 +3586,6 @@ id: MS:1000484 name: orbitrap def: "An ion trapping device that consists of an outer barrel-like electrode and a coaxial inner spindle-like electrode that form an electrostatic field with quadro-logarithmic potential distribution. The frequency of harmonic oscillations of the orbitally trapped ions along the axis of the electrostatic field is independent of the ion velocity and is inversely proportional to the square root of m/z so that the trap can be used as a mass analyzer." [PSI:MS] is_a: MS:1000443 ! mass analyzer type -is_a: MS:1003761 ! instrument class [Term] id: MS:1000485 @@ -3869,6 +3928,7 @@ id: MS:1000532 name: Xcalibur def: "Thermo Finnigan software for data acquisition and analysis." [PSI:MS] is_a: MS:1000693 ! Thermo Finnigan software +is_a: MS:1003961 ! Thermo Scientific software is_a: MS:1001455 ! acquisition software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software @@ -4029,30 +4089,35 @@ is_a: MS:1001457 ! data processing software id: MS:1000554 name: LCQ Deca def: "ThermoFinnigan LCQ Deca." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000555 name: LTQ Orbitrap Discovery def: "LTQ Orbitrap Discovery." [PSI:MS] +is_a: MS:1003768 ! ion trap orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000556 name: LTQ Orbitrap XL def: "LTQ Orbitrap XL." [PSI:MS] +is_a: MS:1003768 ! ion trap orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000557 name: LTQ FT Ultra def: "LTQ FT Ultra." [PSI:MS] +is_a: MS:1003971 ! ion trap fourier transform ion cyclotron resonance instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000558 name: GC Quantum def: "GC Quantum." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] @@ -4178,6 +4243,7 @@ is_a: MS:1000499 ! spectrum attribute id: MS:1000578 name: LCQ Fleet def: "LCQ Fleet." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] @@ -4342,6 +4408,7 @@ is_a: MS:1001457 ! data processing software [Term] id: MS:1000601 name: ProteinLynx Global Server +synonym: "PLGS" EXACT [] def: "Waters software for data analysis." [PSI:MS] is_a: MS:1000694 ! Waters software is_a: MS:1001456 ! analysis software @@ -4363,54 +4430,63 @@ is_a: MS:1000124 ! Shimadzu instrument model id: MS:1000604 name: LCMS-IT-TOF def: "Shimadzu Scientific Instruments LCMS-IT-TOF MS." [PSI:MS] +is_a: MS:1003764 ! ion trap time-of-flight instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1000605 name: LCMS-2010EV def: "Shimadzu Scientific Instruments LCMS-2010EV MS." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1000606 name: LCMS-2010A def: "Shimadzu Scientific Instruments LCMS-2010A MS." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1000607 name: AXIMA CFR MALDI-TOF def: "Shimadzu Biotech AXIMA CFR MALDI-TOF MS." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] id: MS:1000608 name: AXIMA-QIT def: "Shimadzu Biotech AXIMA-QIT MS." [PSI:MS] +is_a: MS:1003764 ! ion trap time-of-flight instrument is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] id: MS:1000609 name: AXIMA-CFR plus def: "Shimadzu Biotech AXIMA-CFR plus MS." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] id: MS:1000610 name: AXIMA Performance MALDI-TOF/TOF def: "Shimadzu Biotech AXIMA Performance MALDI-TOF/TOF MS." [PSI:MS] +is_a: MS:1003946 ! tandem time-of-flight instrument is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] id: MS:1000611 name: AXIMA Confidence MALDI-TOF def: "Shimadzu Biotech AXIMA Confidence MALDI-TOF (curved field reflectron) MS." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] id: MS:1000612 name: AXIMA Assurance Linear MALDI-TOF def: "Shimadzu Biotech AXIMA Assurance Linear MALDI-TOF MS." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] @@ -4561,6 +4637,7 @@ relationship: has_value_type xsd:float ! The allowed value-type for this CV term id: MS:1000632 name: Q-Tof Premier def: "Waters oa-ToF based Q-Tof Premier." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] @@ -4574,84 +4651,98 @@ relationship: has_value_type xsd:int ! The allowed value-type for this CV term id: MS:1000634 name: DSQ def: "ThermoFinnigan DSQ GC-MS." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000635 name: ITQ 700 def: "Thermo Scientific ITQ 700 GC-MS." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000636 name: ITQ 900 def: "Thermo Scientific ITQ 900 GC-MS." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000637 name: ITQ 1100 def: "Thermo Scientific ITQ 1100 GC-MS." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000638 name: LTQ XL ETD def: "Thermo Scientific LTQ XL MS with ETD." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000639 name: LTQ Orbitrap XL ETD def: "Thermo Scientific LTQ Orbitrap XL MS with ETD." [PSI:MS] +is_a: MS:1003768 ! ion trap orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000640 name: DFS def: "Thermo Scientific DFS HR GC-MS." [PSI:MS] +is_a: MS:1003949 ! magnetic sector instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000641 name: DSQ II def: "Thermo Scientific DSQ II GC-MS." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000642 name: MALDI LTQ XL def: "Thermo Scientific MALDI LTQ XL MS." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000643 name: MALDI LTQ Orbitrap def: "Thermo Scientific MALDI LTQ Orbitrap MS." [PSI:MS] +is_a: MS:1003768 ! ion trap orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000644 name: TSQ Quantum Access def: "Thermo Scientific TSQ Quantum Access MS." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000645 name: Element XR def: "Thermo Scientific Element XR HR-ICP-MS." [PSI:MS] +is_a: MS:1003949 ! magnetic sector instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000646 name: Element 2 def: "Thermo Scientific Element 2 HR-ICP-MS." [PSI:MS] +is_a: MS:1003949 ! magnetic sector instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000647 name: Element GD def: "Thermo Scientific Element GD Glow Discharge MS." [PSI:MS] +is_a: MS:1003949 ! magnetic sector instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -4664,6 +4755,7 @@ is_a: MS:1000494 ! Thermo Scientific instrument model id: MS:1000649 name: Exactive def: "Thermo Scientific Exactive MS." [PSI:MS] +is_a: MS:1003953 ! orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -4671,6 +4763,7 @@ id: MS:1000650 name: Proteome Discoverer def: "Thermo Scientific software for data analysis of peptides and proteins." [PSI:MS] is_a: MS:1000693 ! Thermo Finnigan software +is_a: MS:1003961 ! Thermo Scientific software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software @@ -4678,48 +4771,56 @@ is_a: MS:1001457 ! data processing software id: MS:1000651 name: 3200 QTRAP def: "SCIEX or Applied Biosystems|MDS SCIEX QTRAP 3200." [PSI:MS] +is_a: MS:1003765 ! triple quadrupole linear ion trap instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000652 name: 4800 Plus MALDI TOF/TOF def: "SCIEX or Applied Biosystems|MDS SCIEX 4800 Plus MALDI TOF-TOF Analyzer." [PSI:MS] +is_a: MS:1003946 ! tandem time-of-flight instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000653 name: API 3200 def: "SCIEX or Applied Biosystems|MDS SCIEX API 3200 MS." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000654 name: API 5000 def: "SCIEX or Applied Biosystems|MDS SCIEX API 5000 MS." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000655 name: QSTAR Elite def: "SCIEX or Applied Biosystems|MDS SCIEX QSTAR Elite." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000656 name: QSTAR Pulsar def: "Applied Biosystems|MDS SCIEX QSTAR Pulsar." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000657 name: QSTAR XL def: "Applied Biosystems|MDS SCIEX QSTAR XL." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000658 name: 4800 Proteomics Analyzer def: "Applied Biosystems|MDS SCIEX 4800 Proteomics Analyzer." [PSI:MS] +is_a: MS:1003946 ! tandem time-of-flight instrument is_a: MS:1000495 ! Applied Biosystems instrument model [Term] @@ -4735,6 +4836,7 @@ is_a: MS:1001457 ! data processing software id: MS:1000660 name: Xevo MRT MS def: "Waters Corporation Xevo MRT Mass Spectrometer." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] @@ -4850,21 +4952,21 @@ is_a: MS:1001457 ! data processing software id: MS:1000675 name: 6220 Time-of-Flight LC/MS def: "The 6220 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS] -is_a: MS:1000084 ! time-of-flight +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000676 name: 6510 Quadrupole Time-of-Flight LC/MS def: "The 6510 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS] -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000677 name: 6520A Quadrupole Time-of-Flight LC/MS def: "The 6520A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 26,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS] -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] @@ -4995,12 +5097,14 @@ is_a: MS:1000531 ! software id: MS:1000695 name: apex ultra def: "Bruker Daltonics' apex ultra: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR." [PSI:MS] +is_a: MS:1003766 ! quadrupole fourier transform ion cyclotron resonance instrument is_a: MS:1001556 ! Bruker Daltonics apex series [Term] id: MS:1000696 name: autoflex III smartbeam def: "Bruker Daltonics' autoflex III smartbeam: MALDI TOF." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] @@ -5013,48 +5117,56 @@ is_a: MS:1000122 ! Bruker Daltonics instrument model id: MS:1000698 name: HCTultra def: "Bruker Daltonics' HCTultra: ESI TOF, Nanospray, APCI, APPI." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000697 ! Bruker Daltonics HCT Series [Term] id: MS:1000699 name: HCTultra PTM def: "Bruker Daltonics' HCTultra PTM: ESI TOF, Nanospray, APCI, APPI, PTR." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000697 ! Bruker Daltonics HCT Series [Term] id: MS:1000700 name: HCTultra ETD II def: "Bruker Daltonics' HCTultra ETD II: ESI Q-TOF, Nanospray, APCI, APPI, ETD." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000697 ! Bruker Daltonics HCT Series [Term] id: MS:1000701 name: microflex LT def: "Bruker Daltonics' microflex LT: MALDI TOF." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1000702 name: micrOTOF def: "Bruker Daltonics' micrOTOF: ESI TOF, APCI, APPI." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1000703 name: micrOTOF-Q def: "Bruker Daltonics' micrOTOF-Q: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1000704 name: micrOTOF-Q II def: "Bruker Daltonics' micrOTOF-Q II: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1000705 name: ultraflex III TOF/TOF def: "Bruker Daltonics' ultraflex III TOF/TOF: MALDI TOF." [PSI:MS] +is_a: MS:1003946 ! tandem time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] @@ -5316,6 +5428,7 @@ is_a: MS:1001040 ! intermediate analysis format id: MS:1000743 name: TSQ Quantum Ultra AM def: "Thermo Scientific TSQ Quantum Ultra AM." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -5349,24 +5462,28 @@ relationship: has_value_type xsd:dateTime ! The allowed value-type for this CV t id: MS:1000748 name: SSQ 7000 def: "ThermoFinnigan SSQ 7000 MS." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000749 name: TSQ 7000 def: "ThermoFinnigan TSQ 7000 MS." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000750 name: TSQ def: "ThermoFinnigan TSQ MS." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000751 name: TSQ Quantum Ultra def: "Thermo Scientific TSQ Quantum Ultra." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -6104,18 +6221,21 @@ is_a: MS:1000842 ! laser type id: MS:1000854 name: LTQ XL def: "Thermo Scientific LTQ XL MS." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000855 name: LTQ Velos def: "Thermo Scientific LTQ Velos MS." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000856 name: LTQ Velos/ETD def: "Thermo Scientific LTQ Velos MS with ETD." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000494 ! Thermo Scientific instrument model synonym: "LTQ Velos ETD" EXACT [] @@ -6634,12 +6754,14 @@ is_a: MS:1000560 ! mass spectrometer file format id: MS:1000931 name: QTRAP 5500 def: "Applied Biosystems|MDS SCIEX QTRAP 5500." [PSI:MS] +is_a: MS:1003765 ! triple quadrupole linear ion trap instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000932 name: TripleTOF 5600 def: "SCIEX TripleTOF 5600, a quadrupole - quadrupole - time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000121 ! SCIEX instrument model [Term] @@ -6660,21 +6782,21 @@ relationship: has_value_type xsd:string ! The allowed value-type for this CV ter id: MS:1000935 name: 6470A Triple Quadrupole LC/MS def: "The 6470A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1003762 ! triple quadrupole +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000936 name: 6470B Triple Quadrupole LC/MS def: "The 6470B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1003762 ! triple quadrupole +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000937 name: 6495C Triple Quadrupole LC/MS def: "The 6495C Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1003762 ! triple quadrupole +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] @@ -8169,7 +8291,7 @@ id: MS:1001251 name: Trypsin def: "Enzyme trypsin." [PSI:PI] is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001176 ! (?<=[KR])(?!P) +relationship: has_regexp MS:1001176 ! (?<=[KR])(?\!P) [Term] id: MS:1001252 @@ -8453,7 +8575,7 @@ def: "Endoproteinase Arg-C." [PSI:PI] synonym: "Trypsin/R" EXACT [] synonym: "Clostripain" EXACT [] is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001272 ! (?<=R)(?!P) +relationship: has_regexp MS:1001272 ! (?<=R)(?\!P) [Term] id: MS:1001304 @@ -8474,7 +8596,7 @@ id: MS:1001306 name: Chymotrypsin def: "Enzyme chymotrypsin." [PSI:PI] is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001332 ! (?<=[FYWL])(?!P) +relationship: has_regexp MS:1001332 ! (?<=[FYWL])(?\!P) [Term] id: MS:1001307 @@ -8496,7 +8618,7 @@ name: Lys-C def: "Endoproteinase Lys-C." [PSI:PI] synonym: "Trypsin/K" EXACT [] is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001335 ! (?<=K)(?!P) +relationship: has_regexp MS:1001335 ! (?<=K)(?\!P) [Term] id: MS:1001310 @@ -8517,7 +8639,7 @@ id: MS:1001312 name: TrypChymo def: "Cleavage agent TrypChymo." [PSI:PI] is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001338 ! (?<=[FYWLKR])(?!P) +relationship: has_regexp MS:1001338 ! (?<=[FYWLKR])(?\!P) [Term] id: MS:1001313 @@ -8532,14 +8654,14 @@ id: MS:1001314 name: V8-DE def: "Cleavage agent V8-DE." [PSI:PI] is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001340 ! (?<=[BDEZ])(?!P) +relationship: has_regexp MS:1001340 ! (?<=[BDEZ])(?\!P) [Term] id: MS:1001315 name: V8-E def: "Cleavage agent V8-E." [PSI:PI] is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001341 ! (?<=[EZ])(?!P) +relationship: has_regexp MS:1001341 ! (?<=[EZ])(?\!P) [Term] id: MS:1001316 @@ -9631,6 +9753,7 @@ is_a: MS:1000560 ! mass spectrometer file format id: MS:1001482 name: 5800 TOF/TOF def: "SCIEX 5800 TOF-TOF Analyzer." [PSI:MS] +is_a: MS:1003946 ! tandem time-of-flight instrument is_a: MS:1000121 ! SCIEX instrument model [Term] @@ -9820,6 +9943,7 @@ is_a: MS:1000560 ! mass spectrometer file format id: MS:1001510 name: TSQ Vantage def: "TSQ Vantage." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -9996,48 +10120,56 @@ is_a: MS:1000122 ! Bruker Daltonics instrument model id: MS:1001537 name: BioTOF def: "Bruker Daltonics' BioTOF: ESI TOF." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1001535 ! Bruker Daltonics BioTOF series [Term] id: MS:1001538 name: BioTOF III def: "Bruker Daltonics' BioTOF III: ESI TOF." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1001535 ! Bruker Daltonics BioTOF series [Term] id: MS:1001539 name: UltroTOF-Q def: "Bruker Daltonics' UltroTOF-Q: ESI Q-TOF (MALDI optional)." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1001535 ! Bruker Daltonics BioTOF series [Term] id: MS:1001540 name: micrOTOF II def: "Bruker Daltonics' micrOTOF II: ESI TOF, Nanospray, APCI, APPI." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1001541 name: maXis def: "Bruker Daltonics' maXis: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1001547 ! Bruker Daltonics maXis series [Term] id: MS:1001542 name: amaZon ETD def: "Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1001545 ! Bruker Daltonics amaZon series [Term] id: MS:1001543 name: microflex LRF def: "Bruker Daltonics' microflex LRF: MALDI TOF." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1001544 name: ultrafleXtreme def: "Bruker Daltonics' ultrafleXtreme: MALDI TOF." [PSI:MS] +is_a: MS:1003946 ! tandem time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] @@ -10050,6 +10182,7 @@ is_a: MS:1000122 ! Bruker Daltonics instrument model id: MS:1001546 name: amaZon X def: "Bruker Daltonics' amaZon X: ESI quadrupole ion trap, APCI, APPI, ETD, PTR." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1001545 ! Bruker Daltonics amaZon series [Term] @@ -10068,30 +10201,35 @@ is_a: MS:1000122 ! Bruker Daltonics instrument model id: MS:1001549 name: solariX def: "Bruker Daltonics' solariX: ESI, MALDI, Qh-FT_ICR." [PSI:MS] +is_a: MS:1003766 ! quadrupole fourier transform ion cyclotron resonance instrument is_a: MS:1001548 ! Bruker Daltonics solarix series [Term] id: MS:1001550 name: microflex II def: "Bruker Daltonics' microflex II: MALDI TOF." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1001553 name: autoflex II TOF/TOF def: "Bruker Daltonics' autoflex II TOF/TOF: MALDI TOF." [PSI:MS] +is_a: MS:1003946 ! tandem time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1001554 name: autoflex III TOF/TOF smartbeam def: "Bruker Daltonics' autoflex III TOF/TOF smartbeam: MALDI TOF." [PSI:MS] +is_a: MS:1003946 ! tandem time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1001555 name: autoflex def: "Bruker Daltonics' autoflex: MALDI TOF." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] @@ -11452,6 +11590,7 @@ relationship: has_value_type xsd:string ! The allowed value-type for this CV ter id: MS:1001742 name: LTQ Orbitrap Velos def: "Finnigan LTQ Orbitrap Velos MS." [PSI:MS] +is_a: MS:1003768 ! ion trap orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -11650,120 +11789,140 @@ is_a: MS:1003591 ! ultra-performance liquid chromatography system id: MS:1001770 name: GCT Premier def: "Waters oa-ToF based GCT Premier." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001771 name: MALDI Synapt G2 HDMS def: "Waters oa-ToF based MALDI Synapt G2 HDMS." [PSI:MS] +is_a: MS:1003767 ! quadrupole ion mobility time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001772 name: MALDI Synapt G2 MS def: "Waters oa-ToF based MALDI Synapt G2 MS." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001773 name: MALDI Synapt G2-S HDMS def: "Waters oa-ToF based MALDI Synapt G2 MS." [PSI:MS] +is_a: MS:1003767 ! quadrupole ion mobility time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001774 name: MALDI Synapt G2-S MS def: "Waters oa-ToF based MALDI Synapt G2-S MS." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001775 name: MALDI Synapt HDMS def: "Waters oa-ToF based MALDI Synapt HDMS." [PSI:MS] +is_a: MS:1003767 ! quadrupole ion mobility time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001776 name: MALDI Synapt MS def: "Waters oa-ToF based MALDI Synapt MS." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001777 name: Synapt G2 HDMS def: "Waters oa-ToF based Synapt G2 HDMS." [PSI:MS] +is_a: MS:1003767 ! quadrupole ion mobility time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001778 name: Synapt G2 MS def: "Waters oa-ToF based Synapt G2 MS." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001779 name: Synapt G2-S HDMS def: "Waters oa-ToF based Synapt G2-S HDMS." [PSI:MS] +is_a: MS:1003767 ! quadrupole ion mobility time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001780 name: Synapt G2-S MS def: "Waters oa-ToF based Synapt G2-S MS." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001781 name: Synapt HDMS def: "Waters oa-ToF based Synapt HDMS." [PSI:MS] +is_a: MS:1003767 ! quadrupole ion mobility time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001782 name: Synapt MS def: "Waters oa-ToF based Synapt MS." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001783 name: Xevo G2 Q-Tof def: "Waters oa-ToF based Xevo G2 Q-Tof." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001784 name: Xevo G2 Tof def: "Waters oa-ToF based Xevo G2 Tof." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001785 name: Xevo Q-Tof def: "Waters oa-ToF based Xevo Q-Tof." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001786 name: 3100 def: "Waters quadrupole based 3100." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001787 name: Acquity SQD def: "Waters quadrupole based Acquity SQD." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001788 name: Acquity TQD def: "Waters quadrupole based Acquity TQD." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001789 name: Quattro micro GC def: "Waters (triple) quadrupole based Quattro micro GC." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000126 ! Waters instrument model [Term] @@ -11771,18 +11930,20 @@ id: MS:1001790 name: Xevo TQ MS def: "Waters quadrupole based Xevo TQ MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model -is_a: MS:1003762 ! triple quadrupole mass spectrometer +is_a: MS:1003762 ! triple quadrupole instrument [Term] id: MS:1001791 name: Xevo TQD def: "Waters quadrupole based Xevo TQD." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001792 name: Xevo TQ-S def: "Waters quadrupole based Xevo TQ-S." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000126 ! Waters instrument model [Term] @@ -11841,24 +12002,31 @@ is_a: MS:1000031 ! instrument model id: MS:1001801 name: Pegasus HRT def: "LECO high resolution time-of-flight GC mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1001800 ! LECO instrument model [Term] id: MS:1001802 name: Citius HRT def: "LECO high resolution time-of-flight LC mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1001800 ! LECO instrument model [Term] id: MS:1001803 name: Pegasus def: "LECO GC time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1001800 ! LECO instrument model [Term] id: MS:1001804 name: TruTOF def: "LECO bench-top GC time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1001800 ! LECO instrument model [Term] @@ -12563,18 +12731,21 @@ relationship: has_value_type xsd:float ! The allowed value-type for this CV term id: MS:1001908 name: ISQ def: "Thermo Scientific ISQ single quadrupole MS with the ExtractraBrite source." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1001909 name: Velos Plus def: "Thermo Scientific second generation Velos." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1001910 name: Orbitrap Elite def: "Thermo Scientific Orbitrap Elite, sometimes referred to as the LTQ Orbitrap Elite." [PSI:MS] +is_a: MS:1003768 ! ion trap orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model synonym: "LTQ Orbitrap Elite" EXACT [] @@ -12582,6 +12753,7 @@ synonym: "LTQ Orbitrap Elite" EXACT [] id: MS:1001911 name: Q Exactive def: "Thermo Scientific Q Exactive." [PSI:MS] +is_a: MS:1003769 ! quadrupole orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -12589,6 +12761,7 @@ id: MS:1001912 name: PinPoint def: "Thermo Scientific PinPoint SRM analysis software." [PSI:MS] is_a: MS:1000693 ! Thermo Finnigan software +is_a: MS:1003961 ! Thermo Scientific software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software @@ -12611,14 +12784,14 @@ id: MS:1001915 name: leukocyte elastase def: "Enzyme leukocyte elastase (EC 3.4.21.37)." [BRENDA:3.4.21.37] is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001957 ! (?<=[ALIV])(?!P) +relationship: has_regexp MS:1001957 ! (?<=[ALIV])(?\!P) [Term] id: MS:1001916 name: proline endopeptidase def: "Enzyme proline endopeptidase (EC 3.4.21.26)." [BRENDA:3.4.21.26] is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001958 ! (?<=[HKR]P)(?!P) +relationship: has_regexp MS:1001958 ! (?<=[HKR]P)(?\!P) [Term] id: MS:1001917 @@ -12656,7 +12829,7 @@ name: Digital Object Identifier (DOI) def: "DOI unique identifier of a publication." [PSI:PI, http://dx.doi.org] synonym: "doi" EXACT [] is_a: MS:1000878 ! external reference identifier -relationship: has_regexp MS:1002480 ! (10[.][0-9]\{4,\}(?:[.][0-9]+)*/(?:(?![\"&\'<>])[^ \t\\r\n\\v\\f])+) +relationship: has_regexp MS:1002480 ! (10[.][0-9]\\{4,\\}(?:[.][0-9]+)*/(?:(?\![\\"&\\'<>])[^ \\t\\r\\n\\v\\f])+) relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] @@ -12810,6 +12983,8 @@ relationship: has_value_type xsd:float ! The allowed value-type for this CV term id: MS:1001945 name: Pegasus 4D def: "LECO nominal mass resolution time-of-flight GCxGC mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1001800 ! LECO instrument model [Term] @@ -12891,13 +13066,13 @@ is_a: MS:1001045 ! cleavage agent name [Term] id: MS:1001957 -name: (?<=[ALIV])(?!P) +name: (?<=[ALIV])(?\!P) def: "Regular expression for leukocyte elastase." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001958 -name: (?<=[HKR]P)(?!P) +name: (?<=[HKR]P)(?\!P) def: "Regular expression for proline endopeptidase." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression @@ -13729,6 +13904,7 @@ is_a: MS:1001456 ! analysis software id: MS:1002077 name: impact def: "Bruker Daltonics' impact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] @@ -14698,7 +14874,7 @@ relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002231 name: regular expressions for a GUID -def: "([A-Fa-f0-9]\{8\}-([A-Fa-f0-9]\{4\}-)\{3\}[A-Fa-f0-9]\{12\})." [PSI:PI] +def: "([A-Fa-f0-9]\\{8\\}-([A-Fa-f0-9]\\{4\\}-)\\{3\\}[A-Fa-f0-9]\\{12\\})." [PSI:PI] is_a: MS:1002479 ! regular expression [Term] @@ -14998,42 +15174,50 @@ relationship: has_value_type xsd:float ! The allowed value-type for this CV term id: MS:1002274 name: SQ Detector 2 def: "Waters quadrupole based SQ Detector 2." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1002275 name: Xevo G2-S Tof def: "Waters oa-ToF based Xevo G2-S Tof." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1002276 name: Xevo G2-S QTof def: "Waters oa-ToF based Xevo G2-S QTof." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1002277 name: AutoSpec Premier def: "Waters AutoSpec Premier magnetic sector instrument." [PSI:MS] +is_a: MS:1003949 ! magnetic sector instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1002278 name: Pegasus III def: "LECO nominal mass resolution time-of-flight GC mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1001800 ! LECO instrument model [Term] id: MS:1002279 name: maXis 4G def: "Bruker Daltonics' maXis 4G: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1001547 ! Bruker Daltonics maXis series [Term] id: MS:1002280 name: compact def: "Bruker Daltonics' compact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] @@ -15127,42 +15311,49 @@ is_a: MS:1000122 ! Bruker Daltonics instrument model id: MS:1002295 name: SCION SQ def: "Bruker Daltonics' SCION SQ: GC-single quadrupole." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1002293 ! Bruker Daltonics SCION series [Term] id: MS:1002296 name: SCION TQ def: "Bruker Daltonics' SCION TQ: GC-triple quadrupole." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1002293 ! Bruker Daltonics SCION series [Term] id: MS:1002297 name: EVOQ Elite def: "Bruker Daltonics' EVOQ Elite: LC-triple quadrupole." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1002294 ! Bruker Daltonics EVOQ series [Term] id: MS:1002298 name: EVOQ Qube def: "Bruker Daltonics' EVOQ Qube: LC-triple quadrupole." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1002294 ! Bruker Daltonics EVOQ series [Term] id: MS:1002299 name: micrOTOF-Q III def: "Bruker Daltonics' micrOTOF-Q III: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1002300 name: amaZon Speed ETD def: "Bruker Daltonics' amaZon Speed ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR, GC-APCI, CaptiveSpray." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1001545 ! Bruker Daltonics amaZon series [Term] id: MS:1002301 name: amaZon Speed def: "Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1001545 ! Bruker Daltonics amaZon series [Term] @@ -15742,6 +15933,7 @@ is_a: MS:1001557 ! Shimadzu Corporation software id: MS:1002382 name: Shimadzu MALDI-7090 def: "Shimadzu MALDI-7090: MALDI-TOF-TOF." [PSI:PI] +is_a: MS:1003946 ! tandem time-of-flight instrument is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] @@ -15973,24 +16165,28 @@ relationship: has_value_type xsd:boolean ! The allowed value-type for this CV te id: MS:1002416 name: Orbitrap Fusion def: "Thermo Scientific Orbitrap Fusion." [PSI:PI] +is_a: MS:1003770 ! quadrupole ion trap orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002417 name: Orbitrap Fusion ETD def: "Thermo Scientific Orbitrap Fusion with ETD." [PSI:PI] +is_a: MS:1003770 ! quadrupole ion trap orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002418 name: TSQ Quantiva def: "Thermo Scientific TSQ Quantiva MS." [PSI:PI] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002419 name: TSQ Endura def: "Thermo Scientific TSQ Endura MS." [PSI:PI] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -16157,21 +16353,21 @@ is_a: MS:1002442 ! chromatograph file format id: MS:1002444 name: 6420 Triple Quadrupole LC/MS def: "The 6420 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1003762 ! triple quadrupole +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002445 name: 6460 Triple Quadrupole LC/MS def: "The 6460 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds Agilent Jet Stream (AJS) technology to increase sensitivity." [PSI:MS] -is_a: MS:1003762 ! triple quadrupole +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002446 name: 6490 Triple Quadrupole LC/MS def: "The 6490 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds the Agilent iFunnel technology to increase sensitivity." [PSI:MS] -is_a: MS:1003762 ! triple quadrupole +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] @@ -16416,7 +16612,7 @@ relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrom [Term] id: MS:1002480 name: regular expression for a digital object identifier (DOI) -def: "(10[.][0-9]\{4,\}(?:[.][0-9]+)*/(?:(?![\"&\'<>])[^ \t\\r\n\\v\\f])+)." [PSI:PI, http://dx.doi.org/] +def: "(10[.][0-9]\\{4,\\}(?:[.][0-9]+)*/(?:(?![\\\"&\\'<>])[^ \\t\\r\\n\\v\\f])+)." [PSI:PI, http://dx.doi.org/] is_a: MS:1002479 ! regular expression [Term] @@ -16574,7 +16770,7 @@ relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002505 name: regular expression for modification localization scoring -def: "(?[0-9]+):(?[01][.][0-9]+(?:[Ee][+\-]?[0-9]+)?):(?[0-9]+(?:[|][0-9]+)*):(?true|false)" [PSI:PI] +def: "(?[0-9]+):(?[01][.][0-9]+(?:[Ee][+\\-]?[0-9]+)?):(?[0-9]+(?:[|][0-9]+)*):(?true|false)" [PSI:PI] is_a: MS:1002479 ! regular expression [Term] @@ -16702,24 +16898,28 @@ relationship: has_value_type xsd:string ! The allowed value-type for this CV ter id: MS:1002523 name: Q Exactive HF def: "Thermo Scientific Q Exactive." [PSI:PI] +is_a: MS:1003769 ! quadrupole orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002524 name: PepFinder def: "Thermo Scientific PepFinder BioPharma analysis software." [PSI:PI] +is_a: MS:1003961 ! Thermo Scientific software is_a: MS:1001457 ! data processing software [Term] id: MS:1002525 name: TSQ 8000 Evo def: "Thermo Scientific TSQ 8000 Evo MS." [PSI:PI] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002526 name: Exactive Plus def: "Thermo Scientific Exactive Plus MS." [PSI:PI] +is_a: MS:1003953 ! orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -16767,6 +16967,7 @@ is_a: MS:1000767 ! native spectrum identifier format id: MS:1002533 name: TripleTOF 6600 def: "SCIEX TripleTOF 6600, a quadrupole - quadrupole - time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000121 ! SCIEX instrument model [Term] @@ -17072,114 +17273,133 @@ is_a: MS:1001040 ! intermediate analysis format id: MS:1002577 name: 2000 QTRAP def: "SCIEX 2000 QTRAP." [PSI:MS] +is_a: MS:1003765 ! triple quadrupole linear ion trap instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002578 name: 2500 QTRAP def: "SCIEX 2500 QTRAP." [PSI:MS] +is_a: MS:1003765 ! triple quadrupole linear ion trap instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002579 name: 3500 QTRAP def: "SCIEX 3500 QTRAP." [PSI:MS] +is_a: MS:1003765 ! triple quadrupole linear ion trap instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002580 name: QTRAP 4500 def: "SCIEX QTRAP 4500." [PSI:MS] +is_a: MS:1003765 ! triple quadrupole linear ion trap instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002581 name: QTRAP 6500 def: "SCIEX QTRAP 6500." [PSI:MS] +is_a: MS:1003765 ! triple quadrupole linear ion trap instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002582 name: QTRAP 6500+ def: "SCIEX QTRAP 6500+." [PSI:MS] +is_a: MS:1003765 ! triple quadrupole linear ion trap instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002583 name: TripleTOF 4600 def: "SCIEX TripleTOF 4600 time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002584 name: TripleTOF 5600+ def: "SCIEX TripleTOF 5600+ time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002585 name: API 100 def: "Applied Biosystems/MDS SCIEX API 100 MS." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002586 name: API 100LC def: "Applied Biosystems/MDS SCIEX API 100LC MS." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002587 name: API 165 def: "Applied Biosystems/MDS SCIEX API 165 MS." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002588 name: API 300 def: "Applied Biosystems/MDS SCIEX API 300 MS." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002589 name: API 350 def: "Applied Biosystems/MDS SCIEX API 350 MS." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002590 name: API 365 def: "Applied Biosystems/MDS SCIEX API 365 MS." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002591 name: Triple Quad 3500 def: "SCIEX Triple Quad 3500." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002592 name: Triple Quad 4500 def: "SCIEX Triple Quad 4500." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002593 name: Triple Quad 5500 def: "SCIEX Triple Quad 5500." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002594 name: Triple Quad 6500 def: "SCIEX Triple Quad 6500." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002595 name: Triple Quad 6500+ def: "SCIEX Triple Quad 6500+." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] @@ -17219,6 +17439,7 @@ id: MS:1002601 name: mzTab def: "Tabular result format for proteomics and metabolomics experiments." [PMID:24980485, http://www.psidev.info/mztab/] is_a: MS:1000914 ! tab delimited text format +is_a: MS:1002130 ! identification file format [Term] id: MS:1002602 @@ -17420,6 +17641,7 @@ relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV ter id: MS:1002634 name: Q Exactive Plus def: "Thermo Scientific Q Exactive Plus." [PSI:PI] +is_a: MS:1003769 ! quadrupole orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -17649,12 +17871,14 @@ is_a: MS:1002479 ! regular expression id: MS:1002666 name: impact II def: "Bruker Daltonics' impact II." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1002667 name: impact HD def: "Bruker Daltonics' impact HD." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] @@ -17701,6 +17925,7 @@ is_a: MS:1000752 ! TOPP software id: MS:1002674 name: X500R QTOF def: "SCIEX X500R QTOF, a quadrupole - quadrupole - time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000121 ! SCIEX instrument model [Term] @@ -17997,6 +18222,8 @@ is_a: MS:1001457 ! data processing software id: MS:1002719 name: Pegasus BT def: "LECO bench-top GC time-of-flight mass spectrometer." [PSI:PI] +is_a: MS:1003951 ! time-of-flight instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1001800 ! LECO instrument model [Term] @@ -18050,42 +18277,48 @@ id: MS:1002726 name: SYNAPT G2-Si def: "Waters Corporation SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI] is_a: MS:1000126 ! Waters instrument model -is_a: MS:1003767 ! quadrupole ion mobility time-of-flight mass spectrometer +is_a: MS:1003767 ! quadrupole ion mobility time-of-flight instrument [Term] id: MS:1002727 name: MALDI SYNAPT G2-Si def: "Waters Corporation MALDI SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI] +is_a: MS:1003767 ! quadrupole ion mobility time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1002728 name: Vion IMS QTof def: "Waters Corporation Vion IMS QTof orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI] +is_a: MS:1003767 ! quadrupole ion mobility time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1002729 name: Xevo G2-XS Tof def: "Waters Corporation Xevo G2 XS Tof orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1002730 name: Xevo TQ-XS def: "Waters Corporation Xevo TQ-XS triple quadrupole mass spectrometer." [PSI:PI] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1002731 name: Xevo TQ-S micro def: "Waters Corporation Xevo TQ-S micro triple quadrupole mass spectrometer." [PSI:PI] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1002732 name: Orbitrap Fusion Lumos def: "Thermo Scientific Orbitrap Fusion Lumos mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:PI] +is_a: MS:1003770 ! quadrupole ion trap orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -18407,70 +18640,70 @@ is_a: MS:1002778 ! DiLeu reagent id: MS:1002783 name: 6550 iFunnel Q-TOF LC/MS def: "The 6550 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002784 name: 6550A iFunnel Q-TOF LC/MS def: "The 6550A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002785 name: 6520B Q-TOF LC/MS def: "The 6520B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002786 name: 6530A Q-TOF LC/MS def: "The 6530A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002787 name: 6530B Q-TOF LC/MS def: "The 6530B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002788 name: 6538 Q-TOF LC/MS def: "The 6538 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002789 name: 6540 Q-TOF LC/MS def: "The 6540 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002790 name: 6542 Q-TOF LC/MS def: "The 6542 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002791 name: 6545 Q-TOF LC/MS def: "The 6545 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002792 name: 6560 Q-TOF LC/MS def: "The 6560 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1003767 ! quadrupole ion mobility time-of-flight +is_a: MS:1003767 ! quadrupole ion mobility time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] @@ -18478,91 +18711,93 @@ id: MS:1002793 name: 6570 Q-TOF LC/MS def: "The 6570 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] comment: Web search verification (2026-01-16) found no evidence that this Agilent model exists. -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002794 name: 6120B Quadrupole LC/MS def: "The 6120B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers." [PSI:MS] -is_a: MS:1000081 ! quadrupole +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002795 name: 6150 Quadrupole LC/MS def: "The 6150 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers." [PSI:MS] -is_a: MS:1000081 ! quadrupole +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002796 name: 6224 Time-of-Flight LC/MS def: "The 6224 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1000084 ! time-of-flight +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002797 name: 6230A Time-of-Flight LC/MS def: "The 6230A Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1000084 ! time-of-flight +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002798 name: 6230B Time-of-Flight LC/MS def: "The 6230B Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1000084 ! time-of-flight +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002799 name: 6430 Triple Quadrupole LC/MS def: "The 6430 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1003762 ! triple quadrupole +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002800 name: 6495A Triple Quadrupole LC/MS def: "The 6495A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1003762 ! triple quadrupole +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002801 name: 6495B Triple Quadrupole LC/MS def: "The 6495B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1003762 ! triple quadrupole +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002802 name: 7000A Triple Quadrupole GC/MS def: "The 7000A Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1003762 ! triple quadrupole -is_a: MS:1003914 ! Agilent gas chromatography mass spectrometry system model +is_a: MS:1003762 ! triple quadrupole instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002803 name: 7000B Triple Quadrupole GC/MS def: "The 7000B Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1003762 ! triple quadrupole -is_a: MS:1003914 ! Agilent gas chromatography mass spectrometry system model +is_a: MS:1003762 ! triple quadrupole instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002804 name: 7800 Quadrupole ICP-MS def: "The 7800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002805 name: 8800 Triple Quadrupole ICP-MS def: "The 8800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] @@ -18607,7 +18842,7 @@ relationship: has_value_type xsd:string ! The allowed value-type for this CV ter [Term] id: MS:1002812 name: Regular expression for adduct ion formula -def: "(\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-])." [PSI:PI] +def: "(\\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\\][:digit:]{0,1}[+-])." [PSI:PI] is_a: MS:1002479 ! regular expression [Term] @@ -18615,7 +18850,7 @@ id: MS:1002813 name: adduct ion formula def: "Adduct formation formula of the form M+X or M-X, as constrained by the provided regular expression." [PSI:MS] is_a: MS:1002809 ! adduct ion attribute -relationship: has_regexp MS:1002812 ! (\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-]) +relationship: has_regexp MS:1002812 ! (\\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\\][:digit:]{0,1}[+-]) relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] @@ -18755,7 +18990,7 @@ relationship: has_value_type xsd:double ! The allowed value-type for this CV ter id: MS:1002833 name: alternating polarity acquisition def: "The scans of a run are acquired with polarities switching in a strictly alternating sequence (e.g., positive, negative, positive, negative), such that consecutive scans or scan cycles differ in polarity." [PSI:PI] -is_a: MS:1000524 ! data file content +is_a: MS:1003776 ! acquisition polarity [Term] id: MS:1002834 @@ -18768,6 +19003,7 @@ relationship: has_value_type xsd:float ! The allowed value-type for this CV term id: MS:1002835 name: LTQ Orbitrap Classic def: "Thermo Fisher Scientific LTQ Orbitrap Classic." [PSI:MS] +is_a: MS:1003768 ! ion trap orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -19027,24 +19263,28 @@ relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV ter id: MS:1002874 name: TSQ Altis def: "Thermo Scientific TSQ Altis Triple Quadrupole MS." [PSI:PI] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002875 name: TSQ Quantis def: "Thermo Scientific TSQ Quantis Triple Quadrupole MS." [PSI:PI] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002876 name: TSQ 9000 def: "Thermo Scientific TSQ 9000 Triple Quadrupole MS." [PSI:PI] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002877 name: Q Exactive HF-X def: "Thermo Scientific Q Exactive HF-X Hybrid Quadrupole Orbitrap MS." [PSI:PI] +is_a: MS:1003769 ! quadrupole orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -19063,6 +19303,7 @@ is_a: MS:1002878 ! small molecule analysis software id: MS:1002880 name: Compound Discoverer def: "Metabolomics analysis software from Thermo Fisher Scientific." [PSI:PI] +is_a: MS:1003961 ! Thermo Scientific software is_a: MS:1002878 ! small molecule analysis software [Term] @@ -19824,18 +20065,21 @@ is_a: MS:1002333 ! conversion software id: MS:1002992 name: Orbitrap Exploris GC-MS def: "Thermo Scientific Orbitrap Exploris GC-MS." [PSI:PI] +is_a: MS:1003769 ! quadrupole orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002993 name: Q Exactive Focus def: "Q Exactive Focus Hybrid Quadrupole-Orbitrap Mass Spectrometer." [PSI:PI] +is_a: MS:1003769 ! quadrupole orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002994 name: Orbitrap Excedion Pro def: "Thermo Scientific Orbitrap Excedion Pro." [PSI:MS] +is_a: MS:1003769 ! quadrupole orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -19864,48 +20108,56 @@ relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for id: MS:1002998 name: LCMS-9030 def: "Shimadzu Scientific Instruments LCMS-9030 Q-TOF MS." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1002999 name: LCMS-8060 def: "Shimadzu Scientific Instruments LCMS-8060 MS." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003000 name: LCMS-8050 def: "Shimadzu Scientific Instruments LCMS-8050 MS." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003001 name: LCMS-8045 def: "Shimadzu Scientific Instruments LCMS-8045 MS." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003002 name: LCMS-8040 def: "Shimadzu Scientific Instruments LCMS-8040 MS." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003003 name: LCMS-2020 def: "Shimadzu Scientific Instruments LCMS-2020." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003004 name: maXis II def: "Bruker Daltonics' maXis II." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1001547 ! Bruker Daltonics maXis series [Term] id: MS:1003005 name: timsTOF Pro def: "Bruker Daltonics' timsTOF Pro." [PSI:MS] +is_a: MS:1003970 ! ion mobility quadrupole time-of-flight instrument is_a: MS:1003123 ! Bruker Daltonics timsTOF series [Term] @@ -20066,12 +20318,14 @@ is_a: MS:1003025 ! named element id: MS:1003028 name: Orbitrap Exploris 480 def: "Thermo Scientific Orbitrap Exploris 480 Quadrupole Orbitrap MS." [PSI:PI] +is_a: MS:1003769 ! quadrupole orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003029 name: Orbitrap Eclipse def: "Thermo Scientific Orbitrap Eclipse mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:PI] +is_a: MS:1003770 ! quadrupole ion trap orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -20498,18 +20752,21 @@ relationship: has_regexp MS:1001335 ! (?=K) id: MS:1003094 name: Orbitrap Exploris 240 def: "Thermo Scientific Orbitrap Exploris 240 Quadrupole Orbitrap MS." [PSI:PI] +is_a: MS:1003769 ! quadrupole orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003095 name: Orbitrap Exploris 120 def: "Thermo Scientific Orbitrap Exploris 120 Quadrupole Orbitrap MS." [PSI:PI] +is_a: MS:1003769 ! quadrupole orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003096 name: Orbitrap Velos Pro def: "Thermo Scientific LTQ Orbitrap Velos Pro, often just referred to as the Orbitrap Velos Pro." [PSI:MS] +is_a: MS:1003768 ! ion trap orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model synonym: "LTQ Orbitrap Velos Pro" EXACT [] @@ -20618,6 +20875,7 @@ is_a: MS:1001139 ! quantitation software name id: MS:1003112 name: Orbitrap ID-X def: "Thermo Scientific Orbitrap ID-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:MS] +is_a: MS:1003770 ! quadrupole ion trap orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -20687,6 +20945,7 @@ relationship: has_value_type xsd:double ! The allowed value-type for this CV ter id: MS:1003122 name: rapifleX def: "Bruker Daltonics' rapiflex: MALDI TOF/TOF." [PSI:MS] +is_a: MS:1003946 ! tandem time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] @@ -20699,6 +20958,7 @@ is_a: MS:1000122 ! Bruker Daltonics instrument model id: MS:1003124 name: timsTOF fleX def: "Bruker Daltonics' timsTOF fleX" [PSI:MS] +is_a: MS:1003970 ! ion mobility quadrupole time-of-flight instrument is_a: MS:1003123 ! Bruker Daltonics timsTOF series [Term] @@ -20828,7 +21088,9 @@ relationship: has_value_type xsd:boolean ! The allowed value-type for this CV te id: MS:1003141 name: ProSight def: "ProSight: Database search engine for top-down proteomics." [PSI:MS] +is_a: MS:1003961 ! Thermo Scientific software is_a: MS:1001456 ! analysis software +synonym: "ProSightPD" EXACT [] [Term] id: MS:1003142 @@ -20849,6 +21111,7 @@ relationship: has_units UO:0000221 ! dalton id: MS:1003144 name: Triple Quad 7500 def: "SCIEX Triple Quad 7500." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] @@ -20902,6 +21165,7 @@ relationship: has_value_type xsd:string ! The allowed value-type for this CV ter id: MS:1003152 name: GCMS-QP2010SE def: "Shimadzu Scientific Instruments GCMS-QP2010SE." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] @@ -21128,18 +21392,21 @@ is_a: MS:1003181 ! combined dissociation method id: MS:1003183 name: Synapt XS def: "Waters oa-ToF based Synapt XS." [PSI:PI] +is_a: MS:1003767 ! quadrupole ion mobility time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1003184 name: SELECT SERIES Cyclic IMS def: "Waters oa-ToF based SELECT SERIES Cyclic IMS." [PSI:PI] +is_a: MS:1003767 ! quadrupole ion mobility time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1003185 name: SELECT SERIES MRT def: "Waters oa-ToF based SELECT SERIES MRT." [PSI:PI] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] @@ -21279,7 +21546,7 @@ relationship: has_value_type xsd:string ! The allowed value-type for this CV ter [Term] id: MS:1003206 name: library creation log -def: "String of logging information generated when the library was constructed from its constituent files. Multiple lines should be separated with escaped \n" [PSI:PI] +def: "String of logging information generated when the library was constructed from its constituent files. Multiple lines should be separated with escaped \\n" [PSI:PI] is_a: MS:1003201 ! library provenance attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term @@ -21449,18 +21716,21 @@ is_a: MS:1003213 ! mass spectrometry acquisition method id: MS:1003229 name: timsTOF def: "Bruker Daltonics' timsTOF." [PSI:MS] +is_a: MS:1003970 ! ion mobility quadrupole time-of-flight instrument is_a: MS:1003123 ! Bruker Daltonics timsTOF series [Term] id: MS:1003230 name: timsTOF Pro 2 def: "Bruker Daltonics' timsTOF Pro 2." [PSI:MS] +is_a: MS:1003970 ! ion mobility quadrupole time-of-flight instrument is_a: MS:1003123 ! Bruker Daltonics timsTOF series [Term] id: MS:1003231 name: timsTOF SCP def: "Bruker Daltonics' timsTOF SCP." [PSI:MS] +is_a: MS:1003970 ! ion mobility quadrupole time-of-flight instrument is_a: MS:1003123 ! Bruker Daltonics timsTOF series [Term] @@ -21539,6 +21809,7 @@ relationship: has_value_type xsd:string ! The allowed value-type for this CV ter id: MS:1003245 name: Q Exactive UHMR def: "Thermo Scientific Q Exactive UHMR (Ultra High Mass Range) Hybrid Quadrupole Orbitrap MS." [PSI:PI] +is_a: MS:1003769 ! quadrupole orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -21593,6 +21864,7 @@ relationship: has_units UO:0000189 ! count unit id: MS:1003252 name: Xevo G2-XS QTof def: "Waters Corporation Xevo G2-XS QTof quadrupole time-of-flight mass spectrometer." [PSI:PI] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] @@ -21864,12 +22136,14 @@ relationship: has_regexp MS:1002505 ! regular expression for modification locali id: MS:1003292 name: TSQ Altis Plus def: "Thermo Scientific TSQ Altis Plus Triple Quadrupole MS." [PSI:PI] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003293 name: ZenoTOF 7600 def: "SCIEX ZenoTOF 7600." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000121 ! SCIEX instrument model [Term] @@ -22302,6 +22576,7 @@ is_a: MS:1003350 ! mass spectrometry proteomics id: MS:1003356 name: Orbitrap Ascend def: "Thermo Scientific Orbitrap Ascend mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:PI] +is_a: MS:1003770 ! quadrupole ion trap orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -22453,6 +22728,7 @@ is_a: MS:1001457 ! data processing software id: MS:1003378 name: Orbitrap Astral def: "Thermo Scientific Orbitrap Astral mass spectrometer contains three mass analyzers: a quadrupole analyzer, an Orbitrap analyzer, and the Astral analyzer." [PSI:MS] +is_a: MS:1003771 ! quadrupole orbitrap astral instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -22466,12 +22742,14 @@ is_a: MS:1000084 ! time-of-flight id: MS:1003380 name: Xevo G3 QTof def: "Waters Corporation Xevo G3 QTof quadrupole time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1003381 name: ACQUITY RDa Detector def: "Waters Corporation RDa time-of-flight mass detector." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] @@ -22487,6 +22765,7 @@ is_a: MS:1001457 ! data processing software id: MS:1003383 name: timsTOF Ultra def: "Bruker Daltonics' timsTOF Ultra." [PSI:MS] +is_a: MS:1003970 ! ion mobility quadrupole time-of-flight instrument is_a: MS:1003123 ! Bruker Daltonics timsTOF series [Term] @@ -22541,7 +22820,7 @@ relationship: has_value_type xsd:string ! The allowed value-type for this CV ter [Term] id: MS:1003391 name: crosslinker cleavage regular expression -def: "^(?[A-Za-z]):(?[+-]?[0-9]+(\.[0-9]+)?([eE][+-]?[0-9]+(\.[0-9]+)?)?):(?[A-Za-z]+)$" [PSI:PI] +def: "^(?[A-Za-z]):(?[+-]?[0-9]+(\\.[0-9]+)?([eE][+-]?[0-9]+(\\.[0-9]+)?)?):(?[A-Za-z]+)$" [PSI:PI] is_a: MS:1002479 ! regular expression [Term] @@ -22572,6 +22851,7 @@ relationship: has_value_type xsd:float ! The allowed value-type for this CV term id: MS:1003395 name: Q Exactive GC Orbitrap def: "Q Exactive GC Orbitrap GC-MS/MS hybrid quadrupole Orbitrap mass spectrometer." [PSI:MS] +is_a: MS:1003769 ! quadrupole orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -22584,6 +22864,7 @@ is_a: MS:1003731 ! Agilent gas chromatography system model id: MS:1003397 name: timsTOF fleX MALDI-2 def: "Bruker Daltonics' timsTOF fleX MALDI-2." [PSI:MS] +is_a: MS:1003970 ! ion mobility quadrupole time-of-flight instrument is_a: MS:1003123 ! Bruker Daltonics timsTOF series [Term] @@ -22628,6 +22909,7 @@ relationship: has_value_type xsd:string ! The allowed value-type for this CV ter id: MS:1003404 name: timsTOF HT def: "Bruker Daltonics' timsTOF HT." [PSI:MS] +is_a: MS:1003970 ! ion mobility quadrupole time-of-flight instrument is_a: MS:1003123 ! Bruker Daltonics timsTOF series [Term] @@ -22660,6 +22942,7 @@ relationship: has_value_type xsd:double ! The allowed value-type for this CV ter id: MS:1003409 name: Stellar def: "Thermo Scientific Stellar mass spectrometer contains a quadrupole mass filter, a collision cell, and a quadrupole linear ion trap mass analyzer." [PSI:MS] +is_a: MS:1003972 ! quadrupole ion trap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -22674,12 +22957,14 @@ relationship: has_value_type xsd:float ! The allowed value-type for this CV term id: MS:1003411 name: Orbitrap IQ-X def: "Thermo Scientific Orbitrap IQ-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:MS] +is_a: MS:1003770 ! quadrupole ion trap orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003412 name: timsTOF Ultra 2 def: "Bruker Daltonics timsTOF Ultra 2." [PSI:MS] +is_a: MS:1003970 ! ion mobility quadrupole time-of-flight instrument is_a: MS:1003123 ! Bruker Daltonics timsTOF series [Term] @@ -22766,6 +23051,7 @@ relationship: has_value_type xsd:int ! The allowed value-type for this CV term id: MS:1003423 name: Orbitrap Exploris GC 240 def: "Orbitrap Exploris GC 240 Mass Spectrometer." [PSI:MS] +is_a: MS:1003769 ! quadrupole orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -22898,24 +23184,28 @@ is_a: MS:1003439 ! ion mobility frame representation id: MS:1003442 name: Orbitrap Astral Zoom def: "Thermo Scientific Orbitrap Astral Zoom mass spectrometer contains three mass analyzers: a quadrupole analyzer, an Orbitrap analyzer, and an Astral analyzer." [PSI:PI] +is_a: MS:1003771 ! quadrupole orbitrap astral instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003443 name: ZenoTOF 8600 def: "SCIEX ZenoTOF 8600 system." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1003444 name: ZenoTOF 7600+ def: "SCIEX ZenoTOF 7600+ system." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1003445 name: SCIEX 7500+ def: "SCIEX 7500+ system." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] @@ -22944,6 +23234,7 @@ is_a: MS:1000560 ! mass spectrometer file format id: MS:1003449 name: ISQ 7000 def: "Thermo Scientific ISQ 7000 Single Quadrupole GC-MS System." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -22994,451 +23285,511 @@ is_a: MS:1000031 ! instrument model id: MS:1003456 name: TripleTOF 6600+ def: "SCIEX TripleTOF 6600+ triple quadrupole - time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1003457 name: Triple Quad 5500+ def: "SCIEX Triple Quad 5500+ triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1003458 name: Triple Quad 5500+ QTRAP Ready def: "SCIEX Triple Quad 5500+ QTRAP Ready quadrupole - linear ion trap mass spectrometer." [PSI:MS] +is_a: MS:1003765 ! triple quadrupole linear ion trap instrument is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1003459 name: APEX-Qe def: "Bruker APEX-Qe FT-ICR-MS mass spectrometer." [PSI:MS] +is_a: MS:1003766 ! quadrupole fourier transform ion cyclotron resonance instrument is_a: MS:1001556 ! Bruker Daltonics apex series [Term] id: MS:1003460 name: autoflex speed TOF/TOF def: "Bruker autoflex speed TOF/TOF MALDI TOF/TOF mass spectrometer." [PSI:MS] +is_a: MS:1003946 ! tandem time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1003461 name: esquire 3000 def: "Bruker esquire 3000 ion trap mass spectrometer." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1001533 ! Bruker Daltonics esquire series [Term] id: MS:1003462 name: maXis impact def: "Bruker maXis impact quadrupole time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1001547 ! Bruker Daltonics maXis series [Term] id: MS:1003463 name: maXis impact HD def: "Bruker maXis impact HD quadrupole time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1001547 ! Bruker Daltonics maXis series [Term] id: MS:1003464 name: maXis 3G def: "Bruker maXis 3G quadrupole time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1001547 ! Bruker Daltonics maXis series [Term] id: MS:1003465 name: solariX XR def: "Bruker solariX XR FT-ICR-MS mass spectrometer." [PSI:MS] +is_a: MS:1003766 ! quadrupole fourier transform ion cyclotron resonance instrument is_a: MS:1001548 ! Bruker Daltonics solarix series [Term] id: MS:1003466 name: amaZon SL def: "Bruker amaZon SL ion trap mass spectrometer." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1001545 ! Bruker Daltonics amaZon series [Term] id: MS:1003467 name: EVOQ DART-TQ+ def: "Bruker EVOQ DART-TQ+ triple quadrupole mass spectrometer with Direct Analysis in Real Time (DART) ion source." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1002294 ! Bruker Daltonics EVOQ series [Term] id: MS:1003468 name: EVOQ LC-TQ def: "Bruker EVOQ LC-TQ triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1002294 ! Bruker Daltonics EVOQ series [Term] id: MS:1003469 name: EVOQ GC-TQ def: "Bruker EVOQ GC-TQ gas chromatograph - triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1002294 ! Bruker Daltonics EVOQ series [Term] id: MS:1003470 name: Toxtyper def: "Bruker Toxtyper ion trap mass spectrometer." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1003471 name: impact II VIP def: "Bruker impact II VIP quadrupole time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1003472 name: ecTOF def: "Bruker ecTOF gas chromatograph - time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1003473 name: autoflex maX def: "Bruker autoflex maX MALDI TOF mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1003474 name: rapifleX MALDI PharmaPulse def: "Bruker rapifleX MALDI PharmaPulse MALDI TOF mass spectrometer with ultra-high-throughput screening (uHTS) capability." [PSI:MS] +is_a: MS:1003946 ! tandem time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1003475 name: smartfleX def: "Bruker smartfleX MALDI TOF mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1003476 name: neofleX def: "Bruker neofleX MALDI TOF/TOF mass spectrometer." [PSI:MS] +is_a: MS:1003946 ! tandem time-of-flight instrument is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1003477 name: MALDI Biotyper def: "Bruker MALDI Biotyper MALDI TOF mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1003478 name: scimaX def: "Bruker scimaX FT-ICR-MS mass spectrometer." [PSI:MS] +is_a: MS:1003766 ! quadrupole fourier transform ion cyclotron resonance instrument is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1003479 name: timsMetabo def: "Bruker timsMetabo TIMS-Q-TOF mass spectrometer." [PSI:MS] +is_a: MS:1003970 ! ion mobility quadrupole time-of-flight instrument is_a: MS:1003123 ! Bruker Daltonics timsTOF series [Term] id: MS:1003480 name: timsUltra AIP def: "Bruker timsUltra AIP TIMS-Q-TOF mass spectrometer." [PSI:MS] +is_a: MS:1003970 ! ion mobility quadrupole time-of-flight instrument is_a: MS:1003123 ! Bruker Daltonics timsTOF series [Term] id: MS:1003481 name: timsOmni def: "Bruker timsOmni TIMS-Q-TOF mass spectrometer." [PSI:MS] +is_a: MS:1003970 ! ion mobility quadrupole time-of-flight instrument is_a: MS:1003123 ! Bruker Daltonics timsTOF series [Term] id: MS:1003482 name: timsTOF MALDI PharmaPulse def: "Bruker timsTOF MALDI PharmaPulse MALDI TIMS-Q-TOF mass spectrometer with ultra-high-throughput screening (uHTS) capability." [PSI:MS] +is_a: MS:1003970 ! ion mobility quadrupole time-of-flight instrument is_a: MS:1003123 ! Bruker Daltonics timsTOF series [Term] id: MS:1003483 name: 4000 GC/MS def: "Varian 4000 GC/MS gas chromatograph - ion trap mass spectrometer." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000489 ! Varian instrument model [Term] id: MS:1003484 name: 210-MS GC/MS Ion Trap def: "Varian 210-MS GC/MS Ion Trap gas chromatograph - ion trap mass spectrometer." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000489 ! Varian instrument model [Term] id: MS:1003485 name: LCMS-8030 def: "Shimadzu LCMS-8030 triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003486 name: LCMS-8030 Plus def: "Shimadzu LCMS-8030 Plus triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003487 name: GCMS-QP2010 Plus def: "Shimadzu GCMS-QP2010 Plus gas chromatograph - quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003488 name: LCMS-8060NX def: "Shimadzu LCMS-8060NX triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003489 name: GCMS-TQ8050NX def: "Shimadzu GCMS-TQ8050NX gas chromatograph - triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model -is_a: MS:1003735 ! Shimadzu gas chromatography mass spectrometry system model +is_a: MS:1003733 ! gas chromatography mass spectrometry system [Term] id: MS:1003490 name: GCMS-TQ8040NX def: "Shimadzu GCMS-TQ8040NX gas chromatograph - triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003491 name: GCMS-TQ8040 def: "Shimadzu GCMS-TQ8040 gas chromatograph - triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003492 name: GCMS-QP5000 def: "Shimadzu GCMS-QP5000 gas chromatograph - quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003493 name: GCMS-QP2020 def: "Shimadzu GCMS-QP2020 gas chromatograph - quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003494 name: GCMS-QP2010 Ultra def: "Shimadzu GCMS-QP2010 Ultra gas chromatograph - quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003495 name: Velos Pro def: "Thermo Fisher Scientific Velos Pro ion trap - mass spectrometer." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003496 name: MALDI LTQ Orbitrap XL def: "Thermo Fisher Scientific MALDI LTQ Orbitrap XL linear ion trap - orbitrap mass spectrometer." [PSI:MS] +is_a: MS:1003768 ! ion trap orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003497 name: MALDI LTQ Orbitrap Discovery def: "Thermo Fisher Scientific MALDI LTQ Orbitrap Discovery linear ion trap - orbitrap mass spectrometer." [PSI:MS] +is_a: MS:1003768 ! ion trap orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003498 name: TSQ Quantum Access MAX def: "Thermo Fisher Scientific TSQ Quantum Access MAX triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003499 name: LTQ Orbitrap Velos/ETD def: "Thermo Fisher Scientific LTQ Orbitrap Velos/ETD linear ion trap - orbitrap mass spectrometer." [PSI:MS] +is_a: MS:1003768 ! ion trap orbitrap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003500 name: ISQ LT def: "Thermo Fisher Scientific ISQ LT gas chromatograph - quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003501 name: ITQ def: "Thermo Fisher Scientific ITQ ion trap mass spectrometer." [PSI:MS] +is_a: MS:1003952 ! ion trap instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003502 name: TSQ Quantum XLS def: "Thermo Fisher Scientific TSQ Quantum XLS gas chromatograph - triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003503 name: TSQ 8000 def: "Thermo Fisher Scientific TSQ 8000 gas chromatograph - triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003504 name: DeltaPlus IRMS def: "Thermo Fisher Scientific DeltaPlus IRMS isotope ratio mass spectrometer." [PSI:MS] +is_a: MS:1003949 ! magnetic sector instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003505 name: ACQUITY QDa def: "Waters ACQUITY QDa quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1003506 name: LCT Premier def: "Waters LCT Premier time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1003507 name: Quattro Premier XE def: "Waters Quattro Premier XE triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1003508 name: Synapt G1 HDMS def: "Waters Synapt G1 HDMS quadrupole - ion mobility - time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003767 ! quadrupole ion mobility time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1003509 name: Synapt G2-Si HDMS def: "Waters Synapt G2-Si HDMS quadrupole - ion mobility - time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003767 ! quadrupole ion mobility time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1003510 name: Synapt G1 def: "Waters Synapt G1 quadrupole - ion mobility - time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1003511 name: Synapt G2 XS QTOF def: "Waters Synapt G2 XS QTOF quadrupole - ion mobility - time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003767 ! quadrupole ion mobility time-of-flight instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1003512 name: Xevo TQ Absolute def: "Waters Xevo TQ Absolute triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1003513 name: Xevo TQ Absolute XR def: "Waters Xevo TQ Absolute XR triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1003514 name: 5973 MSD def: "Agilent 5973 MSD gas chromatograph - quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1000081 ! quadrupole -is_a: MS:1003914 ! Agilent gas chromatography mass spectrometry system model +is_a: MS:1003950 ! quadrupole instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003515 name: 5973N MSD def: "Agilent 5973N MSD gas chromatograph - quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1000081 ! quadrupole -is_a: MS:1003914 ! Agilent gas chromatography mass spectrometry system model +is_a: MS:1003950 ! quadrupole instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003516 name: 5975 MSD def: "Agilent 5975 MSD gas chromatograph - quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1000081 ! quadrupole -is_a: MS:1003914 ! Agilent gas chromatography mass spectrometry system model +is_a: MS:1003950 ! quadrupole instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003517 name: 5975B MSD def: "Agilent 5975B MSD gas chromatograph - quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1000081 ! quadrupole -is_a: MS:1003914 ! Agilent gas chromatography mass spectrometry system model +is_a: MS:1003950 ! quadrupole instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003518 name: 5975C inert XL MSD def: "Agilent 5975C inert XL MSD gas chromatograph - quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1000081 ! quadrupole -is_a: MS:1003914 ! Agilent gas chromatography mass spectrometry system model +is_a: MS:1003950 ! quadrupole instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003519 name: 5975C MSD def: "Agilent 5975C MSD gas chromatograph - quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1000081 ! quadrupole -is_a: MS:1003914 ! Agilent gas chromatography mass spectrometry system model +is_a: MS:1003950 ! quadrupole instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003520 name: 5975T MSD def: "Agilent 5975T MSD gas chromatograph - quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1000081 ! quadrupole -is_a: MS:1003914 ! Agilent gas chromatography mass spectrometry system model +is_a: MS:1003950 ! quadrupole instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003521 name: 5977 MSD def: "Agilent 5977 MSD gas chromatograph - quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1000081 ! quadrupole -is_a: MS:1003914 ! Agilent gas chromatography mass spectrometry system model +is_a: MS:1003950 ! quadrupole instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003522 name: 5977A MSD def: "Agilent 5977A MSD gas chromatograph - quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1000081 ! quadrupole -is_a: MS:1003914 ! Agilent gas chromatography mass spectrometry system model +is_a: MS:1003950 ! quadrupole instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003523 name: 5977B MSD def: "Agilent 5977B MSD gas chromatograph - quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1000081 ! quadrupole -is_a: MS:1003914 ! Agilent gas chromatography mass spectrometry system model +is_a: MS:1003950 ! quadrupole instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003524 name: 5977C MSD def: "Agilent 5977C MSD gas chromatograph - quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1000081 ! quadrupole -is_a: MS:1003914 ! Agilent gas chromatography mass spectrometry system model +is_a: MS:1003950 ! quadrupole instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003525 name: 6230 Time-of-Flight LC/MS def: "Agilent 6230 Time-of-Flight LC/MS time-of-flight mass spectrometer." [PSI:MS] -is_a: MS:1000084 ! time-of-flight +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003526 name: 6410A Triple Quadrupole LC/MS def: "Agilent 6410A Triple Quadrupole LC/MS triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1003762 ! triple quadrupole +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] @@ -23446,7 +23797,7 @@ id: MS:1003527 name: 6445 Q-TOF LC/MS def: "Agilent 6445 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer." [PSI:MS] comment: Web search verification (2026-01-16) found no evidence that this Agilent model exists. -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] @@ -23454,42 +23805,42 @@ id: MS:1003528 name: 6456 Q-TOF LC/MS def: "Agilent 6456 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer." [PSI:MS] comment: Web search verification (2026-01-16) found no evidence that this Agilent model exists. -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003529 name: 6470 Triple Quadrupole LC/MS def: "Agilent 6470 Triple Quadrupole LC/MS triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1003762 ! triple quadrupole +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003530 name: 6490A Triple Quadrupole LC/MS def: "Agilent 6490A Triple Quadrupole LC/MS triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1003762 ! triple quadrupole +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003531 name: 6495 Triple Quadrupole LC/MS def: "Agilent 6495 Triple Quadrupole LC/MS triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1003762 ! triple quadrupole +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003532 name: 6520 Q-TOF LC/MS def: "Agilent 6520 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer." [PSI:MS] -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003533 name: 6530 Q-TOF LC/MS def: "Agilent 6530 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer." [PSI:MS] -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] @@ -23497,21 +23848,21 @@ id: MS:1003534 name: 6543 Q-TOF LC/MS def: "Agilent 6543 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer." [PSI:MS] comment: Web search verification (2026-01-16) found no evidence that this Agilent model exists. -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003535 name: 6545XT Q-TOF LC/MS def: "Agilent 6545XT Q-TOF LC/MS quadrupole time-of-flight mass spectrometer." [PSI:MS] -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003536 name: 6546 Q-TOF LC/MS def: "Agilent 6546 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer." [PSI:MS] -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] @@ -23519,250 +23870,284 @@ id: MS:1003537 name: 6600 Q-TOF LC/MS def: "Agilent 6600 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer." [PSI:MS] comment: Web search verification (2026-01-16) found no evidence that this Agilent model exists. -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003538 name: 7000C Triple Quadrupole GC/MS def: "Agilent 7000C Triple Quadrupole GC/MS gas chromatograph - triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1003762 ! triple quadrupole -is_a: MS:1003914 ! Agilent gas chromatography mass spectrometry system model +is_a: MS:1003762 ! triple quadrupole instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003539 name: 7000D Triple Quadrupole GC/MS def: "Agilent 7000D Triple Quadrupole GC/MS gas chromatograph - triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1003762 ! triple quadrupole -is_a: MS:1003914 ! Agilent gas chromatography mass spectrometry system model +is_a: MS:1003762 ! triple quadrupole instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003540 name: 7010 Triple Quadrupole GC/MS def: "Agilent 7010 Triple Quadrupole GC/MS gas chromatograph - triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1003762 ! triple quadrupole -is_a: MS:1003914 ! Agilent gas chromatography mass spectrometry system model +is_a: MS:1003762 ! triple quadrupole instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003541 name: 7010B Triple Quadrupole GC/MS def: "Agilent 7010B Triple Quadrupole GC/MS gas chromatograph - triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1003762 ! triple quadrupole -is_a: MS:1003914 ! Agilent gas chromatography mass spectrometry system model +is_a: MS:1003762 ! triple quadrupole instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003542 name: 7200 Q-TOF GC/MS def: "Agilent 7200 Q-TOF GC/MS gas chromatograph - quadrupole time-of-flight mass spectrometer." [PSI:MS] -is_a: MS:1003763 ! quadrupole time-of-flight -is_a: MS:1003914 ! Agilent gas chromatography mass spectrometry system model +is_a: MS:1003763 ! quadrupole time-of-flight instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003543 name: 7250 Q-TOF GC/MS def: "Agilent 7250 Q-TOF GC/MS gas chromatograph - quadrupole time-of-flight mass spectrometer." [PSI:MS] -is_a: MS:1003763 ! quadrupole time-of-flight -is_a: MS:1003914 ! Agilent gas chromatography mass spectrometry system model +is_a: MS:1003763 ! quadrupole time-of-flight instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003544 name: CE-TOFMS def: "Agilent CE-TOFMS capillary electrophoresis - time-of-flight mass spectrometer." [PSI:MS] -is_a: MS:1000084 ! time-of-flight +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003545 name: G3250AA Time-of-Flight LC/MS def: "Agilent G3250AA Time-of-Flight LC/MS time-of-flight mass spectrometer." [PSI:MS] -is_a: MS:1000084 ! time-of-flight +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003546 name: Revident Q-TOF LC/MS def: "Agilent Revident Q-TOF LC/MS quadrupole time-of-flight mass spectrometer." [PSI:MS] -is_a: MS:1003763 ! quadrupole time-of-flight +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003547 name: Pegasus BT 4D def: "LECO Pegasus BT 4D GCxGC - time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1001800 ! LECO instrument model [Term] id: MS:1003548 name: Pegasus HT def: "LECO Pegasus HT gas chromatograph - time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1001800 ! LECO instrument model [Term] id: MS:1003549 name: Pegasus IV def: "LECO Pegasus IV time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1001800 ! LECO instrument model [Term] id: MS:1003550 name: PTR-TOF 8000 def: "Ionicon Analytik PTR-TOF 8000 proton-transfer-reaction - time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1003452 ! Ionicon Analytik instrument model [Term] id: MS:1003551 name: AccuTOF GCv def: "JEOL AccuTOF GCv gas chromatograph - time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1003453 ! JEOL instrument model [Term] id: MS:1003552 name: TOF.SIMS 5 def: "IONTOF TOF.SIMS 5 time-of-flight secondary ion mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1003454 ! IONTOF instrument model [Term] id: MS:1003553 name: TurboMass GC/MS def: "PerkinElmer TurboMass GC/MS gas chromatograph - quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument +is_a: MS:1003733 ! gas chromatography mass spectrometry system is_a: MS:1003455 ! PerkinElmer instrument model [Term] id: MS:1003554 name: ThermoQuest Voyager def: "Thermo Finnigan ThermoQuest Voyager gas chromatograph - quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1003555 name: AXIMA-LNR def: "Shimadzu AXIMA-LNR MALDI TOF mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] id: MS:1003556 name: AXIMA-TOF² def: "Shimadzu AXIMA-TOF² MALDI TOF/TOF mass spectrometer." [PSI:MS] +is_a: MS:1003946 ! tandem time-of-flight instrument is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] id: MS:1003557 name: AXIMA Resonance def: "Shimadzu AXIMA Resonance MALDI TOF mass spectrometerwith Ion Trap for MSn." [PSI:MS] +is_a: MS:1003764 ! ion trap time-of-flight instrument is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] id: MS:1003558 name: MALDI-8020 def: "Shimadzu MALDI-8020 benchtop MALDI TOF mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] id: MS:1003559 name: MALDI-8030 def: "Shimadzu MALDI-8030 benchtop MALDI TOF mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] id: MS:1003560 name: MALDI-8020 EasyCare def: "Shimadzu MALDI-8020 EasyCare benchtop MALDI TOF mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] id: MS:1003561 name: MALDI-8030 EasyCare def: "Shimadzu MALDI-8030 EasyCare benchtop MALDI TOF mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] id: MS:1003562 name: LCMS-2010 def: "Shimadzu LCMS-2010 quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003563 name: LCMS-2050 def: "Shimadzu LCMS-2050 quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003564 name: LCMS-8045RX def: "Shimadzu LCMS-8045RX triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003565 name: LCMS-8050RX def: "Shimadzu LCMS-8050RX triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003566 name: LCMS-8060RX def: "Shimadzu LCMS-8060RX triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003567 name: LCMS-8065XE def: "Shimadzu LCMS-8065XE triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003568 name: LCMS-9050 def: "Shimadzu LCMS-9050 quadrupole time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1003763 ! quadrupole time-of-flight instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003569 name: GCMS-QP5050A def: "Shimadzu GCMS-QP5050A gas chromatograph - quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003570 name: GCMS-QP2010S def: "Shimadzu GCMS-QP2010S gas chromatograph - quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003571 name: GCMS-QP2010 def: "Shimadzu GCMS-QP2010 gas chromatograph - quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003572 name: GCMS-QP2020NX def: "Shimadzu GCMS-QP2020NX gas chromatograph - quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003573 name: GCMS-QP2050 def: "Shimadzu GCMS-QP2050 gas chromatograph - quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003950 ! quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003574 name: GCMS-TQ 8030 def: "Shimadzu GCMS-TQ 8030 gas chromatograph - triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003575 name: GCMS-TQ 8050 def: "Shimadzu GCMS-TQ 8050 gas chromatograph - triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] @@ -23882,8 +24267,8 @@ is_a: MS:1003589 ! liquid chromatography system [Term] id: MS:1003595 -name: planar chomatography system -def: "A system for on-line planar chomatography." [PSI:MS] +name: planar chromatography system +def: "A system for on-line planar chromatography." [PSI:MS] is_a: MS:1003589 ! liquid chromatography system [Term] @@ -24800,18 +25185,6 @@ name: gas chromatography mass spectrometry system def: "A gas chromatography mass spectrometry system (GC–MS) integrates a gas chromatograph for volatile analyte separation with a mass spectrometer for ionization and detection, enabling sensitive qualitative or quantitative analysis." [PSI:MS] is_a: MS:1003588 ! hyphenated separation system -[Term] -id: MS:1003734 -name: gas chromatography mass spectrometry system model -def: "Gas chromatography mass spectrometry system model name not including the vendor's name." [PSI:MS] -is_a: MS:1003733 ! gas chromatography mass spectrometry system - -[Term] -id: MS:1003735 -name: Shimadzu gas chromatography mass spectrometry system model -def: "Shimadzu Corporation gas chromatography mass spectrometry system model." [PSI:MS] -is_a: MS:1003734 ! gas chromatography mass spectrometry system model - [Term] id: MS:1003737 name: separation system @@ -24964,75 +25337,75 @@ relationship: part_of MS:1000463 ! instrument [Term] id: MS:1003762 -name: triple quadrupole -def: "A triple quadrupole mass spectrometer (TQMS; QqQ) is a tandem mass spectrometry (MS/MS) system that employs three linear quadrupoles in series to achieve highly selective and sensitive targeted quantification of specific compounds. The first quadrupole (Q1) may select a precursor ion, the second (Q2) induces fragmentation via collision-induced dissociation (CID), and the third (Q3) monitors specific product ions, typically through Multiple Reaction Monitoring (MRM)." [PSI:MS] +name: triple quadrupole instrument +def: "A tandem instrument that employs three quadrupoles in series, where the first (Q1) acts as a mass filter for precursor ion selection, the second (q2) serves as a collision cell for fragmentation, and the third (Q3) as a mass filter for product ion detection." [PSI:MS] synonym: "QqQ" EXACT [] is_a: MS:1003761 ! instrument class [Term] id: MS:1003763 -name: quadrupole time-of-flight -def: "A quadrupole time-of-flight (Q-TOF) mass spectrometer is a hybrid instrument that combines a quadrupole mass filter with a time-of-flight (TOF) mass analyzer to provide both highly accurate mass measurements and fragmentation data. The quadrupole may be used to select a specific precursor ion which is then fragmented, and the resulting product ions are measured by the TOF analyzer, providing high resolution and mass accuracy for structural elucidation and quantification." [PSI:MS] +name: quadrupole time-of-flight instrument +def: "A hybrid instrument that combines a quadrupole mass filter for precursor ion selection with a time-of-flight mass analyzer for high-resolution, accurate-mass detection of product ions." [PSI:MS] synonym: "Q-TOF" EXACT [] is_a: MS:1003761 ! instrument class [Term] id: MS:1003764 -name: ion trap time-of-flight -def: "An ion trap time-of-flight (IT-TOF) mass spectrometer is a hybrid instrument that uses an ion trap to accumulate, store, and often fragment ions, which are then periodically injected into a time-of-flight (TOF) mass analyzer for high-resolution mass analysis. This combination allows for sensitive MSn experiments (multiple stages of mass spectrometry) within the ion trap for structural elucidation and provides high mass accuracy and resolution via the TOF component." [PSI:MS] +name: ion trap time-of-flight instrument +def: "A hybrid instrument that combines an ion trap for ion accumulation, storage, and fragmentation with a time-of-flight mass analyzer for high-resolution, accurate-mass detection." [PSI:MS] synonym: "IT-TOF" EXACT [] is_a: MS:1003761 ! instrument class [Term] id: MS:1003765 -name: triple quadrupole linear ion trap -def: "A triple quadrupole linear ion trap (QqLIT) mass spectrometer is a hybrid instrument that can operate as a conventional triple quadrupole for high-sensitivity quantification (e.g., in Multiple Reaction Monitoring mode) or as a linear ion trap for qualitative analysis, such as MSn experiments and structural elucidation. The final quadrupole (Q3) of the system can be rapidly switched between functioning as a mass-resolving filter and a high-capacity linear ion trap, allowing for both precise quantification and comprehensive structural information to be acquired in a single analytical run." [PSI:MS] +name: triple quadrupole linear ion trap instrument +def: "A hybrid instrument that combines a triple quadrupole configuration with a linear ion trap, where the third quadrupole can function either as a conventional mass filter or as a linear ion trap for MSn analysis." [PSI:MS] synonym: "QqLIT" EXACT [] is_a: MS:1003761 ! instrument class [Term] id: MS:1003766 -name: quadrupole fourier transform ion cyclotron resonance -def: "A quadrupole Fourier-transform ion cyclotron resonance (Q-FT-ICR) mass spectrometer is a hybrid instrument that uses an initial quadrupole for ion guiding or mass filtering before the ions are introduced into a Penning trap, where the mass analysis occurs. Once in the Penning trap, the ions' mass-to-charge ratios (m/z) are determined with ultra-high resolution and mass accuracy by measuring their unique cyclotron frequencies in a strong magnetic field and converting the resulting image current signal into a mass spectrum via a Fourier transform. " [PSI:MS] +name: quadrupole fourier transform ion cyclotron resonance instrument +def: "A hybrid instrument that combines a quadrupole for ion guiding or mass filtering with a Fourier transform ion cyclotron resonance mass analyzer for ultra-high resolution and mass accuracy." [PSI:MS] synonym: "Q-FT-ICR" EXACT [] is_a: MS:1003761 ! instrument class [Term] id: MS:1003767 -name: quadrupole ion mobility time-of-flight -def: "A quadrupole ion mobility time-of-flight (Q-IMS-TOF) mass spectrometer is a hybrid instrument that adds an ion mobility spectrometry (IMS) cell between the quadrupole and the time-of-flight (TOF) analyzer, providing an additional dimension of separation based on ion size, shape, and charge in a buffer gas. This configuration allows for the separation of isobars and isomers that have the same mass-to-charge ratio (m/z) but different three-dimensional structures, which significantly enhances analytical confidence for complex samples such as in proteomics, environmental analysis, and drug screening." [PSI:MS] +name: quadrupole ion mobility time-of-flight instrument +def: "A hybrid instrument that combines a quadrupole mass filter, an ion mobility spectrometry separation cell, and a time-of-flight mass analyzer, enabling separation of ions by size and shape in addition to mass-to-charge ratio." [PSI:MS] synonym: "Q-IMS-TOF" EXACT [] is_a: MS:1003761 ! instrument class [Term] id: MS:1003768 -name: ion trap orbitrap -def: "A hybrid instrument that combines an ion trap for ion storage and fragmentation with an Orbitrap mass analyzer for high-resolution, accurate-mass (HRAM) detection." [PSI:MS] +name: ion trap orbitrap instrument +def: "A hybrid instrument that combines an ion trap for ion storage and fragmentation with an Orbitrap mass analyzer for high-resolution, accurate-mass detection." [PSI:MS] is_a: MS:1003761 ! instrument class [Term] id: MS:1003769 -name: quadrupole orbitrap -def: "A quadrupole Orbitrap mass spectrometer is a hybrid instrument that uses a quadrupole mass filter for precursor ion selection, a collision cell for fragmentation, followed by an Orbitrap mass analyzer which determines the precise mass-to-charge ratios of ions with high resolution and mass accuracy via Fourier transform." [PSI:MS] +name: quadrupole orbitrap instrument +def: "A hybrid instrument that combines a quadrupole mass filter for precursor ion selection with an Orbitrap mass analyzer for high-resolution, accurate-mass detection." [PSI:MS] is_a: MS:1003761 ! instrument class [Term] id: MS:1003770 -name: quadrupole ion trap orbitrap -def: "A mass spectrometer that integrates a quadrupole mass filter, a linear ion trap, and an Orbitrap mass analyzer to provide precursor ion selection, multiple-stage fragmentation (MSn), and ultra-high resolution mass analysis." [PSI:MS] +name: quadrupole ion trap orbitrap instrument +def: "A hybrid instrument that combines a quadrupole mass filter, a linear ion trap for MSn fragmentation, and an Orbitrap mass analyzer for high-resolution, accurate-mass detection." [PSI:MS] is_a: MS:1003761 ! instrument class [Term] id: MS:1003771 -name: quadrupole orbitrap astral -def: "A instrument that integrates a quadrupole mass filter, an Orbitrap mass analyzer, and the ASTRAL analyzer for high performance in ion selection, high-resolution analysis, and high-speed, high-sensitivity MS2 measurements." [PSI:MS] +name: quadrupole orbitrap astral instrument +def: "A hybrid instrument that combines a quadrupole mass filter, an Orbitrap mass analyzer, and an asymmetric track lossless (ASTRAL) analyzer for high-resolution analysis and high-speed MS/MS measurements." [PSI:MS] is_a: MS:1003761 ! instrument class [Term] id: MS:1003774 name: mixed polarity acquisition def: "The scans of a run include both positive and negative polarity acquisitions in a pattern that is not strictly alternating, such as discrete blocks of each polarity, irregular switching sequences, or other non-alternating arrangements." [PSI:MS] -is_a: MS:1000524 ! data file content +is_a: MS:1003776 ! acquisition polarity [Term] id: MS:1003775 @@ -25040,6 +25413,12 @@ name: secondary electrospray ionization def: "Secondary electrospray ionization (SESI) is an atmospheric pressure ionization (API) technique that uses a primary nano-electrospray plume of solvent ions to ionize neutral gaseous molecules in the gas phase via efficient proton transfer reactions. Operating at atmospheric pressure, SESI allows for the sensitive and real-time detection of volatile organic compounds (VOCs) and vapors with minimal sample preparation, making it ideal for applications like breath analysis and environmental monitoring." [PSI:MS] is_a: MS:1000240 ! atmospheric pressure ionization +[Term] +id: MS:1003776 +name: acquisition polarity +def: "The ion polarity configuration used during data acquisition of a sample run." [PSI:MS] +is_a: MS:1000524 ! data file content + [Term] id: MS:1003780 name: zstd compression @@ -25076,10 +25455,45 @@ name: MS-Numpress short logged float compression followed by zstd compression def: "Compression using MS-Numpress short logged float compression and Zstandard." [PSI:MS, https://github.com/ms-numpress/ms-numpress] is_a: MS:1000572 ! binary data compression type +[Term] +id: MS:1003786 +name: electrophoretic separation +def: "Electrophoretic separation is a technique in which charged analytes are separated by differential migration in an applied electric field." [PSI:MS] +is_a: MS:1000857 ! run attribute + +[Term] +id: MS:1003787 +name: capillary electrophoresis +def: "Capillary electrophoresis (CE) is an electrophoretic separation technique performed in narrow-bore capillaries, in which analytes migrate through an electrolyte solution under the influence of an electric field and separate according to their electrophoretic mobility." [PSI:MS] +is_a: MS:1003786 ! electrophoretic separation +synonym: "capilliary zone electrophoresis" EXACT [] +synonym: "CE" EXACT [] + +[Term] +id: MS:1003788 +name: electrochromatography +def: "Electrochromatography is a liquid chromatography technique in which the mobile phase is driven through a stationary phase by electroosmotic flow generated by an applied electric field, combining electrophoretic migration with chromatographic retention." [PSI:MS] +is_a: MS:1002271 ! liquid chromatography separation + +[Term] +id: MS:1003789 +name: ion-pair reversed phase chromatography +def: "Ion-pair reversed-phase chromatography is a reversed-phase chromatography technique in which an ion-pairing reagent is added to the mobile phase to enable retention and separation of charged or ionizable analytes on a nonpolar stationary phase." [PSI:MS] +is_a: MS:1003582 ! reversed phase chromatography + +[Term] +id: MS:1003790 +name: supercritical fluid chromatography +def: "Supercritical fluid chromatography (SFC) is a separation technique in which the mobile phase is a fluid above and relatively close to its critical temperature and pressure." [PSI:MS] +is_a: MS:1002270 ! chromatography separation +synonym: "SFC" EXACT [] +synonym: "UPC2" RELATED [] + [Term] id: MS:1003800 name: TSQ Certis def: "Thermo Scientific TSQ Certis Triple Quadrupole MS." [PSI:PI] +is_a: MS:1003762 ! triple quadrupole instrument is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -25088,6 +25502,128 @@ name: AccurateMassSearch def: "OpenMS TOPP tool to assemble metabolite features from singleton mass traces." [PSI:MS] is_a: MS:1000752 ! TOPP software +[Term] +id: MS:1003802 +name: Ionoptika instrument model +def: "Ionoptika Ltd. instrument model." [PSI:MS] +is_a: MS:1000031 ! instrument model + +[Term] +id: MS:1003803 +name: Ionoptika software +def: "Ionoptika software for data acquisition and analysis." [PSI:MS] +is_a: MS:1000531 ! software + +[Term] +id: MS:1003804 +name: Ionoptika J105 +def: "Ionoptika J105 time-of-flight secondary ion mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument +is_a: MS:1003802 ! Ionoptika instrument model + +[Term] +id: MS:1003805 +name: J Series III +def: "Ionoptika J Series III time-of-flight secondary ion mass spectrometer." [PSI:MS] +is_a: MS:1003951 ! time-of-flight instrument +is_a: MS:1003802 ! Ionoptika instrument model + +[Term] +id: MS:1003806 +name: NeoSIMS +def: "Ionoptika software for data acquisition." [PSI:MS] +is_a: MS:1001455 ! acquisition software +is_a: MS:1003803 ! Ionoptika software + +[Term] +id: MS:1003807 +name: Ionoptika Image Analyser +def: "Ionoptika software for image data analysis." [PSI:MS] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software +is_a: MS:1003803 ! Ionoptika software + +[Term] +id: MS:1003808 +name: J105 Ionoptika Mass Imager +def: "Ionoptika J105 software for mass spectrometry imaging data analysis." [PSI:MS] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software +is_a: MS:1003803 ! Ionoptika software + +[Term] +id: MS:1003809 +name: IoDataConverter +def: "Ionoptika software for converting Ionoptika data formats to imzML or HDF5." [PSI:MS] +is_a: MS:1001457 ! data processing software +is_a: MS:1003803 ! Ionoptika software + +[Term] +id: MS:1003810 +name: Ionoptika V1 format +def: "Ionoptika data format generated by J105 TOF-SIMS instrument." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1003811 +name: Ionoptika V3 format +def: "Ionoptika data format generated by J105 TOF-SIMS instrument." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1003812 +name: lambda max +def: "The wavelength of maximum absorbance for a substance. This is analogous to the base peak m/z for UV-Vis spectroscopy." [PSI:MS] +synonym: "λ-max" EXACT [] +is_a: MS:1003058 ! spectrum property +relationship: has_units UO:0000018 ! nanometer +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003813 +name: list of doubles +def: "A list of xsd:double." [] +is_a: MS:1002710 ! list of type +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003820 +name: coordinate spacing model +def: "Defines a model for calculating or correcting the spacing between points along a continuous dimension." [PSI:MS] +is_a: MS:1000499 ! spectrum attribute +relationship: has_value_type MS:1003813 ! The allowed value-type for this CV term + +[Term] +id: MS:1003821 +name: polynomial delta coordinate interpolation +def: "A coordinate spacing model that predicts the next coordinate as a function of a low degree polynomial on the current coordinate, for instance a 2nd degree $x_{i + 1} = (a*x_i^2 + b*x_i + c) + x_i$. It is assumed that the parameters are inferred from the value list and the number implies the polynomial degree." [PSI:MS] +is_a: MS:1003820 ! coordinate spacing model + +[Term] +id: MS:1003822 +name: grid coordinate interpolation +def: "A coordinate spacing model that uses some form of interpolation to calculate coordinate values between a fixed minimum and maximum value. This includes formula for (potentially lossily) converting a coordinate to an integer index and vice-versa. The grid model and recalibration function parameters are given by the value list. The recalibration function may be the identity function, or a more complex model defined in a child term." [PSI:MS] +is_a: MS:1003820 ! coordinate spacing model + +[Term] +id: MS:1003824 +name: linear grid interpolation +def: "A coordinate spacing model that uses linear interpolation to map grid indices to coordinates $x_i = f_x(b + i * a)$ where $f$ is some recalibration function." [PSI:MS] +is_a: MS:1003822 ! grid coordinate interpolation + +[Term] +id: MS:1003825 +name: square root grid interpolation +def: "A coordinate spacing model that maps grid indices to coordinates $x_i = f_x((b + i * a)^2)$ where $f$ is some recalibration function. The square root of the coordinate is linear with respect to the index. This mirrors the formula relating time-of-flight to m/z, $t = k\\sqrt{m/z}$" [PSI:MS] +is_a: MS:1003822 ! grid coordinate interpolation + +[Term] +id: MS:1003826 +name: coordinate grid encoding +def: "This array stores indices or spans into some form of coordinate space model rather than the coordinates themselves, and that grid is stored externally from this data array. The objective being that these coordinates are more compact to store than the raw coordinates themselves. The value of this parameter is the grid identifier, if there are multiple to choose from. A separate coordinate spacing model parameter will signify what form of coordinate space model is used." [PSI:MS] +is_a: MS:1000572 ! binary data compression type +relationship: has_value_type xsd:string ! The allowed valute-type for this CV term + [Term] id: MS:1003901 name: zero intensity point trimming @@ -25135,10 +25671,656 @@ is_a: MS:1003213 ! mass spectrometry acquisition method relationship: part_of MS:1003905 ! targeted analysis [Term] -id: MS:1003914 -name: Agilent gas chromatography mass spectrometry system model -def: "Agilent Technologies gas chromatography mass spectrometry system model." [PSI:MS] -is_a: MS:1003734 ! gas chromatography mass spectrometry system model +id: MS:1003908 +name: centroid peak +def: "A peak represented as a single discrete data point defined by a distinct coordinate value (e.g. m/z; wavelength; drift time) and a corresponding intensity value." [PSI:MS] +is_a: MS:1000231 ! peak + +[Term] +id: MS:1003915 +name: two-dimensional gas chromatography +def: "Comprehensive two-dimensional gas chromatography (GCxGC) is a multidimensional separation technique that utilizes two columns with different stationary phases connected by a modulator, which traps, focuses and reinjects fractions from the first column to the second. This approach leads to a 2D chromatogram offering higher peak capacity and separation power." [PSI:MS] +synonym: "GCxGC" EXACT [] +is_a: MS:1002272 ! gas chromatography separation + +[Term] +id: MS:1003916 +name: SpectroSwiss software +def: "SpectroSwiss software for mass spectrometry data processing and analysis." [PSI:MS] +is_a: MS:1000531 ! software + +[Term] +id: MS:1003917 +name: Peak-by-Peak +def: "SpectroSwiss software for Fourier transform mass spectrometry (FTMS) data processing and analysis, providing advanced workflows including the processing of unreduced, transient data." [PSI:MS] +synonym: "PeakByPeak" EXACT [] +is_a: MS:1003916 ! SpectroSwiss software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003920 +name: chromatographic column +def: "A tube or housing containing a stationary phase, through which a mobile phase flows to achieve chromatographic separation of analytes." [PSI:MS] +is_a: MS:1000857 ! run attribute +relationship: part_of MS:1002270 ! chromatographic separation + +[Term] +id: MS:1003921 +name: liquid chromatographic column +def: "A chromatographic column designed for use with a liquid mobile phase, housing a stationary phase for analyte separation." [PSI:MS] +comment: Column or stationary phase name, not including the vendor's name. +is_a: MS:1003945 ! chromatographic column type + +[Term] +id: MS:1003922 +name: chromatographic stationary phase +def: "The immobile phase in a chromatographic system with which analytes interact differentially, enabling separation based on chemical or physical properties." [PSI:MS] +is_a: MS:1000857 ! run attribute +relationship: part_of MS:1003920 ! chromatographic column + +[Term] +id: MS:1003923 +name: chromatographic stationary phase attribute +def: "Chromatographic stationary phase properties that are associated with a value." [PSI:MS] +is_a: MS:1000857 ! run attribute +relationship: part_of MS:1003922 ! chromatographic stationary phase + +[Term] +id: MS:1003924 +name: pore size +def: "The average diameter of the pores within the particles of the stationary phase, typically represented in angstroms (Å)" [PSI:MS] +is_a: MS:1003923 ! chromatographic stationary phase attribute +relationship: has_units UO:0000019 ! angstrom +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003925 +name: particle diameter +def: "The average diameter of the solid particles that constitute the stationary phase." [PSI:MS] +is_a: MS:1003923 ! chromatographic stationary phase attribute +relationship: has_units UO:0000017 ! micrometer +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003926 +name: chromatographic column attribute +def: "Properties of the chromatographic column hardware that are associated with a value." [PSI:MS] +is_a: MS:1000857 ! run attribute +relationship: part_of MS:1003920 ! chromatographic column + +[Term] +id: MS:1003927 +name: column length +def: "The length of the chromatographic column, representing the path length available for separation." [PSI:MS] +is_a: MS:1003926 ! chromatographic column attribute +relationship: has_units UO:0000016 ! millimeter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003928 +name: column internal diameter +def: "The inner diameter of the chromatographic column." [PSI:MS] +synonym: "column I.D." EXACT [] +is_a: MS:1003926 ! chromatographic column attribute +relationship: has_units UO:0000016 ! millimeter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003929 +name: particle porosity +def: "The porosity of the particles composing the chromatographic stationary phase." [PSI:MS] +is_a: MS:1003923 ! chromatographic stationary phase attribute + +[Term] +id: MS:1003930 +name: fully porous +def: "A chromatographic stationary phase particle with pores distributed throughout its entire volume." [PSI:MS] +is_a: MS:1003929 ! particle porosity + +[Term] +id: MS:1003931 +name: superficially porous +def: "A chromatographic stationary phase particle consisting of a solid, non-porous core surrounded by a porous shell." [PSI:MS] +synonym: "core-shell particle" EXACT [] +is_a: MS:1003929 ! particle porosity + +[Term] +id: MS:1003932 +name: non-porous +def: "A solid chromatographic stationary phase particle without internal pores." [PSI:MS] +is_a: MS:1003929 ! particle porosity + +[Term] +id: MS:1003933 +name: support material +def: "The base material from which the chromatographic stationary phase is constructed." [PSI:MS] +is_a: MS:1003923 ! chromatographic stationary phase attribute + +[Term] +id: MS:1003934 +name: silica-based +def: "A chromatographic stationary phase constructed from silica particles, optionally with surface chemical modification." [PSI:MS] +is_a: MS:1003933 ! support material + +[Term] +id: MS:1003935 +name: hybrid particle +def: "A chromatographic stationary phase constructed from organic-inorganic hybrid particles, such as ethylene-bridged hybrid (BEH), providing enhanced chemical stability and pH range." [PSI:MS] +synonym: "BEH stationary phase" RELATED [] +is_a: MS:1003933 ! support material + +[Term] +id: MS:1003936 +name: polymer-based +def: "A chromatographic stationary phase constructed from organic polymer particles such as polystyrene-divinylbenzene or methacrylate-based polymers." [PSI:MS] +is_a: MS:1003933 ! support material + +[Term] +id: MS:1003937 +name: monolithic +def: "A chromatographic stationary phase consisting of a single continuous porous rod rather than packed discrete particles." [PSI:MS] +is_a: MS:1003933 ! support material + +[Term] +id: MS:1003938 +name: porous graphitic carbon +def: "A chromatographic stationary phase composed of porous graphitic carbon, providing strong retention of polar compounds and chemical robustness across a wide pH range." [PSI:MS] +synonym: "PGC stationary phase" EXACT [] +is_a: MS:1003933 ! support material + +[Term] +id: MS:1003939 +name: trap column +def: "A short chromatographic column used for on-line sample loading, concentration, and desalting prior to separation on the analytical column." [PSI:MS] +synonym: "precolumn" RELATED [] +is_a: MS:1003944 ! chromatographic column role + +[Term] +id: MS:1003940 +name: guard column +def: "A short protective chromatographic column placed upstream of the analytical column to capture contaminants and extend analytical column lifetime." [PSI:MS] +is_a: MS:1003944 ! chromatographic column role + +[Term] +id: MS:1003941 +name: analytical column +def: "The primary chromatographic column in which analyte separation occurs." [PSI:MS] +is_a: MS:1003944 ! chromatographic column role + +[Term] +id: MS:1003943 +name: gas chromatographic column +def: "A chromatographic column designed for use with a gaseous mobile phase." [PSI:MS] +is_a: MS:1003945 ! chromatographic column type + +[Term] +id: MS:1003944 +name: chromatographic column role +def: "The functional role of a chromatographic column within the separation workflow." [PSI:MS] +is_a: MS:1000857 ! run attribute +relationship: part_of MS:1003920 ! chromatographic column + +[Term] +id: MS:1003945 +name: chromatographic column type +def: "The type of chromatographic column classified by the mobile phase it is designed to operate with." [PSI:MS] +is_a: MS:1000857 ! run attribute +relationship: part_of MS:1003920 ! chromatographic column + +[Term] +id: MS:1003946 +name: tandem time-of-flight instrument +def: "A tandem instrument that combines two time-of-flight mass analyzers in series, where the first selects precursor ions and the second analyzes fragment ions produced by collision-induced dissociation or post-source decay." [PSI:MS] +synonym: "TOF/TOF" EXACT [] +synonym: "TOF-TOF" EXACT [] +is_a: MS:1003761 ! instrument class + +[Term] +id: MS:1003947 +name: magnetic sector ion trap instrument +def: "A hybrid instrument that combines a double-focusing magnetic sector analyzer for high-resolution precursor ion selection with an ion trap for MSn fragmentation analysis." [PSI:MS] +is_a: MS:1003761 ! instrument class + +[Term] +id: MS:1003948 +name: fourier transform ion cyclotron resonance instrument +def: "An instrument that uses a Fourier transform ion cyclotron resonance mass analyzer as its primary means of mass analysis." [PSI:MS] +is_a: MS:1003761 ! instrument class + +[Term] +id: MS:1003949 +name: magnetic sector instrument +def: "An instrument that uses a magnetic sector mass analyzer as its primary means of mass analysis." [PSI:MS] +is_a: MS:1003761 ! instrument class + +[Term] +id: MS:1003950 +name: quadrupole instrument +def: "An instrument that uses a single quadrupole mass analyzer as its primary means of mass analysis." [PSI:MS] +is_a: MS:1003761 ! instrument class + +[Term] +id: MS:1003951 +name: time-of-flight instrument +def: "An instrument that uses a time-of-flight mass analyzer as its primary means of mass analysis." [PSI:MS] +is_a: MS:1003761 ! instrument class + +[Term] +id: MS:1003952 +name: ion trap instrument +def: "An instrument that uses an ion trap mass analyzer as its primary means of mass analysis." [PSI:MS] +is_a: MS:1003761 ! instrument class + +[Term] +id: MS:1003953 +name: orbitrap instrument +def: "An instrument that uses an Orbitrap mass analyzer as its primary means of mass analysis." [PSI:MS] +is_a: MS:1003761 ! instrument class + +[Term] +id: MS:1003954 +name: argon gas cluster ion beam +def: "Argon gas cluster ion beam (Ar GCIB) bombardment uses a focused beam of large argon cluster ions, typically [Ar500]+ to [Ar10000]+, accelerated to high energies to sputter and generate secondary ions from a surface, enabling molecular depth profiling and imaging of organic and biological materials with reduced subsurface damage compared to monatomic ion beams." [PSI:MS] +synonym: "Ar GCIB" EXACT [] +is_a: MS:1003959 ! gas cluster ion beam + +[Term] +id: MS:1003955 +name: singly charged bismuth trimer liquid metal ion gun +def: "A beam of singly charged bismuth trimer ([Bi3]+) ions for desorption and ionisation from a surface, providing high spatial resolution imaging and enhanced molecular secondary ion yields compared to monatomic primary ion beams." [PSI:MS] +synonym: "[Bi3]+ LMIG" EXACT [] +is_a: MS:1003958 ! bismuth liquid metal ion gun + +[Term] +id: MS:1003956 +name: doubly charged bismuth trimer liquid metal ion gun +def: "A beam of doubly charged bismuth trimer ([Bi3]2+) ions for desorption and ionisation from a surface. Ions achieve a higher velocity at a given acceleration voltage compared to singly charged [Bi3]+, resulting in enhanced secondary ion yields for surface analysis." [PSI:MS] +synonym: "[Bi3]2+ LMIG" EXACT [] +is_a: MS:1003958 ! bismuth liquid metal ion gun + +[Term] +id: MS:1003957 +name: two-dimensional liquid chromatography +def: "Two-dimensional liquid chromatography (2D-LC) is a multidimensional separation technique that couples two liquid chromatography columns with different selectivities, such as strong cation exchange and reversed phase, connected by a switching valve or modulator to provide significantly higher peak capacity and resolving power for complex mixtures than one-dimensional liquid chromatography." [PSI:MS] +synonym: "2D-LC" EXACT [] +synonym: "LCxLC" EXACT [] +is_a: MS:1002271 ! liquid chromatography separation + +[Term] +id: MS:1003958 +name: bismuth liquid metal ion gun +def: "Bismuth liquid metal ion gun (Bi LMIG) bombardment uses a focused beam of bismuth ions emitted from a liquid metal ion source to desorb and ionize molecules from a surface. The LMIG source generates a diversity of monomers and clusters, which are filtered prior to the sample in order to select the specific ionisation characteristics." [PSI:MS] +synonym: "Bi LMIG" EXACT [] +is_a: MS:1003960 ! liquid metal ion gun + +[Term] +id: MS:1003959 +name: gas cluster ion beam +def: "A gas cluster ion beam (GCIB) is an ion source that generates and accelerates large aggregates of gas atoms or molecules to high energies. The low energy per constituent atom minimizes surface damage and molecular fragmentation, making it highly effective for molecular depth profiling and the analysis of fragile organic and biological materials." [PSI:MS] +synonym: "GCIB" EXACT [] +is_a: MS:1000446 ! fast ion bombardment + +[Term] +id: MS:1003960 +name: liquid metal ion gun +def: "A liquid metal ion gun (LMIG) is an ion source that extracts and ionizes a thin layer of liquid metal from a fine heated needle using a high-voltage electric field. It produces a high-brightness, tightly focused beam of metal ions or clusters, enabling high-resolution imaging and analysis in Secondary Ion Mass Spectrometry (SIMS)." [PSI:MS] +synonym: "LMIG" EXACT [] +is_a: MS:1000446 ! fast ion bombardment + +[Term] +id: MS:1003961 +name: Thermo Scientific software +def: "Thermo Scientific software for data acquisition and analysis." [PSI:MS] +is_a: MS:1000531 ! software + +[Term] +id: MS:1003962 +name: TraceFinder +def: "Thermo Scientific software for targeted quantitative and screening analysis of LC-MS, GC-MS, and IC-MS data, supporting automated data acquisition, processing, and reporting for diverse workflows." [PSI:MS] +is_a: MS:1003961 ! Thermo Scientific software +is_a: MS:1001455 ! acquisition software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003963 +name: FreeStyle +def: "Thermo Scientific software for interactive qualitative visualization and review of mass spectrometry data, including chromatographic peak detection, spectral library searching, and high-resolution deconvolution." [PSI:MS] +is_a: MS:1003961 ! Thermo Scientific software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003964 +name: Chromeleon CDS +def: "Thermo Scientific enterprise chromatography data system with integrated mass spectrometry instrument control and data processing, supporting GC-MS, LC-MS, and IC-MS platforms with GxP/21 CFR Part 11 compliance." [PSI:MS] +synonym: "Chromeleon Chromatography Data System" EXACT [] +is_a: MS:1003961 ! Thermo Scientific software +is_a: MS:1001455 ! acquisition software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003965 +name: Mass Frontier +def: "Thermo Scientific software for mass spectral interpretation and structural elucidation of small molecules, featuring the HighChem fragmentation library, fragmentation prediction, and spectral tree searching." [PSI:MS] +is_a: MS:1003961 ! Thermo Scientific software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003966 +name: LipidSearch +def: "Thermo Scientific software for automated identification of lipid molecular species from LC-MS and LC-MS/MS data using a comprehensive database of predicted lipid ion fragments." [PSI:MS] +is_a: MS:1003961 ! Thermo Scientific software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003967 +name: mzVault +def: "Thermo Scientific software for offline storage, searching, and management of high-resolution accurate-mass spectral libraries, including curated mzCloud content and user-generated in-house libraries." [PSI:MS] +is_a: MS:1003961 ! Thermo Scientific software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003968 +name: SIEVE +def: "Thermo Scientific software for label-free differential expression analysis of LC-MS and GC-MS data, providing chromatographic alignment, feature detection, and statistical comparison for proteomics and metabolomics." [PSI:MS] +is_a: MS:1003961 ! Thermo Scientific software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003969 +name: BioPharma Finder +def: "Thermo Scientific software for complex biotherapeutic characterization by LC-MS, supporting intact protein analysis, peptide mapping, oligonucleotide analysis, multi-attribute method workflows, and top-down or middle-down approaches." [PSI:MS] +is_a: MS:1003961 ! Thermo Scientific software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003970 +name: ion mobility quadrupole time-of-flight instrument +def: "An instrument that uses an ion mobility analyzer followed by a quadrupole mass filter and a time-of-flight mass analyzer as its primary means of mass analysis." [PSI:MS] +synonym: "IMS-Q-TOF" EXACT [] +is_a: MS:1003761 ! instrument class + +[Term] +id: MS:1003971 +name: ion trap fourier transform ion cyclotron resonance instrument +def: "An instrument that uses a linear ion trap coupled to a fourier transform ion cyclotron resonance mass analyzer as its primary means of mass analysis." [PSI:MS] +is_a: MS:1003761 ! instrument class + +[Term] +id: MS:1003972 +name: quadrupole ion trap instrument +def: "An instrument that uses a quadrupole mass filter followed by an ion trap mass analyzer as its primary means of mass analysis." [PSI:MS] +is_a: MS:1003761 ! instrument class + +[Term] +id: MS:1003973 +name: LECO PEG format +def: "Proprietary binary data format with extension '.peg', used by LECO ChromaTOF software to store raw and processed data from LECO Pegasus series mass spectrometers." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1003974 +name: JEOL JPF format +def: "Proprietary binary data format with extension '.jpf', used by JEOL mass spectrometry systems and associated data processing software to store mass spectral data." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + + +[Term] +id: MS:1003975 +name: peak group +def: "A collection of co-eluting chromatographic peaks with matching profiles, derived from a single source analyte. Examples include: related product ion peaks of a single precursor; related peaks derived from different adducts, multimers or isotopologues of a given analyte; and related peaks derived from in-source fragmentation of a given analyte." [PSI:MS] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: MS:1003976 +name: retention time window target +def: "The reference retention time from which a retention time window is defined. The target may be derived from a predicted, expected, observed, or user-specified retention time." [PSI:MS] +is_a: MS:1000915 ! retention time window attribute +relationship: has_units UO:0000010 ! second +relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + + +[Term] +id: MS:1003977 +name: Monocle +def: "A software program for converting Thermo Scientific RAW file format to mzXML, mzML, or CSV with improved monoisotopic mass estimation. Monocle was originally developed at the Gygi Lab at Harvard Medical School." [DOI:10.1021/acs.jproteome.0c00563, https://github.com/gygilab/Monocle] +synonym: "Monocle RAW converter" RELATED [] +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003978 +name: (?<=[^DE])(?=[AFILMV][^P]) +def: "Regular expression for Thermolysin." [BRENDA:3.4.24.27, DOI:10.1007/978-3-642-48380-6] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1003979 +name: Thermolysin +def: "Thermostable extracellular metalloendopeptidase containing four calcium ions" [BRENDA:3.4.24.27, DOI:10.1007/978-3-642-48380-6] +synonym: "Bacillus thermoproteolyticus neutral proteinase" EXACT [] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1003978 ! (?<=[^DE])(?=[AFILMV][^P]) + +[Term] +id: MS:1003980 +name: (?=[AEFILTVWY]) +def: "Regular expression for peptidase K." [BRENDA:3.4.21.64, DOI:10.1007/978-3-642-48380-6] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1003981 +name: peptidase K +def: "Peptidase from the mold Tritirachium album Limber" [BRENDA:3.4.21.64, DOI:10.1007/978-3-642-48380-6] +synonym: "endopeptidase K" EXACT [] +synonym: "proteinase K" EXACT [] +synonym: "Tritirachium album proteinase K" EXACT [] +synonym: "Tritirachium alkaline proteinase" EXACT [] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1003980 ! (?=[AEFILTVWY]) + +[Term] +id: MS:1003982 +name: (?<=N)(?=G) +def: "Regular expression for hydroxylamine." [https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Hydro, DOI:10.1016/0076-6879(77)47016-2] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1003983 +name: hydroxylamine +def: "NH2OH" [https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Hydro, DOI:10.1016/0076-6879(77)47016-2] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1003982 ! (?<=N)(?=G) + +[Term] +id: MS:1003984 +name: amino acid confidence level +def: "The confidence level of the PSM assignment per amino acid, where 0 is not confident and 1 is maximally confident." [PSI:MS] +is_a: MS:1002347 ! PSM-level identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type MS:1002713 ! The allowed value-type for this CV term + +[Term] +id: MS:1003985 +name: peptidoform token confidence level +def: "The confidence level of the PSM assignment per peptidoform token, so separately for each amino acid and modification, where 0 is not confident and 1 is maximally confident." [PSI:MS] +is_a: MS:1002347 ! PSM-level identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type MS:1002713 ! The allowed value-type for this CV term + +[Term] +id: MS:1003986 +name: protein sequence +def: "The protein sequence of a protein in a database." [PSI:MS] +is_a: MS:1000884 ! protein attribute +relationship: has_value_type MS:1001344 ! AA sequence + +[Term] +id: MS:1003987 +name: Orbitrap Tribrid Apex +def: "Thermo Scientific Orbitrap Tribrid Apex mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:MS] +is_a: MS:1003770 ! quadrupole ion trap orbitrap instrument +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003988 +name: Xevo MRT P10 +def: "Waters Xevo MRT P10 quadrupole - multi-reflecting time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model +is_a: MS:1003763 ! quadrupole time-of-flight instrument + +[Term] +id: MS:1003989 +name: Cyclic IMS P20 +def: "Waters Cyclic IMS P20 multipass cyclic ion mobility quadrupole time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model +is_a: MS:1003767 ! quadrupole ion mobility time-of-flight instrument + +[Term] +id: MS:1003990 +name: Orbitrap Excedion +def: "Thermo Scientific Orbitrap Excedion mass spectrometer." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model +is_a: MS:1003769 ! quadrupole orbitrap instrument + +[Term] +id: MS:1003991 +name: novus V55 +def: "SCIEX novus V55 triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model +is_a: MS:1003762 ! triple quadrupole instrument + +[Term] +id: MS:1003992 +name: 9500 Triple Quadrupole ICP-MS +def: "Agilent 9500 Triple Quadrupole ICP-MS inductively coupled plasma triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model +is_a: MS:1003762 ! triple quadrupole instrument + +[Term] +id: MS:1003993 +name: InfinityLab Pro iQ +def: "Agilent InfinityLab Pro iQ single quadrupole LC mass detector." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model +is_a: MS:1003950 ! quadrupole instrument + +[Term] +id: MS:1003994 +name: ion mobility quadrupole FT-ICR instrument +def: "Instrument class combining trapped ion mobility spectrometry (TIMS) with a quadrupole mass filter and fourier transform ion cyclotron resonance (magnetic resonance) mass analysis." [PSI:MS] +is_a: MS:1003761 ! instrument class + +[Term] +id: MS:1003995 +name: timsMRMS +def: "Bruker timsMRMS instrument combining trapped ion mobility spectrometry with magnetic resonance (FT-ICR) mass spectrometry." [PSI:MS] +is_a: MS:1000122 ! Bruker Daltonics instrument model +is_a: MS:1003994 ! ion mobility quadrupole FT-ICR instrument + +[Term] +id: MS:1003996 +name: DeepNovo +def: "DeepNovo is a deep-learning based de novo peptide sequencer for DDA." [PSI:MS, DOI:10.1073/pnas.1705691114, https://github.com/nh2tran/DeepNovo] +is_a: MS:1001456 ! analysis software +is_a: MS:1001949 ! BSI software + +[Term] +id: MS:1003997 +name: DeepNovo-DIA +def: "DeepNovo is a deep-learning based de novo peptide sequencer for DDA and DIA." [PSI:MS, DOI:10.1038/s41592-018-0260-3, https://github.com/nh2tran/DeepNovo-DIA] +is_a: MS:1001456 ! analysis software +is_a: MS:1001949 ! BSI software + +[Term] +id: MS:1003998 +name: PointNovo +def: "PointNovo is neural network based de novo peptide sequencing model." [PSI:MS, DOI:10.1038/s42256-021-00304-3, http://github.com/volpato30/PointNovo] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003999 +name: PGPointNovo +def: "PGPointNovo is a modification of PointNovo that allows parallel processing and a better optimization strategy." [PSI:MS, DOI:10.1093/bioadv/vbad057, https://github.com/shallFun4Learning/PGPointNovo] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1004000 +name: BiATNovo +def: "BiATNovo an attention based bidirectional de novo peptide sequencing software." [PSI:MS, DOI:10.1101/2023.05.11.540352, https://github.com/yangshu729/buaa-BiATnovo, https://github.com/yangshu729/BiATNovo-DDA] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1004001 +name: NovoB +def: "NovoB a transformer based bidirectional de novo peptide sequencing software." [PSI:MS, DOI:10.1371/journal.pcbi.1011892, https://github.com/ProteomeTeam/NovoB ] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1004002 +name: PepNet +def: "PepNet a convolutional neural network de novo peptide sequencing software." [PSI:MS, DOI:10.1038/s41467-023-43010-x, https://github.com/lkytal/pepnet ] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1004003 +name: π-HelixNovo +synonym: "pi-HelixNovo" EXACT [] +def: "π-HelixNovo a transformer based de novo peptide sequencing software." [PSI:MS, DOI:10.1093/bib/bbae021, https://github.com/PHOENIXcenter/pi-HelixNovo] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1004004 +name: π-PrimeNovo +synonym: "pi-PrimeNovo" EXACT [] +def: "π-PrimeNovo a non-autoregressive de novo peptide sequencing software." [PSI:MS, DOI:10.1038/s41467-024-55021-3, https://github.com/PHOENIXcenter/pi-PrimeNovo] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1004005 +name: PowerNovo +def: "PowerNovo a BERT and transformer ensemble de novo peptide sequencing software." [PSI:MS, DOI:10.1038/s41598-024-65861-0, https://github.com/protdb/PowerNovo] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1004006 +name: pUniFind +def: "pUniFind a open modification de novo peptide sequencing and rescoring software." [PSI:MS, DOI:10.1038/s42256-026-01234-8, https://github.com/pFindStudio/pUniFind] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1004007 +name: Sage +def: "A database search based peptide identification software with retention time prediction, quantification, rescoring, and false discovery rate control." [PSI:MS, DOI:10.1021/acs.jproteome.3c00486, https://github.com/lazear/sage] +is_a: MS:1001456 ! analysis software +is_a: MS:1001139 ! quantitation software name + +[Term] +id: MS:1004008 +name: BiblioSpec Spectrum Sequence List +def: "Tabular result format for proteomics and small molecule experiments, saved with extension '.ssl'." [PSI:MS, https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BiblioSpec%20input%20and%20output%20file%20formats] +is_a: MS:1000914 ! tab delimited text format +is_a: MS:1002130 ! identification file format + +[Term] +id: MS:1004009 +name: ProteoScape +def: "Bruker ProteoScape is a GPU-powered platform delivering parallel computing capabilities and real-time database search results for bottom-up proteomics." [PSI:MS, https://www.bruker.com/en/products-and-solutions/mass-spectrometry/ms-software/proteoscape.html] +is_a: MS:1001456 ! analysis software +is_a: MS:1000692 ! Bruker software + +[Term] +id: MS:1004010 +name: Stitch +def: "Template-based assembly of PSMs for de novo protein sequencing." [PSI:MS, DOI:10.1021/acs.analchem.2c01300, DOI:10.1021/acs.jproteome.4c00188, https://github.com/snijderlab/stitch] +is_a: MS:1001456 ! analysis software [Term] id: MS:4000000 @@ -27437,7 +28619,7 @@ is_obsolete: true [Term] id: PEFF:0000015 name: NumberOfEntries -def: "PEFF keyword for the sumber of sequence entries in the database." [PSI:PEFF] +def: "PEFF keyword for the number of sequence entries in the database." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term relationship: has_value_type xsd:integer ! The allowed value-type for this CV term @@ -27598,7 +28780,7 @@ relationship: has_value_type xsd:string ! The allowed value-type for this CV ter [Term] id: PEFF:0001013 name: ModRes -def: "PEFF keyword for the modified residue without aPSI-MOD or UniMod identifier." [PSI:PEFF] +def: "PEFF keyword for the modified residue without a PSI-MOD or Unimod identifier." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment relationship: has_value_type xsd:string ! The allowed value-type for this CV term @@ -27702,7 +28884,7 @@ relationship: has_value_type xsd:string ! The allowed value-type for this CV ter [Term] id: PEFF:0001027 name: ModResUnimod -def: "PEFF keyword for the modified residue with UniMod identifier." [PSI:PEFF] +def: "PEFF keyword for the modified residue with Unimod identifier." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment relationship: has_value_type xsd:string ! The allowed value-type for this CV term @@ -27875,6 +29057,17 @@ is_a: UO:0000005 is_a: UO:0000045 created_by: george gkoutos +[Term] +id: UO:0000016 +name: millimeter +namespace: unit.ontology +def: "A length unit which is equal to one thousandth of a meter or 10^[-3] m." [NIST:NIST] +subset: unit_slim +synonym: "millimetre" EXACT [] +synonym: "mm" EXACT [] +is_a: UO:0000001 +created_by: george gkoutos + [Term] id: UO:0000017 name: micrometer @@ -27898,6 +29091,15 @@ synonym: "nm" EXACT [] is_a: UO:0000001 created_by: george gkoutos +[Term] +id: UO:0000019 +name: angstrom +namespace: unit.ontology +def: "A length unit which is equal to 10 [-10] m." [NIST:NIST] +synonym: "Å" EXACT [] +is_a: UO:0000001 +created_by: george gkoutos + [Term] id: UO:0000021 name: gram @@ -28305,4 +29507,3 @@ synonym: "A^[2]" RELATED [] is_a: UO:0000047 created_by: gkoutos creation_date: 2013-06-27T05:06:40Z - diff --git a/pwiz/data/common/unimod.obo b/pwiz/data/common/unimod.obo index ad4aaed5c36..fb7145cb49d 100644 --- a/pwiz/data/common/unimod.obo +++ b/pwiz/data/common/unimod.obo @@ -1,5 +1,5 @@ format-version: 1.4 -date: 17:06:2025 11:31 +date: 17:02:2026 11:36 saved-by: psi-pi_team default-namespace: UNIMOD @@ -46584,3 +46584,215 @@ xref: spec_6_classification "Chemical derivative" is_a: UNIMOD:0 ! unimod root node +[Term] +id: UNIMOD:2138 +name: HCCA-Lys +def: "Lysine labelled with HCCA tag." [PMID:17591739, UNIMODURL:http\://www.unimod.org/modifications_view.php?editid1=2138] +xref: record_id "2138" +xref: delta_mono_mass "412.211056" +xref: delta_avge_mass "412.4821" +xref: delta_composition "H(28) C(22) N(4) O(4)" +xref: username_of_poster "Lomane" +xref: group_of_poster "" +xref: date_time_posted "2025-07-10 14:26:02" +xref: date_time_modified "2026-02-17 11:34:13" +xref: approved "0" +xref: spec_1_group "1" +xref: spec_1_hidden "1" +xref: spec_1_site "K" +xref: spec_1_position "Anywhere" +xref: spec_1_classification "Chemical derivative" +is_a: UNIMOD:0 ! unimod root node + + +[Term] +id: UNIMOD:2139 +name: Phosphocholine +def: "Serine/Threonine/Tyrosine of a protein becomes posttranslationally modified with a phosphocholine moiety.." [UNIMODURL:http\://www.unimod.org/modifications_view.php?editid1=2139] +comment: Serine/Threonine/Tyrosine of a protein becomes posttranslationally modified with a phosphocholine moiety. Phosphocholine itself has a molecular weight of 183,1426 Da for (C5H14NO4P), but in classic LC-MS it would be protonated due to the acidic environment (C5H15NO4P) and would have a molecular weight of 184,1205 Da. Since the modification is attached to the protein in an enzymatic process the actual mass gain of a phosphocholination to a peptide is: 166,1357 Da if no acidic environment is present and 167,1436 Da for evironments that are acidic. +synonym: "C5H14NO3P PC" RELATED [] +xref: record_id "2139" +xref: delta_mono_mass "165.05548" +xref: delta_avge_mass "165.1274" +xref: delta_composition "H(12) C(5) N O(3) P" +xref: username_of_poster "sandkamm" +xref: group_of_poster "" +xref: date_time_posted "2025-07-11 12:43:21" +xref: date_time_modified "2026-02-17 11:34:50" +xref: approved "0" +xref: spec_1_group "1" +xref: spec_1_hidden "1" +xref: spec_1_site "S" +xref: spec_1_position "Anywhere" +xref: spec_1_classification "Post-translational" +xref: spec_2_group "2" +xref: spec_2_hidden "1" +xref: spec_2_site "T" +xref: spec_2_position "Anywhere" +xref: spec_2_classification "Post-translational" +xref: spec_3_group "3" +xref: spec_3_hidden "1" +xref: spec_3_site "Y" +xref: spec_3_position "Anywhere" +xref: spec_3_classification "Post-translational" +is_a: UNIMOD:0 ! unimod root node + + +[Term] +id: UNIMOD:2140 +name: Methyl:13C(1)2H(2) +def: "Heavy-Methyl:13C(1)2H(2)." [PMID:27644970, PMID:16335955, UNIMODURL:http\://www.unimod.org/modifications_view.php?editid1=2140] +xref: record_id "2140" +xref: delta_mono_mass "17.031558" +xref: delta_avge_mass "17.0316" +xref: delta_composition "2H(2) 13C" +xref: username_of_poster "NilsBurger" +xref: group_of_poster "" +xref: date_time_posted "2025-08-04 14:10:56" +xref: date_time_modified "2026-02-17 11:35:15" +xref: approved "0" +xref: spec_1_group "1" +xref: spec_1_hidden "1" +xref: spec_1_site "K" +xref: spec_1_position "Anywhere" +xref: spec_1_classification "Isotopic label" +xref: spec_2_group "2" +xref: spec_2_hidden "1" +xref: spec_2_site "N-term" +xref: spec_2_position "Anywhere" +xref: spec_2_classification "Isotopic label" +is_a: UNIMOD:0 ! unimod root node + + +[Term] +id: UNIMOD:2141 +name: c-type-ion +def: "Cleavage at the N atom from the N+1 residue as reaction inside the mass spectrometer." [PMID:2074849, UNIMODURL:http\://www.unimod.org/modifications_view.php?editid1=2141] +comment: Search engines that analyze MS3 spectra derived from c-ions from the MS2 stage must recognize this virtual modification for this purpose. +xref: record_id "2141" +xref: delta_mono_mass "-0.984016" +xref: delta_avge_mass "-0.9848" +xref: delta_composition "H N O(-1)" +xref: username_of_poster "edeutsch" +xref: group_of_poster "" +xref: date_time_posted "2025-10-03 16:31:57" +xref: date_time_modified "2025-10-03 17:04:13" +xref: approved "0" +xref: spec_1_group "1" +xref: spec_1_hidden "1" +xref: spec_1_site "C-term" +xref: spec_1_position "Any C-term" +xref: spec_1_classification "Other" +xref: spec_1_misc_notes "Virtual modification for MS/MS of c-type ions" +is_a: UNIMOD:0 ! unimod root node + + +[Term] +id: UNIMOD:2142 +name: x-type-ion +def: "Cleavage at the carbonyl from the N-1 residue as reaction inside the mass spectrometer." [PMID:2074849, UNIMODURL:http\://www.unimod.org/modifications_view.php?editid1=2142] +comment: Search engines that analyze MS3 spectra derived from x-ions from the MS2 stage must recognize this virtual modification for this purpose. +xref: record_id "2142" +xref: delta_mono_mass "25.979265" +xref: delta_avge_mass "25.9942" +xref: delta_composition "H(-2) C O" +xref: username_of_poster "edeutsch" +xref: group_of_poster "" +xref: date_time_posted "2025-10-03 16:50:58" +xref: date_time_modified "2025-10-03 17:06:22" +xref: approved "0" +xref: spec_1_group "1" +xref: spec_1_hidden "1" +xref: spec_1_site "N-term" +xref: spec_1_position "Any N-term" +xref: spec_1_classification "Other" +xref: spec_1_misc_notes "Virtual modification for MS/MS of x-type ions" +is_a: UNIMOD:0 ! unimod root node + + +[Term] +id: UNIMOD:2143 +name: z-type-ion +def: "Ammonia loss from N-terminus as reaction inside the mass spectrometer." [PMID:2074849, UNIMODURL:http\://www.unimod.org/modifications_view.php?editid1=2143] +comment: Search engines that analyze MS3 spectra derived from z-ions from the MS2 stage must recognize this virtual modification for this purpose. +xref: record_id "2143" +xref: delta_mono_mass "-17.026549" +xref: delta_avge_mass "-17.0305" +xref: delta_composition "H(-3) N(-1)" +xref: username_of_poster "edeutsch" +xref: group_of_poster "" +xref: date_time_posted "2025-10-03 16:56:40" +xref: date_time_modified "2025-10-03 16:56:40" +xref: approved "0" +xref: spec_1_group "1" +xref: spec_1_hidden "1" +xref: spec_1_site "N-term" +xref: spec_1_position "Any N-term" +xref: spec_1_classification "Other" +xref: spec_1_misc_notes "Virtual modification for MS/MS of z-type ions. This is for the Biemann z-type ion, but the most common ETD z-dot ion has one more hydrogen." +is_a: UNIMOD:0 ! unimod root node + + +[Term] +id: UNIMOD:2144 +name: Dehydromethionine +def: "Intramolecular cyclization product of N-terminal methionine, forming a five-membered azasulfonium ion where the sulfur atom bonds to the amine group." [UNIMODURL:http\://www.unimod.org/modifications_view.php?editid1=2144] +xref: record_id "2144" +xref: delta_mono_mass "-2.01565" +xref: delta_avge_mass "-2.0159" +xref: delta_composition "H(-2)" +xref: username_of_poster "rnascimento" +xref: group_of_poster "" +xref: date_time_posted "2025-10-15 13:12:00" +xref: date_time_modified "2026-02-17 11:35:59" +xref: approved "0" +xref: spec_1_group "1" +xref: spec_1_hidden "1" +xref: spec_1_site "M" +xref: spec_1_position "Protein N-term" +xref: spec_1_classification "Post-translational" +is_a: UNIMOD:0 ! unimod root node + + +[Term] +id: UNIMOD:2146 +name: Label:2H(8) +def: "SILAC: Lysine_D8." [URL:https\://isotope.com/silac-reagents-and-sets/l-lysine-2hcl-3-3-4-4-5-5-6-6-d8-dlm-2641-025, UNIMODURL:http\://www.unimod.org/modifications_view.php?editid1=2146] +xref: record_id "2146" +xref: delta_mono_mass "8.050214" +xref: delta_avge_mass "8.0493" +xref: delta_composition "H(-8) 2H(8)" +xref: username_of_poster "FengmingLI" +xref: group_of_poster "" +xref: date_time_posted "2025-12-10 02:42:54" +xref: date_time_modified "2026-02-17 11:36:11" +xref: approved "0" +xref: spec_1_group "1" +xref: spec_1_hidden "1" +xref: spec_1_site "K" +xref: spec_1_position "Anywhere" +xref: spec_1_classification "Isotopic label" +is_a: UNIMOD:0 ! unimod root node + + +[Term] +id: UNIMOD:2147 +name: imidazolone +def: "Imidazolone from 3-DG." [UNIMODURL:http\://www.unimod.org/modifications_view.php?editid1=2147] +xref: record_id "2147" +xref: delta_mono_mass "144.042259" +xref: delta_avge_mass "144.1253" +xref: delta_composition "H(8) C(6) O(4)" +xref: username_of_poster "hoaianhtran" +xref: group_of_poster "" +xref: date_time_posted "2025-12-10 10:24:37" +xref: date_time_modified "2026-02-17 11:36:21" +xref: approved "0" +xref: spec_1_group "1" +xref: spec_1_hidden "1" +xref: spec_1_site "R" +xref: spec_1_position "Anywhere" +xref: spec_1_classification "Non-standard residue" +is_a: UNIMOD:0 ! unimod root node + + diff --git a/pwiz/data/identdata/IdentData.cpp b/pwiz/data/identdata/IdentData.cpp index 7834021706c..e16c35107ac 100644 --- a/pwiz/data/identdata/IdentData.cpp +++ b/pwiz/data/identdata/IdentData.cpp @@ -1256,6 +1256,10 @@ PWIZ_API_DECL void snapModificationsToUnimod(const SpectrumIdentification& si) // skip AA substitutions if (possibleMod.specificities[0].classification == unimod::Classification::Substitution) continue; + // skip fragment ion-type pseudo-modifications (e.g. "c-type-ion"), whose masses + // collide with real modifications (c-type-ion has the same -0.984 Da as Amidated) + if (bal::ends_with(possibleMod.name, "-type-ion")) + continue; mod.set(possibleMod.cvid); } } @@ -1313,6 +1317,10 @@ PWIZ_API_DECL void snapModificationsToUnimod(const SpectrumIdentification& si) // skip AA substitutions if (possibleMod.specificities[0].classification == unimod::Classification::Substitution) continue; + // skip fragment ion-type pseudo-modifications (e.g. "c-type-ion"), whose masses + // collide with real modifications (c-type-ion has the same -0.984 Da as Amidated) + if (bal::ends_with(possibleMod.name, "-type-ion")) + continue; mod.set(possibleMod.cvid); } } diff --git a/pwiz/data/identdata/Serializer_pepXML.cpp b/pwiz/data/identdata/Serializer_pepXML.cpp index e0526475edc..6646b054ccc 100644 --- a/pwiz/data/identdata/Serializer_pepXML.cpp +++ b/pwiz/data/identdata/Serializer_pepXML.cpp @@ -2074,10 +2074,24 @@ PWIZ_API_DECL PepXMLSpecificity pepXMLSpecificity(const Enzyme& ez) case MS_2_iodobenzoate: cut="W"; nocut=""; sense="C"; break; case MS_LysargiNase: cut="KR"; nocut=""; sense="N"; break; case MS_AlphaLP: cut="TASV"; nocut=""; sense="C"; break; + case MS_Thermolysin: cut="AFILMV"; nocut="DE"; sense="N"; break; // (?<=[^DE])(?=[AFILMV][^P]); the not-followed-by-P restriction is not representable in pepXML case MS_unspecific_cleavage: cut="X"; nocut=""; sense="C"; break; case MS_no_cleavage: cut=""; nocut=""; sense="C"; break; default: + { + // Newer PSI-MS cleavage agents may lack a curated case above; derive the + // cut/no-cut sets from the agent's CV-defined cleavage regex when possible. + string cvRegex; + try { cvRegex = proteome::Digestion::getCleavageAgentRegex(cleavageAgent); } + catch (exception&) {} + if (!cvRegex.empty() && bxp::regex_match(cvRegex, what, cutNoCutRegex)) + { + Enzyme ezFromRegex(ez); + ezFromRegex.siteRegexp = cvRegex; + return pepXMLSpecificity(ezFromRegex); + } throw runtime_error("[pepXMLSpecificity] No case supporting enzyme \"" + cvTermInfo(cleavageAgent).name + "\""); + } } } else diff --git a/pwiz/data/msdata/LegacyAdapter.cpp b/pwiz/data/msdata/LegacyAdapter.cpp index 2d60ec12c91..466c6b29e47 100644 --- a/pwiz/data/msdata/LegacyAdapter.cpp +++ b/pwiz/data/msdata/LegacyAdapter.cpp @@ -148,8 +148,20 @@ PWIZ_API_DECL string LegacyAdapter_Instrument::manufacturer() const if (modelInfo.parentsIsA.empty()) throw runtime_error("[LegacyAdapter_Instrument::manufacturer()] Model has no parents."); + // find the manufacturer/brand parent (named " instrument model"); a model may + // also have instrument-type parents (e.g. "ion trap instrument") which are not brands + CVID manufacturerCvid = CVID_Unknown; + for (CVID parentCvid : modelInfo.parentsIsA) + if (bal::ends_with(cvTermInfo(parentCvid).name, "instrument model")) + { + manufacturerCvid = parentCvid; + break; + } + if (manufacturerCvid == CVID_Unknown) + manufacturerCvid = modelInfo.parentsIsA[0]; + // s/ instrument model// - string result = cvTermInfo(modelInfo.parentsIsA[0]).name; + string result = cvTermInfo(manufacturerCvid).name; string::size_type index_suffix = result.find(" instrument model"); if (index_suffix != string::npos) result.erase(index_suffix); return result; diff --git a/pwiz/data/vendor_readers/Thermo/Reader_Thermo_Detail.cpp b/pwiz/data/vendor_readers/Thermo/Reader_Thermo_Detail.cpp index c57eb607998..49405420cc4 100644 --- a/pwiz/data/vendor_readers/Thermo/Reader_Thermo_Detail.cpp +++ b/pwiz/data/vendor_readers/Thermo/Reader_Thermo_Detail.cpp @@ -129,6 +129,8 @@ PWIZ_API_DECL CVID translateAsInstrumentModel(InstrumentModelType instrumentMode case InstrumentModelType_Orbitrap_Fusion_ETD: return MS_Orbitrap_Fusion_ETD; case InstrumentModelType_Orbitrap_Ascend: return MS_Orbitrap_Ascend; case InstrumentModelType_Orbitrap_Excedion_Pro: return MS_Orbitrap_Excedion_Pro; + case InstrumentModelType_Orbitrap_Excedion: return MS_Orbitrap_Excedion; + case InstrumentModelType_Orbitrap_Tribrid_Apex: return MS_Orbitrap_Tribrid_Apex; case InstrumentModelType_Orbitrap_ID_X: return MS_Orbitrap_ID_X; case InstrumentModelType_Orbitrap_IQ_X: return MS_Orbitrap_IQ_X; case InstrumentModelType_TSQ_Quantiva: return MS_TSQ_Quantiva; @@ -268,6 +270,7 @@ vector createInstrumentConfigurations(const Component& case InstrumentModelType_Orbitrap_Exploris_GC: case InstrumentModelType_Orbitrap_GC: case InstrumentModelType_Orbitrap_Excedion_Pro: + case InstrumentModelType_Orbitrap_Excedion: configurations.push_back(InstrumentConfiguration()); configurations.back().componentList.push_back(commonSource); configurations.back().componentList.push_back(Component(MS_quadrupole, 2)); @@ -318,6 +321,7 @@ vector createInstrumentConfigurations(const Component& case InstrumentModelType_Orbitrap_ID_X: case InstrumentModelType_Orbitrap_IQ_X: case InstrumentModelType_Orbitrap_Eclipse: + case InstrumentModelType_Orbitrap_Tribrid_Apex: configurations.push_back(InstrumentConfiguration()); configurations.back().componentList.push_back(commonSource); configurations.back().componentList.push_back(Component(MS_quadrupole, 2)); diff --git a/pwiz/utility/bindings/CLI/common/cv.hpp b/pwiz/utility/bindings/CLI/common/cv.hpp index 754f3112799..0a42502ecd0 100644 --- a/pwiz/utility/bindings/CLI/common/cv.hpp +++ b/pwiz/utility/bindings/CLI/common/cv.hpp @@ -38,9 +38,9 @@ // ["psi-ms.obo"] // format-version: 1.2 -// data-version: 4.1.232 -// date: 16:01:2026 12:00 -// saved-by: Jonathan Hunter +// data-version: 4.1.257 +// date: 23:06:2026 22:00 +// saved-by: Douwe Schulte // default-namespace: MS // namespace-id-rule: * MS:$sequence(7,0,9999999)$ // namespace-id-rule: * PEFF:$sequence(7,0,9999999)$ @@ -67,6 +67,7 @@ // remark: creator: Jonathan Hunter ebi.ac.uk> // remark: creator: Samuel Wein openms.de> // remark: creator: Jeroen Van Goey instadeep.com> +// remark: creator: Jannick Kappelmann gmail.com> // remark: publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics Working Group // remark: When appropriate the definition and synonyms of a term are reported exactly as in the chapter 12 of IUPAC orange book. See http://www.iupac.org/projects/2003/2003-056-2-500.html and http://mass-spec.lsu.edu/msterms/index.php/Main_Page // remark: For any queries contact psidev-ms-vocab@lists.sourceforge.net @@ -77,7 +78,7 @@ // // ["unimod.obo"] // format-version: 1.4 -// date: 17:06:2025 11:31 +// date: 17:02:2026 11:36 // // ["unit.obo"] // format-version: 1.2 @@ -132,7 +133,7 @@ public enum class CVID /// DbDate: PEFF keyword for the database date (release or file date of the source) according to database provider. PEFF_DbDate_OBSOLETE = 200000014, - /// NumberOfEntries: PEFF keyword for the sumber of sequence entries in the database. + /// NumberOfEntries: PEFF keyword for the number of sequence entries in the database. PEFF_NumberOfEntries = 200000015, /// Conversion: PEFF keyword for the description of the conversion from original format to this current one. @@ -198,7 +199,7 @@ public enum class CVID /// ModResPsi: PEFF keyword for the modified residue with PSI-MOD identifier. PEFF_ModResPsi = 200001012, - /// ModRes: PEFF keyword for the modified residue without aPSI-MOD or UniMod identifier. + /// ModRes: PEFF keyword for the modified residue without a PSI-MOD or Unimod identifier. PEFF_ModRes = 200001013, /// AltAC: PEFF keyword for the Alternative Accession Code. @@ -240,7 +241,7 @@ public enum class CVID /// ID: PEFF keyword for the UniProtKB specific Protein identifier ID; a UniProtKB term. PEFF_ID = 200001026, - /// ModResUnimod: PEFF keyword for the modified residue with UniMod identifier. + /// ModResUnimod: PEFF keyword for the modified residue with Unimod identifier. PEFF_ModResUnimod = 200001027, /// VariantSimple: PEFF keyword for the simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term. @@ -777,19 +778,19 @@ public enum class CVID /// Waters instrument model: Waters Corporation instrument model. MS_Waters_instrument_model = 1000126, - /// centroid spectrum: Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset. + /// centroid spectrum: A spectrum representation in which each peak is recorded as a single discrete data point at a distinct coordinate value (e.g. m/z; wavelength; drift time) with a corresponding intensity. MS_centroid_spectrum = 1000127, - /// Discrete Mass Spectrum: Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset. + /// Discrete Mass Spectrum: A spectrum representation in which each peak is recorded as a single discrete data point at a distinct coordinate value (e.g. m/z; wavelength; drift time) with a corresponding intensity. MS_Discrete_Mass_Spectrum = MS_centroid_spectrum, - /// profile spectrum: A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis. + /// profile spectrum: A spectrum representation in which ion signal for each peak is recorded as a distribution of intensity values across the coordinate range (e.g. m/z; wavelength; drift time). MS_profile_spectrum = 1000128, - /// continuous mass spectrum: A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis. + /// continuous mass spectrum: A spectrum representation in which ion signal for each peak is recorded as a distribution of intensity values across the coordinate range (e.g. m/z; wavelength; drift time). MS_continuous_mass_spectrum = MS_profile_spectrum, - /// Continuum Mass Spectrum: A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis. + /// Continuum Mass Spectrum: A spectrum representation in which ion signal for each peak is recorded as a distribution of intensity values across the coordinate range (e.g. m/z; wavelength; drift time). MS_Continuum_Mass_Spectrum = MS_profile_spectrum, /// negative scan: Polarity of the scan is negative. @@ -2523,6 +2524,9 @@ public enum class CVID /// ProteinLynx Global Server: Waters software for data analysis. MS_ProteinLynx_Global_Server = 1000601, + /// PLGS: Waters software for data analysis. + MS_PLGS = MS_ProteinLynx_Global_Server, + /// Shimadzu MALDI-TOF instrument model: Shimadzu MALDI-TOF instrument model. MS_Shimadzu_MALDI_TOF_instrument_model = 1000602, @@ -7233,7 +7237,7 @@ public enum class CVID /// ProteomeDiscoverer:Mascot:Significance High: Calculated relaxed significance when performing a decoy search for medium-confidence peptides. MS_ProteomeDiscoverer_Mascot_Significance_High = 1002230, - /// regular expressions for a GUID: ([A-Fa-f0-9]\{8\}-([A-Fa-f0-9]\{4\}-)\{3\}[A-Fa-f0-9]\{12\}). + /// regular expressions for a GUID: ([A-Fa-f0-9]\\{8\\}-([A-Fa-f0-9]\\{4\\}-)\\{3\\}[A-Fa-f0-9]\\{12\\}). MS_regular_expressions_for_a_GUID = 1002231, /// ProteomeDiscoverer:Default FDR calculator: The default FDR calculator as globally unique identifier (GUID). @@ -7989,7 +7993,7 @@ public enum class CVID /// regular expression: Regular expression. MS_regular_expression = 1002479, - /// regular expression for a digital object identifier (DOI): (10[.][0-9]\{4,\}(?:[.][0-9]+)*/(?:(?![\"&\'<>])[^ \t\\r\n\\v\\f])+). + /// regular expression for a digital object identifier (DOI): (10[.][0-9]\\{4,\\}(?:[.][0-9]+)*/(?:(?![\\\"&\\'<>])[^ \\t\\r\\n\\v\\f])+). MS_regular_expression_for_a_digital_object_identifier__DOI_ = 1002480, /// higher energy beam-type collision-induced dissociation: A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV. @@ -8067,7 +8071,7 @@ public enum class CVID /// modification index: The order of modifications to be referenced elsewhere in the document. MS_modification_index = 1002504, - /// regular expression for modification localization scoring: (?[0-9]+):(?[01][.][0-9]+(?:[Ee][+\-]?[0-9]+)?):(?[0-9]+(?:[|][0-9]+)*):(?true|false) + /// regular expression for modification localization scoring: (?[0-9]+):(?[01][.][0-9]+(?:[Ee][+\\-]?[0-9]+)?):(?[0-9]+(?:[|][0-9]+)*):(?true|false) MS_regular_expression_for_modification_localization_scoring = 1002505, /// modification position score: Modification position score. @@ -9018,7 +9022,7 @@ public enum class CVID /// adduct ion isotope: Isotope of the matrix molecule M of an adduct formation. MS_adduct_ion_isotope = 1002811, - /// Regular expression for adduct ion formula: (\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-]). + /// Regular expression for adduct ion formula: (\\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\\][:digit:]{0,1}[+-]). MS_Regular_expression_for_adduct_ion_formula = 1002812, /// adduct ion formula: Adduct formation formula of the form M+X or M-X, as constrained by the provided regular expression. @@ -10026,6 +10030,9 @@ public enum class CVID /// ProSight: ProSight: Database search engine for top-down proteomics. MS_ProSight = 1003141, + /// ProSightPD: ProSight: Database search engine for top-down proteomics. + MS_ProSightPD = MS_ProSight, + /// TDPortal: TDPortal: Database search engine for top-down proteomics. MS_TDPortal = 1003142, @@ -10230,7 +10237,7 @@ public enum class CVID /// constituent library file: Source library URI which(at least) a subset of spectra were extracted from. MS_constituent_library_file = 1003205, - /// library creation log: String of logging information generated when the library was constructed from its constituent files. Multiple lines should be separated with escaped \n + /// library creation log: String of logging information generated when the library was constructed from its constituent files. Multiple lines should be separated with escaped \\n MS_library_creation_log = 1003206, /// library creation software: Library creation software @@ -10818,7 +10825,7 @@ public enum class CVID /// crosslinker cleavage characteristics: Signifies that the crosslinker is cleavable and on cleavage can leave a given stub. The pattern specifies three slots ::. MS_crosslinker_cleavage_characteristics = 1003390, - /// crosslinker cleavage regular expression: ^(?[A-Za-z]):(?[+-]?[0-9]+(\.[0-9]+)?([eE][+-]?[0-9]+(\.[0-9]+)?)?):(?[A-Za-z]+)$ + /// crosslinker cleavage regular expression: ^(?[A-Za-z]):(?[+-]?[0-9]+(\\.[0-9]+)?([eE][+-]?[0-9]+(\\.[0-9]+)?)?):(?[A-Za-z]+)$ MS_crosslinker_cleavage_regular_expression = 1003391, /// search modification id: A unique identifier within an in mzIdentML document denoting a search modification rule. The same modification may be present multiple times with different id values to reflect different specificities or neutral losses. @@ -11433,8 +11440,8 @@ public enum class CVID /// three-dimensional liquid chromatography system: A system for Three-dimensional liquid chromatography (3D-LC), an advanced separation technique that combines three distinct liquid chromatography (LC) methods to achieve significantly enhanced separation power for complex mixtures, particularly in fields like proteomics. MS_three_dimensional_liquid_chromatography_system = 1003594, - /// planar chomatography system: A system for on-line planar chomatography. - MS_planar_chomatography_system = 1003595, + /// planar chromatography system: A system for on-line planar chromatography. + MS_planar_chromatography_system = 1003595, /// thin layer chromatography system: A system for on-line Thin Layer Chromatography (TLC), based upon a widely used, simple, and cost-effective analytical technique for separating and identifying components in a mixture. MS_thin_layer_chromatography_system = 1003596, @@ -11844,12 +11851,6 @@ public enum class CVID /// gas chromatography mass spectrometry system: A gas chromatography mass spectrometry system (GC–MS) integrates a gas chromatograph for volatile analyte separation with a mass spectrometer for ionization and detection, enabling sensitive qualitative or quantitative analysis. MS_gas_chromatography_mass_spectrometry_system = 1003733, - /// gas chromatography mass spectrometry system model: Gas chromatography mass spectrometry system model name not including the vendor's name. - MS_gas_chromatography_mass_spectrometry_system_model = 1003734, - - /// Shimadzu gas chromatography mass spectrometry system model: Shimadzu Corporation gas chromatography mass spectrometry system model. - MS_Shimadzu_gas_chromatography_mass_spectrometry_system_model = 1003735, - /// separation system: A system to effect separation of compounds. MS_separation_system = 1003737, @@ -11925,53 +11926,53 @@ public enum class CVID /// instrument class: Instruments classified based on their architecture with respect to mass analyzers. MS_instrument_class = 1003761, - /// triple quadrupole: A triple quadrupole mass spectrometer (TQMS; QqQ) is a tandem mass spectrometry (MS/MS) system that employs three linear quadrupoles in series to achieve highly selective and sensitive targeted quantification of specific compounds. The first quadrupole (Q1) may select a precursor ion, the second (Q2) induces fragmentation via collision-induced dissociation (CID), and the third (Q3) monitors specific product ions, typically through Multiple Reaction Monitoring (MRM). - MS_triple_quadrupole = 1003762, + /// triple quadrupole instrument: A tandem instrument that employs three quadrupoles in series, where the first (Q1) acts as a mass filter for precursor ion selection, the second (q2) serves as a collision cell for fragmentation, and the third (Q3) as a mass filter for product ion detection. + MS_triple_quadrupole_instrument = 1003762, - /// QqQ: A triple quadrupole mass spectrometer (TQMS; QqQ) is a tandem mass spectrometry (MS/MS) system that employs three linear quadrupoles in series to achieve highly selective and sensitive targeted quantification of specific compounds. The first quadrupole (Q1) may select a precursor ion, the second (Q2) induces fragmentation via collision-induced dissociation (CID), and the third (Q3) monitors specific product ions, typically through Multiple Reaction Monitoring (MRM). - MS_QqQ = MS_triple_quadrupole, + /// QqQ: A tandem instrument that employs three quadrupoles in series, where the first (Q1) acts as a mass filter for precursor ion selection, the second (q2) serves as a collision cell for fragmentation, and the third (Q3) as a mass filter for product ion detection. + MS_QqQ = MS_triple_quadrupole_instrument, - /// quadrupole time-of-flight: A quadrupole time-of-flight (Q-TOF) mass spectrometer is a hybrid instrument that combines a quadrupole mass filter with a time-of-flight (TOF) mass analyzer to provide both highly accurate mass measurements and fragmentation data. The quadrupole may be used to select a specific precursor ion which is then fragmented, and the resulting product ions are measured by the TOF analyzer, providing high resolution and mass accuracy for structural elucidation and quantification. - MS_quadrupole_time_of_flight = 1003763, + /// quadrupole time-of-flight instrument: A hybrid instrument that combines a quadrupole mass filter for precursor ion selection with a time-of-flight mass analyzer for high-resolution, accurate-mass detection of product ions. + MS_quadrupole_time_of_flight_instrument = 1003763, - /// Q-TOF: A quadrupole time-of-flight (Q-TOF) mass spectrometer is a hybrid instrument that combines a quadrupole mass filter with a time-of-flight (TOF) mass analyzer to provide both highly accurate mass measurements and fragmentation data. The quadrupole may be used to select a specific precursor ion which is then fragmented, and the resulting product ions are measured by the TOF analyzer, providing high resolution and mass accuracy for structural elucidation and quantification. - MS_Q_TOF = MS_quadrupole_time_of_flight, + /// Q-TOF: A hybrid instrument that combines a quadrupole mass filter for precursor ion selection with a time-of-flight mass analyzer for high-resolution, accurate-mass detection of product ions. + MS_Q_TOF = MS_quadrupole_time_of_flight_instrument, - /// ion trap time-of-flight: An ion trap time-of-flight (IT-TOF) mass spectrometer is a hybrid instrument that uses an ion trap to accumulate, store, and often fragment ions, which are then periodically injected into a time-of-flight (TOF) mass analyzer for high-resolution mass analysis. This combination allows for sensitive MSn experiments (multiple stages of mass spectrometry) within the ion trap for structural elucidation and provides high mass accuracy and resolution via the TOF component. - MS_ion_trap_time_of_flight = 1003764, + /// ion trap time-of-flight instrument: A hybrid instrument that combines an ion trap for ion accumulation, storage, and fragmentation with a time-of-flight mass analyzer for high-resolution, accurate-mass detection. + MS_ion_trap_time_of_flight_instrument = 1003764, - /// IT-TOF: An ion trap time-of-flight (IT-TOF) mass spectrometer is a hybrid instrument that uses an ion trap to accumulate, store, and often fragment ions, which are then periodically injected into a time-of-flight (TOF) mass analyzer for high-resolution mass analysis. This combination allows for sensitive MSn experiments (multiple stages of mass spectrometry) within the ion trap for structural elucidation and provides high mass accuracy and resolution via the TOF component. - MS_IT_TOF = MS_ion_trap_time_of_flight, + /// IT-TOF: A hybrid instrument that combines an ion trap for ion accumulation, storage, and fragmentation with a time-of-flight mass analyzer for high-resolution, accurate-mass detection. + MS_IT_TOF = MS_ion_trap_time_of_flight_instrument, - /// triple quadrupole linear ion trap: A triple quadrupole linear ion trap (QqLIT) mass spectrometer is a hybrid instrument that can operate as a conventional triple quadrupole for high-sensitivity quantification (e.g., in Multiple Reaction Monitoring mode) or as a linear ion trap for qualitative analysis, such as MSn experiments and structural elucidation. The final quadrupole (Q3) of the system can be rapidly switched between functioning as a mass-resolving filter and a high-capacity linear ion trap, allowing for both precise quantification and comprehensive structural information to be acquired in a single analytical run. - MS_triple_quadrupole_linear_ion_trap = 1003765, + /// triple quadrupole linear ion trap instrument: A hybrid instrument that combines a triple quadrupole configuration with a linear ion trap, where the third quadrupole can function either as a conventional mass filter or as a linear ion trap for MSn analysis. + MS_triple_quadrupole_linear_ion_trap_instrument = 1003765, - /// QqLIT: A triple quadrupole linear ion trap (QqLIT) mass spectrometer is a hybrid instrument that can operate as a conventional triple quadrupole for high-sensitivity quantification (e.g., in Multiple Reaction Monitoring mode) or as a linear ion trap for qualitative analysis, such as MSn experiments and structural elucidation. The final quadrupole (Q3) of the system can be rapidly switched between functioning as a mass-resolving filter and a high-capacity linear ion trap, allowing for both precise quantification and comprehensive structural information to be acquired in a single analytical run. - MS_QqLIT = MS_triple_quadrupole_linear_ion_trap, + /// QqLIT: A hybrid instrument that combines a triple quadrupole configuration with a linear ion trap, where the third quadrupole can function either as a conventional mass filter or as a linear ion trap for MSn analysis. + MS_QqLIT = MS_triple_quadrupole_linear_ion_trap_instrument, - /// quadrupole fourier transform ion cyclotron resonance: A quadrupole Fourier-transform ion cyclotron resonance (Q-FT-ICR) mass spectrometer is a hybrid instrument that uses an initial quadrupole for ion guiding or mass filtering before the ions are introduced into a Penning trap, where the mass analysis occurs. Once in the Penning trap, the ions' mass-to-charge ratios (m/z) are determined with ultra-high resolution and mass accuracy by measuring their unique cyclotron frequencies in a strong magnetic field and converting the resulting image current signal into a mass spectrum via a Fourier transform. - MS_quadrupole_fourier_transform_ion_cyclotron_resonance = 1003766, + /// quadrupole fourier transform ion cyclotron resonance instrument: A hybrid instrument that combines a quadrupole for ion guiding or mass filtering with a Fourier transform ion cyclotron resonance mass analyzer for ultra-high resolution and mass accuracy. + MS_quadrupole_fourier_transform_ion_cyclotron_resonance_instrument = 1003766, - /// Q-FT-ICR: A quadrupole Fourier-transform ion cyclotron resonance (Q-FT-ICR) mass spectrometer is a hybrid instrument that uses an initial quadrupole for ion guiding or mass filtering before the ions are introduced into a Penning trap, where the mass analysis occurs. Once in the Penning trap, the ions' mass-to-charge ratios (m/z) are determined with ultra-high resolution and mass accuracy by measuring their unique cyclotron frequencies in a strong magnetic field and converting the resulting image current signal into a mass spectrum via a Fourier transform. - MS_Q_FT_ICR = MS_quadrupole_fourier_transform_ion_cyclotron_resonance, + /// Q-FT-ICR: A hybrid instrument that combines a quadrupole for ion guiding or mass filtering with a Fourier transform ion cyclotron resonance mass analyzer for ultra-high resolution and mass accuracy. + MS_Q_FT_ICR = MS_quadrupole_fourier_transform_ion_cyclotron_resonance_instrument, - /// quadrupole ion mobility time-of-flight: A quadrupole ion mobility time-of-flight (Q-IMS-TOF) mass spectrometer is a hybrid instrument that adds an ion mobility spectrometry (IMS) cell between the quadrupole and the time-of-flight (TOF) analyzer, providing an additional dimension of separation based on ion size, shape, and charge in a buffer gas. This configuration allows for the separation of isobars and isomers that have the same mass-to-charge ratio (m/z) but different three-dimensional structures, which significantly enhances analytical confidence for complex samples such as in proteomics, environmental analysis, and drug screening. - MS_quadrupole_ion_mobility_time_of_flight = 1003767, + /// quadrupole ion mobility time-of-flight instrument: A hybrid instrument that combines a quadrupole mass filter, an ion mobility spectrometry separation cell, and a time-of-flight mass analyzer, enabling separation of ions by size and shape in addition to mass-to-charge ratio. + MS_quadrupole_ion_mobility_time_of_flight_instrument = 1003767, - /// Q-IMS-TOF: A quadrupole ion mobility time-of-flight (Q-IMS-TOF) mass spectrometer is a hybrid instrument that adds an ion mobility spectrometry (IMS) cell between the quadrupole and the time-of-flight (TOF) analyzer, providing an additional dimension of separation based on ion size, shape, and charge in a buffer gas. This configuration allows for the separation of isobars and isomers that have the same mass-to-charge ratio (m/z) but different three-dimensional structures, which significantly enhances analytical confidence for complex samples such as in proteomics, environmental analysis, and drug screening. - MS_Q_IMS_TOF = MS_quadrupole_ion_mobility_time_of_flight, + /// Q-IMS-TOF: A hybrid instrument that combines a quadrupole mass filter, an ion mobility spectrometry separation cell, and a time-of-flight mass analyzer, enabling separation of ions by size and shape in addition to mass-to-charge ratio. + MS_Q_IMS_TOF = MS_quadrupole_ion_mobility_time_of_flight_instrument, - /// ion trap orbitrap: A hybrid instrument that combines an ion trap for ion storage and fragmentation with an Orbitrap mass analyzer for high-resolution, accurate-mass (HRAM) detection. - MS_ion_trap_orbitrap = 1003768, + /// ion trap orbitrap instrument: A hybrid instrument that combines an ion trap for ion storage and fragmentation with an Orbitrap mass analyzer for high-resolution, accurate-mass detection. + MS_ion_trap_orbitrap_instrument = 1003768, - /// quadrupole orbitrap: A quadrupole Orbitrap mass spectrometer is a hybrid instrument that uses a quadrupole mass filter for precursor ion selection, a collision cell for fragmentation, followed by an Orbitrap mass analyzer which determines the precise mass-to-charge ratios of ions with high resolution and mass accuracy via Fourier transform. - MS_quadrupole_orbitrap = 1003769, + /// quadrupole orbitrap instrument: A hybrid instrument that combines a quadrupole mass filter for precursor ion selection with an Orbitrap mass analyzer for high-resolution, accurate-mass detection. + MS_quadrupole_orbitrap_instrument = 1003769, - /// quadrupole ion trap orbitrap: A mass spectrometer that integrates a quadrupole mass filter, a linear ion trap, and an Orbitrap mass analyzer to provide precursor ion selection, multiple-stage fragmentation (MSn), and ultra-high resolution mass analysis. - MS_quadrupole_ion_trap_orbitrap = 1003770, + /// quadrupole ion trap orbitrap instrument: A hybrid instrument that combines a quadrupole mass filter, a linear ion trap for MSn fragmentation, and an Orbitrap mass analyzer for high-resolution, accurate-mass detection. + MS_quadrupole_ion_trap_orbitrap_instrument = 1003770, - /// quadrupole orbitrap astral: A instrument that integrates a quadrupole mass filter, an Orbitrap mass analyzer, and the ASTRAL analyzer for high performance in ion selection, high-resolution analysis, and high-speed, high-sensitivity MS2 measurements. - MS_quadrupole_orbitrap_astral = 1003771, + /// quadrupole orbitrap astral instrument: A hybrid instrument that combines a quadrupole mass filter, an Orbitrap mass analyzer, and an asymmetric track lossless (ASTRAL) analyzer for high-resolution analysis and high-speed MS/MS measurements. + MS_quadrupole_orbitrap_astral_instrument = 1003771, /// mixed polarity acquisition: The scans of a run include both positive and negative polarity acquisitions in a pattern that is not strictly alternating, such as discrete blocks of each polarity, irregular switching sequences, or other non-alternating arrangements. MS_mixed_polarity_acquisition = 1003774, @@ -11979,6 +11980,9 @@ public enum class CVID /// secondary electrospray ionization: Secondary electrospray ionization (SESI) is an atmospheric pressure ionization (API) technique that uses a primary nano-electrospray plume of solvent ions to ionize neutral gaseous molecules in the gas phase via efficient proton transfer reactions. Operating at atmospheric pressure, SESI allows for the sensitive and real-time detection of volatile organic compounds (VOCs) and vapors with minimal sample preparation, making it ideal for applications like breath analysis and environmental monitoring. MS_secondary_electrospray_ionization = 1003775, + /// acquisition polarity: The ion polarity configuration used during data acquisition of a sample run. + MS_acquisition_polarity = 1003776, + /// zstd compression: Zstandard compression, a fast, modern, general purpose lossless compression algorithm. MS_zstd_compression = 1003780, @@ -11997,12 +12001,93 @@ public enum class CVID /// MS-Numpress short logged float compression followed by zstd compression: Compression using MS-Numpress short logged float compression and Zstandard. MS_MS_Numpress_short_logged_float_compression_followed_by_zstd_compression = 1003785, + /// electrophoretic separation: Electrophoretic separation is a technique in which charged analytes are separated by differential migration in an applied electric field. + MS_electrophoretic_separation = 1003786, + + /// capillary electrophoresis: Capillary electrophoresis (CE) is an electrophoretic separation technique performed in narrow-bore capillaries, in which analytes migrate through an electrolyte solution under the influence of an electric field and separate according to their electrophoretic mobility. + MS_capillary_electrophoresis = 1003787, + + /// capilliary zone electrophoresis: Capillary electrophoresis (CE) is an electrophoretic separation technique performed in narrow-bore capillaries, in which analytes migrate through an electrolyte solution under the influence of an electric field and separate according to their electrophoretic mobility. + MS_capilliary_zone_electrophoresis = MS_capillary_electrophoresis, + + /// CE: Capillary electrophoresis (CE) is an electrophoretic separation technique performed in narrow-bore capillaries, in which analytes migrate through an electrolyte solution under the influence of an electric field and separate according to their electrophoretic mobility. + MS_CE = MS_capillary_electrophoresis, + + /// electrochromatography: Electrochromatography is a liquid chromatography technique in which the mobile phase is driven through a stationary phase by electroosmotic flow generated by an applied electric field, combining electrophoretic migration with chromatographic retention. + MS_electrochromatography = 1003788, + + /// ion-pair reversed phase chromatography: Ion-pair reversed-phase chromatography is a reversed-phase chromatography technique in which an ion-pairing reagent is added to the mobile phase to enable retention and separation of charged or ionizable analytes on a nonpolar stationary phase. + MS_ion_pair_reversed_phase_chromatography = 1003789, + + /// supercritical fluid chromatography: Supercritical fluid chromatography (SFC) is a separation technique in which the mobile phase is a fluid above and relatively close to its critical temperature and pressure. + MS_supercritical_fluid_chromatography = 1003790, + + /// SFC: Supercritical fluid chromatography (SFC) is a separation technique in which the mobile phase is a fluid above and relatively close to its critical temperature and pressure. + MS_SFC = MS_supercritical_fluid_chromatography, + /// TSQ Certis: Thermo Scientific TSQ Certis Triple Quadrupole MS. MS_TSQ_Certis = 1003800, /// AccurateMassSearch: OpenMS TOPP tool to assemble metabolite features from singleton mass traces. MS_AccurateMassSearch = 1003801, + /// Ionoptika instrument model: Ionoptika Ltd. instrument model. + MS_Ionoptika_instrument_model = 1003802, + + /// Ionoptika software: Ionoptika software for data acquisition and analysis. + MS_Ionoptika_software = 1003803, + + /// Ionoptika J105: Ionoptika J105 time-of-flight secondary ion mass spectrometer. + MS_Ionoptika_J105 = 1003804, + + /// J Series III: Ionoptika J Series III time-of-flight secondary ion mass spectrometer. + MS_J_Series_III = 1003805, + + /// NeoSIMS: Ionoptika software for data acquisition. + MS_NeoSIMS = 1003806, + + /// Ionoptika Image Analyser: Ionoptika software for image data analysis. + MS_Ionoptika_Image_Analyser = 1003807, + + /// J105 Ionoptika Mass Imager: Ionoptika J105 software for mass spectrometry imaging data analysis. + MS_J105_Ionoptika_Mass_Imager = 1003808, + + /// IoDataConverter: Ionoptika software for converting Ionoptika data formats to imzML or HDF5. + MS_IoDataConverter = 1003809, + + /// Ionoptika V1 format: Ionoptika data format generated by J105 TOF-SIMS instrument. + MS_Ionoptika_V1_format = 1003810, + + /// Ionoptika V3 format: Ionoptika data format generated by J105 TOF-SIMS instrument. + MS_Ionoptika_V3_format = 1003811, + + /// lambda max: The wavelength of maximum absorbance for a substance. This is analogous to the base peak m/z for UV-Vis spectroscopy. + MS_lambda_max = 1003812, + + /// λ-max: The wavelength of maximum absorbance for a substance. This is analogous to the base peak m/z for UV-Vis spectroscopy. + MS__xCE__xBB__max = MS_lambda_max, + + /// list of doubles: A list of xsd:double. + MS_list_of_doubles = 1003813, + + /// coordinate spacing model: Defines a model for calculating or correcting the spacing between points along a continuous dimension. + MS_coordinate_spacing_model = 1003820, + + /// polynomial delta coordinate interpolation: A coordinate spacing model that predicts the next coordinate as a function of a low degree polynomial on the current coordinate, for instance a 2nd degree $x_{i + 1} = (a*x_i^2 + b*x_i + c) + x_i$. It is assumed that the parameters are inferred from the value list and the number implies the polynomial degree. + MS_polynomial_delta_coordinate_interpolation = 1003821, + + /// grid coordinate interpolation: A coordinate spacing model that uses some form of interpolation to calculate coordinate values between a fixed minimum and maximum value. This includes formula for (potentially lossily) converting a coordinate to an integer index and vice-versa. The grid model and recalibration function parameters are given by the value list. The recalibration function may be the identity function, or a more complex model defined in a child term. + MS_grid_coordinate_interpolation = 1003822, + + /// linear grid interpolation: A coordinate spacing model that uses linear interpolation to map grid indices to coordinates $x_i = f_x(b + i * a)$ where $f$ is some recalibration function. + MS_linear_grid_interpolation = 1003824, + + /// square root grid interpolation: A coordinate spacing model that maps grid indices to coordinates $x_i = f_x((b + i * a)^2)$ where $f$ is some recalibration function. The square root of the coordinate is linear with respect to the index. This mirrors the formula relating time-of-flight to m/z, $t = k\\sqrt{m/z}$ + MS_square_root_grid_interpolation = 1003825, + + /// coordinate grid encoding: This array stores indices or spans into some form of coordinate space model rather than the coordinates themselves, and that grid is stored externally from this data array. The objective being that these coordinates are more compact to store than the raw coordinates themselves. The value of this parameter is the grid identifier, if there are multiple to choose from. A separate coordinate spacing model parameter will signify what form of coordinate space model is used. + MS_coordinate_grid_encoding = 1003826, + /// zero intensity point trimming: Apply an algorithm to remove excess zero intensity value data points from a spectrum. Data may be retained for interperatbility such as retaining only zeros that flank non-zero intensity value data points from a profile spectrum.. MS_zero_intensity_point_trimming = 1003901, @@ -12027,8 +12112,356 @@ public enum class CVID /// PRM: Parallel Reaction Monitoring (PRM) utilizes high-resolution, accurate-mass mass spectrometry, typically a quadrupole orbitrap or quadrupole time-of-flight instrument, to isolate specific precursor ions and detect all resulting product ions in parallel. Unlike Selected Reaction Monitoring (SRM), which filters for pre-selected transitions, PRM acquires full MS/MS spectra for each target, thereby eliminating the need for transition optimization and providing high specificity through high-resolution interference rejection. MS_PRM = MS_parallel_reaction_monitoring, - /// Agilent gas chromatography mass spectrometry system model: Agilent Technologies gas chromatography mass spectrometry system model. - MS_Agilent_gas_chromatography_mass_spectrometry_system_model = 1003914, + /// centroid peak: A peak represented as a single discrete data point defined by a distinct coordinate value (e.g. m/z; wavelength; drift time) and a corresponding intensity value. + MS_centroid_peak = 1003908, + + /// two-dimensional gas chromatography: Comprehensive two-dimensional gas chromatography (GCxGC) is a multidimensional separation technique that utilizes two columns with different stationary phases connected by a modulator, which traps, focuses and reinjects fractions from the first column to the second. This approach leads to a 2D chromatogram offering higher peak capacity and separation power. + MS_two_dimensional_gas_chromatography = 1003915, + + /// GCxGC: Comprehensive two-dimensional gas chromatography (GCxGC) is a multidimensional separation technique that utilizes two columns with different stationary phases connected by a modulator, which traps, focuses and reinjects fractions from the first column to the second. This approach leads to a 2D chromatogram offering higher peak capacity and separation power. + MS_GCxGC = MS_two_dimensional_gas_chromatography, + + /// SpectroSwiss software: SpectroSwiss software for mass spectrometry data processing and analysis. + MS_SpectroSwiss_software = 1003916, + + /// Peak-by-Peak: SpectroSwiss software for Fourier transform mass spectrometry (FTMS) data processing and analysis, providing advanced workflows including the processing of unreduced, transient data. + MS_Peak_by_Peak = 1003917, + + /// PeakByPeak: SpectroSwiss software for Fourier transform mass spectrometry (FTMS) data processing and analysis, providing advanced workflows including the processing of unreduced, transient data. + MS_PeakByPeak = MS_Peak_by_Peak, + + /// chromatographic column: A tube or housing containing a stationary phase, through which a mobile phase flows to achieve chromatographic separation of analytes. + MS_chromatographic_column = 1003920, + + /// liquid chromatographic column: A chromatographic column designed for use with a liquid mobile phase, housing a stationary phase for analyte separation. + MS_liquid_chromatographic_column = 1003921, + + /// chromatographic stationary phase: The immobile phase in a chromatographic system with which analytes interact differentially, enabling separation based on chemical or physical properties. + MS_chromatographic_stationary_phase = 1003922, + + /// chromatographic stationary phase attribute: Chromatographic stationary phase properties that are associated with a value. + MS_chromatographic_stationary_phase_attribute = 1003923, + + /// pore size: The average diameter of the pores within the particles of the stationary phase, typically represented in angstroms (Å) + MS_pore_size = 1003924, + + /// particle diameter: The average diameter of the solid particles that constitute the stationary phase. + MS_particle_diameter = 1003925, + + /// chromatographic column attribute: Properties of the chromatographic column hardware that are associated with a value. + MS_chromatographic_column_attribute = 1003926, + + /// column length: The length of the chromatographic column, representing the path length available for separation. + MS_column_length = 1003927, + + /// column internal diameter: The inner diameter of the chromatographic column. + MS_column_internal_diameter = 1003928, + + /// column I.D.: The inner diameter of the chromatographic column. + MS_column_I_D_ = MS_column_internal_diameter, + + /// particle porosity: The porosity of the particles composing the chromatographic stationary phase. + MS_particle_porosity = 1003929, + + /// fully porous: A chromatographic stationary phase particle with pores distributed throughout its entire volume. + MS_fully_porous = 1003930, + + /// superficially porous: A chromatographic stationary phase particle consisting of a solid, non-porous core surrounded by a porous shell. + MS_superficially_porous = 1003931, + + /// core-shell particle: A chromatographic stationary phase particle consisting of a solid, non-porous core surrounded by a porous shell. + MS_core_shell_particle = MS_superficially_porous, + + /// non-porous: A solid chromatographic stationary phase particle without internal pores. + MS_non_porous = 1003932, + + /// support material: The base material from which the chromatographic stationary phase is constructed. + MS_support_material = 1003933, + + /// silica-based: A chromatographic stationary phase constructed from silica particles, optionally with surface chemical modification. + MS_silica_based = 1003934, + + /// hybrid particle: A chromatographic stationary phase constructed from organic-inorganic hybrid particles, such as ethylene-bridged hybrid (BEH), providing enhanced chemical stability and pH range. + MS_hybrid_particle = 1003935, + + /// polymer-based: A chromatographic stationary phase constructed from organic polymer particles such as polystyrene-divinylbenzene or methacrylate-based polymers. + MS_polymer_based = 1003936, + + /// monolithic: A chromatographic stationary phase consisting of a single continuous porous rod rather than packed discrete particles. + MS_monolithic = 1003937, + + /// porous graphitic carbon: A chromatographic stationary phase composed of porous graphitic carbon, providing strong retention of polar compounds and chemical robustness across a wide pH range. + MS_porous_graphitic_carbon = 1003938, + + /// PGC stationary phase: A chromatographic stationary phase composed of porous graphitic carbon, providing strong retention of polar compounds and chemical robustness across a wide pH range. + MS_PGC_stationary_phase = MS_porous_graphitic_carbon, + + /// trap column: A short chromatographic column used for on-line sample loading, concentration, and desalting prior to separation on the analytical column. + MS_trap_column = 1003939, + + /// guard column: A short protective chromatographic column placed upstream of the analytical column to capture contaminants and extend analytical column lifetime. + MS_guard_column = 1003940, + + /// analytical column: The primary chromatographic column in which analyte separation occurs. + MS_analytical_column = 1003941, + + /// gas chromatographic column: A chromatographic column designed for use with a gaseous mobile phase. + MS_gas_chromatographic_column = 1003943, + + /// chromatographic column role: The functional role of a chromatographic column within the separation workflow. + MS_chromatographic_column_role = 1003944, + + /// chromatographic column type: The type of chromatographic column classified by the mobile phase it is designed to operate with. + MS_chromatographic_column_type = 1003945, + + /// tandem time-of-flight instrument: A tandem instrument that combines two time-of-flight mass analyzers in series, where the first selects precursor ions and the second analyzes fragment ions produced by collision-induced dissociation or post-source decay. + MS_tandem_time_of_flight_instrument = 1003946, + + /// TOF/TOF: A tandem instrument that combines two time-of-flight mass analyzers in series, where the first selects precursor ions and the second analyzes fragment ions produced by collision-induced dissociation or post-source decay. + MS_TOF_TOF = MS_tandem_time_of_flight_instrument, + + /// magnetic sector ion trap instrument: A hybrid instrument that combines a double-focusing magnetic sector analyzer for high-resolution precursor ion selection with an ion trap for MSn fragmentation analysis. + MS_magnetic_sector_ion_trap_instrument = 1003947, + + /// fourier transform ion cyclotron resonance instrument: An instrument that uses a Fourier transform ion cyclotron resonance mass analyzer as its primary means of mass analysis. + MS_fourier_transform_ion_cyclotron_resonance_instrument = 1003948, + + /// magnetic sector instrument: An instrument that uses a magnetic sector mass analyzer as its primary means of mass analysis. + MS_magnetic_sector_instrument = 1003949, + + /// quadrupole instrument: An instrument that uses a single quadrupole mass analyzer as its primary means of mass analysis. + MS_quadrupole_instrument = 1003950, + + /// time-of-flight instrument: An instrument that uses a time-of-flight mass analyzer as its primary means of mass analysis. + MS_time_of_flight_instrument = 1003951, + + /// ion trap instrument: An instrument that uses an ion trap mass analyzer as its primary means of mass analysis. + MS_ion_trap_instrument = 1003952, + + /// orbitrap instrument: An instrument that uses an Orbitrap mass analyzer as its primary means of mass analysis. + MS_orbitrap_instrument = 1003953, + + /// argon gas cluster ion beam: Argon gas cluster ion beam (Ar GCIB) bombardment uses a focused beam of large argon cluster ions, typically [Ar500]+ to [Ar10000]+, accelerated to high energies to sputter and generate secondary ions from a surface, enabling molecular depth profiling and imaging of organic and biological materials with reduced subsurface damage compared to monatomic ion beams. + MS_argon_gas_cluster_ion_beam = 1003954, + + /// Ar GCIB: Argon gas cluster ion beam (Ar GCIB) bombardment uses a focused beam of large argon cluster ions, typically [Ar500]+ to [Ar10000]+, accelerated to high energies to sputter and generate secondary ions from a surface, enabling molecular depth profiling and imaging of organic and biological materials with reduced subsurface damage compared to monatomic ion beams. + MS_Ar_GCIB = MS_argon_gas_cluster_ion_beam, + + /// singly charged bismuth trimer liquid metal ion gun: A beam of singly charged bismuth trimer ([Bi3]+) ions for desorption and ionisation from a surface, providing high spatial resolution imaging and enhanced molecular secondary ion yields compared to monatomic primary ion beams. + MS_singly_charged_bismuth_trimer_liquid_metal_ion_gun = 1003955, + + /// [Bi3]+ LMIG: A beam of singly charged bismuth trimer ([Bi3]+) ions for desorption and ionisation from a surface, providing high spatial resolution imaging and enhanced molecular secondary ion yields compared to monatomic primary ion beams. + MS__Bi3___LMIG = MS_singly_charged_bismuth_trimer_liquid_metal_ion_gun, + + /// doubly charged bismuth trimer liquid metal ion gun: A beam of doubly charged bismuth trimer ([Bi3]2+) ions for desorption and ionisation from a surface. Ions achieve a higher velocity at a given acceleration voltage compared to singly charged [Bi3]+, resulting in enhanced secondary ion yields for surface analysis. + MS_doubly_charged_bismuth_trimer_liquid_metal_ion_gun = 1003956, + + /// [Bi3]2+ LMIG: A beam of doubly charged bismuth trimer ([Bi3]2+) ions for desorption and ionisation from a surface. Ions achieve a higher velocity at a given acceleration voltage compared to singly charged [Bi3]+, resulting in enhanced secondary ion yields for surface analysis. + MS__Bi3_2__LMIG = MS_doubly_charged_bismuth_trimer_liquid_metal_ion_gun, + + /// two-dimensional liquid chromatography: Two-dimensional liquid chromatography (2D-LC) is a multidimensional separation technique that couples two liquid chromatography columns with different selectivities, such as strong cation exchange and reversed phase, connected by a switching valve or modulator to provide significantly higher peak capacity and resolving power for complex mixtures than one-dimensional liquid chromatography. + MS_two_dimensional_liquid_chromatography = 1003957, + + /// 2D-LC: Two-dimensional liquid chromatography (2D-LC) is a multidimensional separation technique that couples two liquid chromatography columns with different selectivities, such as strong cation exchange and reversed phase, connected by a switching valve or modulator to provide significantly higher peak capacity and resolving power for complex mixtures than one-dimensional liquid chromatography. + MS_2D_LC = MS_two_dimensional_liquid_chromatography, + + /// LCxLC: Two-dimensional liquid chromatography (2D-LC) is a multidimensional separation technique that couples two liquid chromatography columns with different selectivities, such as strong cation exchange and reversed phase, connected by a switching valve or modulator to provide significantly higher peak capacity and resolving power for complex mixtures than one-dimensional liquid chromatography. + MS_LCxLC = MS_two_dimensional_liquid_chromatography, + + /// bismuth liquid metal ion gun: Bismuth liquid metal ion gun (Bi LMIG) bombardment uses a focused beam of bismuth ions emitted from a liquid metal ion source to desorb and ionize molecules from a surface. The LMIG source generates a diversity of monomers and clusters, which are filtered prior to the sample in order to select the specific ionisation characteristics. + MS_bismuth_liquid_metal_ion_gun = 1003958, + + /// Bi LMIG: Bismuth liquid metal ion gun (Bi LMIG) bombardment uses a focused beam of bismuth ions emitted from a liquid metal ion source to desorb and ionize molecules from a surface. The LMIG source generates a diversity of monomers and clusters, which are filtered prior to the sample in order to select the specific ionisation characteristics. + MS_Bi_LMIG = MS_bismuth_liquid_metal_ion_gun, + + /// gas cluster ion beam: A gas cluster ion beam (GCIB) is an ion source that generates and accelerates large aggregates of gas atoms or molecules to high energies. The low energy per constituent atom minimizes surface damage and molecular fragmentation, making it highly effective for molecular depth profiling and the analysis of fragile organic and biological materials. + MS_gas_cluster_ion_beam = 1003959, + + /// GCIB: A gas cluster ion beam (GCIB) is an ion source that generates and accelerates large aggregates of gas atoms or molecules to high energies. The low energy per constituent atom minimizes surface damage and molecular fragmentation, making it highly effective for molecular depth profiling and the analysis of fragile organic and biological materials. + MS_GCIB = MS_gas_cluster_ion_beam, + + /// liquid metal ion gun: A liquid metal ion gun (LMIG) is an ion source that extracts and ionizes a thin layer of liquid metal from a fine heated needle using a high-voltage electric field. It produces a high-brightness, tightly focused beam of metal ions or clusters, enabling high-resolution imaging and analysis in Secondary Ion Mass Spectrometry (SIMS). + MS_liquid_metal_ion_gun = 1003960, + + /// LMIG: A liquid metal ion gun (LMIG) is an ion source that extracts and ionizes a thin layer of liquid metal from a fine heated needle using a high-voltage electric field. It produces a high-brightness, tightly focused beam of metal ions or clusters, enabling high-resolution imaging and analysis in Secondary Ion Mass Spectrometry (SIMS). + MS_LMIG = MS_liquid_metal_ion_gun, + + /// Thermo Scientific software: Thermo Scientific software for data acquisition and analysis. + MS_Thermo_Scientific_software = 1003961, + + /// TraceFinder: Thermo Scientific software for targeted quantitative and screening analysis of LC-MS, GC-MS, and IC-MS data, supporting automated data acquisition, processing, and reporting for diverse workflows. + MS_TraceFinder = 1003962, + + /// FreeStyle: Thermo Scientific software for interactive qualitative visualization and review of mass spectrometry data, including chromatographic peak detection, spectral library searching, and high-resolution deconvolution. + MS_FreeStyle = 1003963, + + /// Chromeleon CDS: Thermo Scientific enterprise chromatography data system with integrated mass spectrometry instrument control and data processing, supporting GC-MS, LC-MS, and IC-MS platforms with GxP/21 CFR Part 11 compliance. + MS_Chromeleon_CDS = 1003964, + + /// Chromeleon Chromatography Data System: Thermo Scientific enterprise chromatography data system with integrated mass spectrometry instrument control and data processing, supporting GC-MS, LC-MS, and IC-MS platforms with GxP/21 CFR Part 11 compliance. + MS_Chromeleon_Chromatography_Data_System = MS_Chromeleon_CDS, + + /// Mass Frontier: Thermo Scientific software for mass spectral interpretation and structural elucidation of small molecules, featuring the HighChem fragmentation library, fragmentation prediction, and spectral tree searching. + MS_Mass_Frontier = 1003965, + + /// LipidSearch: Thermo Scientific software for automated identification of lipid molecular species from LC-MS and LC-MS/MS data using a comprehensive database of predicted lipid ion fragments. + MS_LipidSearch = 1003966, + + /// mzVault: Thermo Scientific software for offline storage, searching, and management of high-resolution accurate-mass spectral libraries, including curated mzCloud content and user-generated in-house libraries. + MS_mzVault = 1003967, + + /// SIEVE: Thermo Scientific software for label-free differential expression analysis of LC-MS and GC-MS data, providing chromatographic alignment, feature detection, and statistical comparison for proteomics and metabolomics. + MS_SIEVE = 1003968, + + /// BioPharma Finder: Thermo Scientific software for complex biotherapeutic characterization by LC-MS, supporting intact protein analysis, peptide mapping, oligonucleotide analysis, multi-attribute method workflows, and top-down or middle-down approaches. + MS_BioPharma_Finder = 1003969, + + /// ion mobility quadrupole time-of-flight instrument: An instrument that uses an ion mobility analyzer followed by a quadrupole mass filter and a time-of-flight mass analyzer as its primary means of mass analysis. + MS_ion_mobility_quadrupole_time_of_flight_instrument = 1003970, + + /// IMS-Q-TOF: An instrument that uses an ion mobility analyzer followed by a quadrupole mass filter and a time-of-flight mass analyzer as its primary means of mass analysis. + MS_IMS_Q_TOF = MS_ion_mobility_quadrupole_time_of_flight_instrument, + + /// ion trap fourier transform ion cyclotron resonance instrument: An instrument that uses a linear ion trap coupled to a fourier transform ion cyclotron resonance mass analyzer as its primary means of mass analysis. + MS_ion_trap_fourier_transform_ion_cyclotron_resonance_instrument = 1003971, + + /// quadrupole ion trap instrument: An instrument that uses a quadrupole mass filter followed by an ion trap mass analyzer as its primary means of mass analysis. + MS_quadrupole_ion_trap_instrument = 1003972, + + /// LECO PEG format: Proprietary binary data format with extension '.peg', used by LECO ChromaTOF software to store raw and processed data from LECO Pegasus series mass spectrometers. + MS_LECO_PEG_format = 1003973, + + /// JEOL JPF format: Proprietary binary data format with extension '.jpf', used by JEOL mass spectrometry systems and associated data processing software to store mass spectral data. + MS_JEOL_JPF_format = 1003974, + + /// peak group: A collection of co-eluting chromatographic peaks with matching profiles, derived from a single source analyte. Examples include: related product ion peaks of a single precursor; related peaks derived from different adducts, multimers or isotopologues of a given analyte; and related peaks derived from in-source fragmentation of a given analyte. + MS_peak_group = 1003975, + + /// retention time window target: The reference retention time from which a retention time window is defined. The target may be derived from a predicted, expected, observed, or user-specified retention time. + MS_retention_time_window_target = 1003976, + + /// Monocle: A software program for converting Thermo Scientific RAW file format to mzXML, mzML, or CSV with improved monoisotopic mass estimation. Monocle was originally developed at the Gygi Lab at Harvard Medical School. + MS_Monocle = 1003977, + + /// (?<=[^DE])(?=[AFILMV][^P]): Regular expression for Thermolysin. + MS_______DE______AFILMV___P__ = 1003978, + + /// Thermolysin: Thermostable extracellular metalloendopeptidase containing four calcium ions + MS_Thermolysin = 1003979, + + /// Bacillus thermoproteolyticus neutral proteinase: Thermostable extracellular metalloendopeptidase containing four calcium ions + MS_Bacillus_thermoproteolyticus_neutral_proteinase = MS_Thermolysin, + + /// (?=[AEFILTVWY]): Regular expression for peptidase K. + MS_____AEFILTVWY__ = 1003980, + + /// peptidase K: Peptidase from the mold Tritirachium album Limber + MS_peptidase_K = 1003981, + + /// endopeptidase K: Peptidase from the mold Tritirachium album Limber + MS_endopeptidase_K = MS_peptidase_K, + + /// proteinase K: Peptidase from the mold Tritirachium album Limber + MS_proteinase_K = MS_peptidase_K, + + /// Tritirachium album proteinase K: Peptidase from the mold Tritirachium album Limber + MS_Tritirachium_album_proteinase_K = MS_peptidase_K, + + /// Tritirachium alkaline proteinase: Peptidase from the mold Tritirachium album Limber + MS_Tritirachium_alkaline_proteinase = MS_peptidase_K, + + /// (?<=N)(?=G): Regular expression for hydroxylamine. + MS_____N____G_ = 1003982, + + /// hydroxylamine: NH2OH + MS_hydroxylamine = 1003983, + + /// amino acid confidence level: The confidence level of the PSM assignment per amino acid, where 0 is not confident and 1 is maximally confident. + MS_amino_acid_confidence_level = 1003984, + + /// peptidoform token confidence level: The confidence level of the PSM assignment per peptidoform token, so separately for each amino acid and modification, where 0 is not confident and 1 is maximally confident. + MS_peptidoform_token_confidence_level = 1003985, + + /// protein sequence: The protein sequence of a protein in a database. + MS_protein_sequence = 1003986, + + /// Orbitrap Tribrid Apex: Thermo Scientific Orbitrap Tribrid Apex mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. + MS_Orbitrap_Tribrid_Apex = 1003987, + + /// Xevo MRT P10: Waters Xevo MRT P10 quadrupole - multi-reflecting time-of-flight mass spectrometer. + MS_Xevo_MRT_P10 = 1003988, + + /// Cyclic IMS P20: Waters Cyclic IMS P20 multipass cyclic ion mobility quadrupole time-of-flight mass spectrometer. + MS_Cyclic_IMS_P20 = 1003989, + + /// Orbitrap Excedion: Thermo Scientific Orbitrap Excedion mass spectrometer. + MS_Orbitrap_Excedion = 1003990, + + /// novus V55: SCIEX novus V55 triple quadrupole mass spectrometer. + MS_novus_V55 = 1003991, + + /// 9500 Triple Quadrupole ICP-MS: Agilent 9500 Triple Quadrupole ICP-MS inductively coupled plasma triple quadrupole mass spectrometer. + MS_9500_Triple_Quadrupole_ICP_MS = 1003992, + + /// InfinityLab Pro iQ: Agilent InfinityLab Pro iQ single quadrupole LC mass detector. + MS_InfinityLab_Pro_iQ = 1003993, + + /// ion mobility quadrupole FT-ICR instrument: Instrument class combining trapped ion mobility spectrometry (TIMS) with a quadrupole mass filter and fourier transform ion cyclotron resonance (magnetic resonance) mass analysis. + MS_ion_mobility_quadrupole_FT_ICR_instrument = 1003994, + + /// timsMRMS: Bruker timsMRMS instrument combining trapped ion mobility spectrometry with magnetic resonance (FT-ICR) mass spectrometry. + MS_timsMRMS = 1003995, + + /// DeepNovo: DeepNovo is a deep-learning based de novo peptide sequencer for DDA. + MS_DeepNovo = 1003996, + + /// DeepNovo-DIA: DeepNovo is a deep-learning based de novo peptide sequencer for DDA and DIA. + MS_DeepNovo_DIA = 1003997, + + /// PointNovo: PointNovo is neural network based de novo peptide sequencing model. + MS_PointNovo = 1003998, + + /// PGPointNovo: PGPointNovo is a modification of PointNovo that allows parallel processing and a better optimization strategy. + MS_PGPointNovo = 1003999, + + /// BiATNovo: BiATNovo an attention based bidirectional de novo peptide sequencing software. + MS_BiATNovo = 1004000, + + /// NovoB: NovoB a transformer based bidirectional de novo peptide sequencing software. + MS_NovoB = 1004001, + + /// PepNet: PepNet a convolutional neural network de novo peptide sequencing software. + MS_PepNet = 1004002, + + /// π-HelixNovo: π-HelixNovo a transformer based de novo peptide sequencing software. + MS__xCF__x80__HelixNovo = 1004003, + + /// pi-HelixNovo: π-HelixNovo a transformer based de novo peptide sequencing software. + MS_pi_HelixNovo = MS__xCF__x80__HelixNovo, + + /// π-PrimeNovo: π-PrimeNovo a non-autoregressive de novo peptide sequencing software. + MS__xCF__x80__PrimeNovo = 1004004, + + /// pi-PrimeNovo: π-PrimeNovo a non-autoregressive de novo peptide sequencing software. + MS_pi_PrimeNovo = MS__xCF__x80__PrimeNovo, + + /// PowerNovo: PowerNovo a BERT and transformer ensemble de novo peptide sequencing software. + MS_PowerNovo = 1004005, + + /// pUniFind: pUniFind a open modification de novo peptide sequencing and rescoring software. + MS_pUniFind = 1004006, + + /// Sage: A database search based peptide identification software with retention time prediction, quantification, rescoring, and false discovery rate control. + MS_Sage = 1004007, + + /// BiblioSpec Spectrum Sequence List: Tabular result format for proteomics and small molecule experiments, saved with extension '.ssl'. + MS_BiblioSpec_Spectrum_Sequence_List = 1004008, + + /// ProteoScape: Bruker ProteoScape is a GPU-powered platform delivering parallel computing capabilities and real-time database search results for bottom-up proteomics. + MS_ProteoScape = 1004009, + + /// Stitch: Template-based assembly of PSMs for de novo protein sequencing. + MS_Stitch = 1004010, /// Number of Occurrences: The number of times something happened. NCIT_Number_of_Occurrences = 103150827, @@ -17319,6 +17752,33 @@ public enum class CVID /// DMA-PEG3: DimethylaminoPEG3ylation. UNIMOD_DMA_PEG3 = 300002136, + /// HCCA-Lys: Lysine labelled with HCCA tag. + UNIMOD_HCCA_Lys = 300002138, + + /// Phosphocholine: Serine/Threonine/Tyrosine of a protein becomes posttranslationally modified with a phosphocholine moiety.. + UNIMOD_Phosphocholine = 300002139, + + /// Methyl:13C(1)2H(2): Heavy-Methyl:13C(1)2H(2). + UNIMOD_Methyl_13C_1_2H_2_ = 300002140, + + /// c-type-ion: Cleavage at the N atom from the N+1 residue as reaction inside the mass spectrometer. + UNIMOD_c_type_ion = 300002141, + + /// x-type-ion: Cleavage at the carbonyl from the N-1 residue as reaction inside the mass spectrometer. + UNIMOD_x_type_ion = 300002142, + + /// z-type-ion: Ammonia loss from N-terminus as reaction inside the mass spectrometer. + UNIMOD_z_type_ion = 300002143, + + /// Dehydromethionine: Intramolecular cyclization product of N-terminal methionine, forming a five-membered azasulfonium ion where the sulfur atom bonds to the amine group. + UNIMOD_Dehydromethionine = 300002144, + + /// Label:2H(8): SILAC: Lysine_D8. + UNIMOD_Label_2H_8_ = 300002146, + + /// imidazolone: Imidazolone from 3-DG. + UNIMOD_imidazolone = 300002147, + /// unit: A unit of measurement is a standardized quantity of a physical quality. UO_unit = 400000000, diff --git a/pwiz/utility/bindings/CLI/common/cvgen_cli.cpp b/pwiz/utility/bindings/CLI/common/cvgen_cli.cpp index ad551c392d8..225f5a74db3 100644 --- a/pwiz/utility/bindings/CLI/common/cvgen_cli.cpp +++ b/pwiz/utility/bindings/CLI/common/cvgen_cli.cpp @@ -149,6 +149,7 @@ void writeHpp(const vector& obos, const string& basename, const bfs::path& os << "/// enumeration of controlled vocabulary (CV) terms, generated from OBO file(s)\n" "public enum class CVID\n{\n" " CVID_Unknown = -1"; + set emittedEnumNames; // track emitted enum names to avoid redefinitions (e.g. synonyms that escape to the same name) for (vector::const_iterator obo=obos.begin(); obo!=obos.end(); ++obo) { multiset enumNames; @@ -166,14 +167,23 @@ void writeHpp(const vector& obos, const string& basename, const bfs::path& os << ",\n\n" << " /// " << term.name << ": " << term.def << "\n" << " " << eName << " = " << enumValue(term, enumMultiplierByPrefix[term.prefix]); + emittedEnumNames.insert(eName); if (term.prefix == "MS") // add synonyms for PSI-MS only { BOOST_FOREACH(const string& synonym, term.exactSynonyms) { + string synonym_enum_name = enumName(term.prefix, synonym, term.isObsolete); + // skip synonyms whose escaped enum name collides with an already-emitted name + // (e.g. a term with both "TOF/TOF" and "TOF-TOF" synonyms both escape to MS_TOF_TOF) + if (!emittedEnumNames.insert(synonym_enum_name).second) + { + cerr << "Warning: skipping duplicate synonym enum name for term id " << term.id << ": " << synonym << ": " << synonym_enum_name << endl; + continue; + } os << ",\n\n" << " /// " << synonym << ": " << term.def << "\n" - << " " << enumName(term.prefix, synonym, term.isObsolete) << " = " << eName; + << " " << synonym_enum_name << " = " << eName; } } } diff --git a/pwiz_aux/msrc/utility/vendor_api/thermo/Jamfile.jam b/pwiz_aux/msrc/utility/vendor_api/thermo/Jamfile.jam index 82a35f05290..258c8ba7150 100644 --- a/pwiz_aux/msrc/utility/vendor_api/thermo/Jamfile.jam +++ b/pwiz_aux/msrc/utility/vendor_api/thermo/Jamfile.jam @@ -163,6 +163,11 @@ rule vendor-api-usage-requirements ( properties * ) result += $(API_PATH)/ThermoFisher.CommonCore.RawFileReader.dll ; #result += $(API_PATH)/ThermoFisher.CommonCore.MassPrecisionEstimator.dll ; #result += $(API_PATH)/ThermoFisher.CommonCore.BackgroundSubtraction.dll ; + # RawFileReader 5.1.0.27 depends on System.Memory (and its deps); declare them as assemblies so they + # are deployed and BindingRedirectGenerator emits binding redirects for native consumers (e.g. msconvert under Wine) + result += $(PWIZ_ROOT_PATH)/pwiz_tools/Shared/Lib/System.Memory.dll ; + result += $(PWIZ_ROOT_PATH)/pwiz_tools/Shared/Lib/System.Buffers.dll ; + result += $(PWIZ_ROOT_PATH)/pwiz_tools/Shared/Lib/System.Numerics.Vectors.dll ; result += $(API_PATH)/EULA.RawFileReader ; result += /wd4564 ; # warning C4564: method 'x' defines unsupported default parameter 'y' } diff --git a/pwiz_aux/msrc/utility/vendor_api/thermo/RawFileTypes.h b/pwiz_aux/msrc/utility/vendor_api/thermo/RawFileTypes.h index 935c44998b4..1334b15846d 100644 --- a/pwiz_aux/msrc/utility/vendor_api/thermo/RawFileTypes.h +++ b/pwiz_aux/msrc/utility/vendor_api/thermo/RawFileTypes.h @@ -140,6 +140,8 @@ enum PWIZ_API_DECL InstrumentModelType InstrumentModelType_Orbitrap_Astral, InstrumentModelType_Orbitrap_Astral_Zoom, InstrumentModelType_Orbitrap_Excedion_Pro, + InstrumentModelType_Orbitrap_Excedion, + InstrumentModelType_Orbitrap_Tribrid_Apex, InstrumentModelType_Q_Exactive_GC_Orbitrap, InstrumentModelType_ISQ_7000, InstrumentModelType_Velos_Pro, @@ -283,9 +285,10 @@ const InstrumentNameToModelMapping nameToModelMapping[] = {"ORBITRAPEXPLORISGC", InstrumentModelType_Orbitrap_Exploris_GC, ContainsNoSpaces}, // predicted {"ORBITRAP EXPLORIS 480", InstrumentModelType_Orbitrap_Exploris_480, Exact}, {"ORBITRAP EXCEDION PRO", InstrumentModelType_Orbitrap_Excedion_Pro, Contains}, - {"ORBITRAP EXCEDION", InstrumentModelType_Orbitrap_Excedion_Pro, Contains}, + {"ORBITRAP EXCEDION", InstrumentModelType_Orbitrap_Excedion, Contains}, {"ORBITRAP GC", InstrumentModelType_Orbitrap_GC, Contains}, {"ECLIPSE", InstrumentModelType_Orbitrap_Eclipse, Contains}, + {"TRIBRID APEX", InstrumentModelType_Orbitrap_Tribrid_Apex, Contains}, {"ASTRAL ZOOM", InstrumentModelType_Orbitrap_Astral_Zoom, Contains}, // predicted {"ASTRAL", InstrumentModelType_Orbitrap_Astral, Contains}, {"MALDI LTQ ORBITRAP XL", InstrumentModelType_MALDI_LTQ_Orbitrap_XL, Exact}, @@ -394,6 +397,8 @@ inline std::vector getIonSourcesForInstrumentModel(InstrumentMod case InstrumentModelType_Orbitrap_Astral: case InstrumentModelType_Orbitrap_Astral_Zoom: case InstrumentModelType_Orbitrap_Excedion_Pro: + case InstrumentModelType_Orbitrap_Excedion: + case InstrumentModelType_Orbitrap_Tribrid_Apex: case InstrumentModelType_Stellar: case InstrumentModelType_TSQ: case InstrumentModelType_TSQ_Quantum: @@ -527,6 +532,7 @@ inline MassAnalyzerType convertScanFilterMassAnalyzer(ScanFilterMassAnalyzerType case InstrumentModelType_Orbitrap_Exploris_480: case InstrumentModelType_Orbitrap_Exploris_GC: case InstrumentModelType_Orbitrap_Excedion_Pro: + case InstrumentModelType_Orbitrap_Excedion: return MassAnalyzerType_Orbitrap; case InstrumentModelType_LTQ_Orbitrap: @@ -548,6 +554,7 @@ inline MassAnalyzerType convertScanFilterMassAnalyzer(ScanFilterMassAnalyzerType case InstrumentModelType_Orbitrap_ID_X: case InstrumentModelType_Orbitrap_IQ_X: case InstrumentModelType_Orbitrap_Eclipse: + case InstrumentModelType_Orbitrap_Tribrid_Apex: case InstrumentModelType_Orbitrap_GC: { switch (scanFilterType) @@ -695,6 +702,7 @@ inline std::vector getMassAnalyzersForInstrumentModel(Instrume case InstrumentModelType_Orbitrap_Exploris_GC: case InstrumentModelType_Orbitrap_GC: case InstrumentModelType_Orbitrap_Excedion_Pro: + case InstrumentModelType_Orbitrap_Excedion: massAnalyzers.push_back(MassAnalyzerType_Orbitrap); break; @@ -716,6 +724,7 @@ inline std::vector getMassAnalyzersForInstrumentModel(Instrume case InstrumentModelType_Orbitrap_ID_X: // ditto case InstrumentModelType_Orbitrap_IQ_X: // ditto case InstrumentModelType_Orbitrap_Eclipse: + case InstrumentModelType_Orbitrap_Tribrid_Apex: // Tribrid: quadrupole (filter only), linear ion trap, and orbitrap massAnalyzers.push_back(MassAnalyzerType_Orbitrap); massAnalyzers.push_back(MassAnalyzerType_Linear_Ion_Trap); break; @@ -862,6 +871,7 @@ inline std::vector getDetectorsForInstrumentModel(InstrumentModelT case InstrumentModelType_Orbitrap_Exploris_GC: case InstrumentModelType_Orbitrap_GC: case InstrumentModelType_Orbitrap_Excedion_Pro: + case InstrumentModelType_Orbitrap_Excedion: detectors.push_back(DetectorType_Inductive); break; @@ -886,6 +896,7 @@ inline std::vector getDetectorsForInstrumentModel(InstrumentModelT case InstrumentModelType_Orbitrap_ID_X: case InstrumentModelType_Orbitrap_IQ_X: case InstrumentModelType_Orbitrap_Eclipse: + case InstrumentModelType_Orbitrap_Tribrid_Apex: case InstrumentModelType_Orbitrap_Astral: case InstrumentModelType_Orbitrap_Astral_Zoom: detectors.push_back(DetectorType_Inductive); diff --git a/pwiz_aux/msrc/utility/vendor_api_Thermo.7z b/pwiz_aux/msrc/utility/vendor_api_Thermo.7z index 602f0fc157b..c1edf8ecbdd 100644 Binary files a/pwiz_aux/msrc/utility/vendor_api_Thermo.7z and b/pwiz_aux/msrc/utility/vendor_api_Thermo.7z differ diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/BumberDash.csproj b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/BumberDash.csproj index 47a94e9b30a..b240222c2ab 100644 --- a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/BumberDash.csproj +++ b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/BumberDash.csproj @@ -10,7 +10,7 @@ Properties BumberDash BumberDash - v4.7.2 + v4.8 512 BumberDash.Program false diff --git a/pwiz_tools/Bumbershoot/bumberdash/CustomDataSourceDialog/CustomDataSourceDialog.csproj b/pwiz_tools/Bumbershoot/bumberdash/CustomDataSourceDialog/CustomDataSourceDialog.csproj index 2ba32c78ff4..e83812dbfe2 100644 --- a/pwiz_tools/Bumbershoot/bumberdash/CustomDataSourceDialog/CustomDataSourceDialog.csproj +++ b/pwiz_tools/Bumbershoot/bumberdash/CustomDataSourceDialog/CustomDataSourceDialog.csproj @@ -10,7 +10,7 @@ Properties CustomDataSourceDialog CustomDataSourceDialog - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Bumbershoot/bumberdash/Deploy/SetupDeployProject.csproj b/pwiz_tools/Bumbershoot/bumberdash/Deploy/SetupDeployProject.csproj index 7971f53d48e..062d595c8c9 100644 --- a/pwiz_tools/Bumbershoot/bumberdash/Deploy/SetupDeployProject.csproj +++ b/pwiz_tools/Bumbershoot/bumberdash/Deploy/SetupDeployProject.csproj @@ -10,7 +10,7 @@ Properties SetupDeployProject SetupDeployProject - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Bumbershoot/bumberdash/Tests/Tests.csproj b/pwiz_tools/Bumbershoot/bumberdash/Tests/Tests.csproj index 3f0826cba4f..dbaccae422b 100644 --- a/pwiz_tools/Bumbershoot/bumberdash/Tests/Tests.csproj +++ b/pwiz_tools/Bumbershoot/bumberdash/Tests/Tests.csproj @@ -10,7 +10,7 @@ Properties Tests Tests - v4.7.2 + v4.8 512 {3AC096D0-A1C2-E12C-1390-A8335801FDAB};{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC} diff --git a/pwiz_tools/Bumbershoot/greazy/GUI/Greazy.csproj b/pwiz_tools/Bumbershoot/greazy/GUI/Greazy.csproj index 3b862ae6e6e..5ddfdfe03cc 100644 --- a/pwiz_tools/Bumbershoot/greazy/GUI/Greazy.csproj +++ b/pwiz_tools/Bumbershoot/greazy/GUI/Greazy.csproj @@ -10,7 +10,7 @@ Properties Greazy GreazyGUI - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Bumbershoot/greazy/GUI/app.config b/pwiz_tools/Bumbershoot/greazy/GUI/app.config index 312bb3f26fc..3e0e37cfc8c 100644 --- a/pwiz_tools/Bumbershoot/greazy/GUI/app.config +++ b/pwiz_tools/Bumbershoot/greazy/GUI/app.config @@ -1,3 +1,3 @@ - + diff --git a/pwiz_tools/Bumbershoot/idpicker/Controls/Controls.csproj b/pwiz_tools/Bumbershoot/idpicker/Controls/Controls.csproj index 5f1b151602e..c7ec8f3976b 100644 --- a/pwiz_tools/Bumbershoot/idpicker/Controls/Controls.csproj +++ b/pwiz_tools/Bumbershoot/idpicker/Controls/Controls.csproj @@ -10,7 +10,7 @@ Properties IDPicker.Controls IDPicker.Controls - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Bumbershoot/idpicker/CustomDataSourceDialog/CustomDataSourceDialog.csproj b/pwiz_tools/Bumbershoot/idpicker/CustomDataSourceDialog/CustomDataSourceDialog.csproj index cd4120fe994..bb19e1349a6 100644 --- a/pwiz_tools/Bumbershoot/idpicker/CustomDataSourceDialog/CustomDataSourceDialog.csproj +++ b/pwiz_tools/Bumbershoot/idpicker/CustomDataSourceDialog/CustomDataSourceDialog.csproj @@ -10,7 +10,7 @@ Properties CustomDataSourceDialog CustomDataSourceDialog - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Bumbershoot/idpicker/DefaultAppDomainManager/DefaultAppDomainManager.csproj b/pwiz_tools/Bumbershoot/idpicker/DefaultAppDomainManager/DefaultAppDomainManager.csproj index 2c5eac13eb8..b54b7ec83dc 100644 --- a/pwiz_tools/Bumbershoot/idpicker/DefaultAppDomainManager/DefaultAppDomainManager.csproj +++ b/pwiz_tools/Bumbershoot/idpicker/DefaultAppDomainManager/DefaultAppDomainManager.csproj @@ -9,7 +9,7 @@ Properties DefaultAppDomainManager DefaultAppDomainManager - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Bumbershoot/idpicker/Deploy/SetupDeployProject.csproj b/pwiz_tools/Bumbershoot/idpicker/Deploy/SetupDeployProject.csproj index e45886c4fa9..eebcab6106e 100644 --- a/pwiz_tools/Bumbershoot/idpicker/Deploy/SetupDeployProject.csproj +++ b/pwiz_tools/Bumbershoot/idpicker/Deploy/SetupDeployProject.csproj @@ -10,7 +10,7 @@ Properties SetupDeployProject SetupDeployProject - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Bumbershoot/idpicker/IDPicker.csproj b/pwiz_tools/Bumbershoot/idpicker/IDPicker.csproj index 468d1714d12..a5b2f87a153 100644 --- a/pwiz_tools/Bumbershoot/idpicker/IDPicker.csproj +++ b/pwiz_tools/Bumbershoot/idpicker/IDPicker.csproj @@ -10,7 +10,7 @@ Properties IDPicker IDPicker - v4.7.2 + v4.8 512 false IDPicker.Program diff --git a/pwiz_tools/Bumbershoot/idpicker/Model/Model.csproj b/pwiz_tools/Bumbershoot/idpicker/Model/Model.csproj index b8b3e36611a..8eeae61ad37 100644 --- a/pwiz_tools/Bumbershoot/idpicker/Model/Model.csproj +++ b/pwiz_tools/Bumbershoot/idpicker/Model/Model.csproj @@ -10,7 +10,7 @@ Properties IDPicker.DataModel IDPicker.DataModel - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Bumbershoot/idpicker/PureControls/PureControls.csproj b/pwiz_tools/Bumbershoot/idpicker/PureControls/PureControls.csproj index 0458eb308b1..139ccd9fb64 100644 --- a/pwiz_tools/Bumbershoot/idpicker/PureControls/PureControls.csproj +++ b/pwiz_tools/Bumbershoot/idpicker/PureControls/PureControls.csproj @@ -9,7 +9,7 @@ Properties PureControls PureControls - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Bumbershoot/idpicker/Test/Test.csproj b/pwiz_tools/Bumbershoot/idpicker/Test/Test.csproj index 51c53488ec5..73ffdf9902d 100644 --- a/pwiz_tools/Bumbershoot/idpicker/Test/Test.csproj +++ b/pwiz_tools/Bumbershoot/idpicker/Test/Test.csproj @@ -10,7 +10,7 @@ Properties Test Test - v4.7.2 + v4.8 512 {3AC096D0-A1C2-E12C-1390-A8335801FDAB};{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC} diff --git a/pwiz_tools/Bumbershoot/idpicker/Util/STL_Containers/STL_Containers.csproj b/pwiz_tools/Bumbershoot/idpicker/Util/STL_Containers/STL_Containers.csproj index 949cb0fea02..ebd810ae650 100644 --- a/pwiz_tools/Bumbershoot/idpicker/Util/STL_Containers/STL_Containers.csproj +++ b/pwiz_tools/Bumbershoot/idpicker/Util/STL_Containers/STL_Containers.csproj @@ -15,7 +15,7 @@ 3.5 - v4.7.2 + v4.8 publish\ diff --git a/pwiz_tools/Bumbershoot/idpicker/Util/Util.csproj b/pwiz_tools/Bumbershoot/idpicker/Util/Util.csproj index 7fc6589771a..63c931e447d 100644 --- a/pwiz_tools/Bumbershoot/idpicker/Util/Util.csproj +++ b/pwiz_tools/Bumbershoot/idpicker/Util/Util.csproj @@ -10,7 +10,7 @@ Properties IDPicker IDPicker.Util - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Bumbershoot/scanranker/GUI/IonMatcher/IonMatcher.csproj b/pwiz_tools/Bumbershoot/scanranker/GUI/IonMatcher/IonMatcher.csproj index 8ffd934bbc1..0c5d0588cb7 100644 --- a/pwiz_tools/Bumbershoot/scanranker/GUI/IonMatcher/IonMatcher.csproj +++ b/pwiz_tools/Bumbershoot/scanranker/GUI/IonMatcher/IonMatcher.csproj @@ -10,7 +10,7 @@ Properties IonMatcher IonMatcher - v4.7.2 + v4.8 512 publish\ true diff --git a/pwiz_tools/Bumbershoot/scanranker/GUI/ScanRanker.csproj b/pwiz_tools/Bumbershoot/scanranker/GUI/ScanRanker.csproj index d8fcb172770..23f2d3eccc2 100644 --- a/pwiz_tools/Bumbershoot/scanranker/GUI/ScanRanker.csproj +++ b/pwiz_tools/Bumbershoot/scanranker/GUI/ScanRanker.csproj @@ -10,7 +10,7 @@ Properties ScanRanker ScanRanker - v4.7.2 + v4.8 512 down.ico false diff --git a/pwiz_tools/MSConvertGUI/CustomDataSourceDialog/CustomDataSourceDialog.csproj b/pwiz_tools/MSConvertGUI/CustomDataSourceDialog/CustomDataSourceDialog.csproj index 05f95110967..0115b334a52 100644 --- a/pwiz_tools/MSConvertGUI/CustomDataSourceDialog/CustomDataSourceDialog.csproj +++ b/pwiz_tools/MSConvertGUI/CustomDataSourceDialog/CustomDataSourceDialog.csproj @@ -10,7 +10,7 @@ Properties CustomDataSourceDialog CustomDataSourceDialog - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/MSConvertGUI/CustomDataSourceDialog/app.config b/pwiz_tools/MSConvertGUI/CustomDataSourceDialog/app.config index 1b63797b93a..b1d9068847b 100644 --- a/pwiz_tools/MSConvertGUI/CustomDataSourceDialog/app.config +++ b/pwiz_tools/MSConvertGUI/CustomDataSourceDialog/app.config @@ -12,4 +12,4 @@ - + diff --git a/pwiz_tools/MSConvertGUI/MSConvertGUI.csproj b/pwiz_tools/MSConvertGUI/MSConvertGUI.csproj index 90628cdb003..5a5adc792b8 100644 --- a/pwiz_tools/MSConvertGUI/MSConvertGUI.csproj +++ b/pwiz_tools/MSConvertGUI/MSConvertGUI.csproj @@ -10,7 +10,7 @@ Properties MSConvertGUI MSConvertGUI - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/MSConvertGUI/Test/Test.csproj b/pwiz_tools/MSConvertGUI/Test/Test.csproj index cdf60ad7291..dcbe3adcd26 100644 --- a/pwiz_tools/MSConvertGUI/Test/Test.csproj +++ b/pwiz_tools/MSConvertGUI/Test/Test.csproj @@ -10,7 +10,7 @@ Properties Test MSConvertGUITest - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/MSConvertGUI/Test/app.config b/pwiz_tools/MSConvertGUI/Test/app.config index 5a18fdecebe..36a8cea17d1 100644 --- a/pwiz_tools/MSConvertGUI/Test/app.config +++ b/pwiz_tools/MSConvertGUI/Test/app.config @@ -8,11 +8,11 @@ - + - + diff --git a/pwiz_tools/MSConvertGUI/TestConnected/TestConnected.csproj b/pwiz_tools/MSConvertGUI/TestConnected/TestConnected.csproj index 1070ce9855d..85fb0bf7ecb 100644 --- a/pwiz_tools/MSConvertGUI/TestConnected/TestConnected.csproj +++ b/pwiz_tools/MSConvertGUI/TestConnected/TestConnected.csproj @@ -8,7 +8,7 @@ Properties MSConvertGUI.TestConnected MSConvertGUI.TestConnected - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/MSConvertGUI/TestConnected/app.config b/pwiz_tools/MSConvertGUI/TestConnected/app.config index 5a18fdecebe..36a8cea17d1 100644 --- a/pwiz_tools/MSConvertGUI/TestConnected/app.config +++ b/pwiz_tools/MSConvertGUI/TestConnected/app.config @@ -8,11 +8,11 @@ - + - + diff --git a/pwiz_tools/SeeMS/seems.csproj b/pwiz_tools/SeeMS/seems.csproj index 048e7356422..e9ea4b57d30 100644 --- a/pwiz_tools/SeeMS/seems.csproj +++ b/pwiz_tools/SeeMS/seems.csproj @@ -11,7 +11,7 @@ seems seems Misc\SpectrumIcon.ico - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Shared/BiblioSpec/BiblioSpec.csproj b/pwiz_tools/Shared/BiblioSpec/BiblioSpec.csproj index 23e66e6e8bd..94a42f1fd25 100644 --- a/pwiz_tools/Shared/BiblioSpec/BiblioSpec.csproj +++ b/pwiz_tools/Shared/BiblioSpec/BiblioSpec.csproj @@ -10,7 +10,7 @@ Properties pwiz.BiblioSpec BiblioSpec - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Shared/BindingRedirectGenerator/App.config b/pwiz_tools/Shared/BindingRedirectGenerator/App.config index 20939707c81..033746a4a20 100644 --- a/pwiz_tools/Shared/BindingRedirectGenerator/App.config +++ b/pwiz_tools/Shared/BindingRedirectGenerator/App.config @@ -1,6 +1,6 @@ - + \ No newline at end of file diff --git a/pwiz_tools/Shared/BindingRedirectGenerator/BindingRedirectGenerator.csproj b/pwiz_tools/Shared/BindingRedirectGenerator/BindingRedirectGenerator.csproj index ba9e7dab554..410a0f0198d 100644 --- a/pwiz_tools/Shared/BindingRedirectGenerator/BindingRedirectGenerator.csproj +++ b/pwiz_tools/Shared/BindingRedirectGenerator/BindingRedirectGenerator.csproj @@ -8,7 +8,7 @@ Exe BindingRedirectGenerator BindingRedirectGenerator - v4.7.2 + v4.8 512 true true diff --git a/pwiz_tools/Shared/Common/Common.csproj b/pwiz_tools/Shared/Common/Common.csproj index 58f1ed5c0d0..388d81d3fbb 100644 --- a/pwiz_tools/Shared/Common/Common.csproj +++ b/pwiz_tools/Shared/Common/Common.csproj @@ -10,7 +10,7 @@ Properties pwiz.Common pwiz.Common - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Shared/Common/CommonUtil.csproj b/pwiz_tools/Shared/Common/CommonUtil.csproj index 44324434fb1..22db221d9cf 100644 --- a/pwiz_tools/Shared/Common/CommonUtil.csproj +++ b/pwiz_tools/Shared/Common/CommonUtil.csproj @@ -10,7 +10,7 @@ Properties pwiz.Common pwiz.CommonUtil - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Shared/CommonFileDialogs/CommonFileDialogs.csproj b/pwiz_tools/Shared/CommonFileDialogs/CommonFileDialogs.csproj index 4d81c91533b..954ce267ddf 100644 --- a/pwiz_tools/Shared/CommonFileDialogs/CommonFileDialogs.csproj +++ b/pwiz_tools/Shared/CommonFileDialogs/CommonFileDialogs.csproj @@ -9,7 +9,7 @@ Properties pwiz.CommonFileDialogs pwiz.CommonFileDialogs - v4.7.2 + v4.8 512 true diff --git a/pwiz_tools/Shared/CommonMsData/CommonMsData.csproj b/pwiz_tools/Shared/CommonMsData/CommonMsData.csproj index ec6855f03fc..ebd7734e432 100644 --- a/pwiz_tools/Shared/CommonMsData/CommonMsData.csproj +++ b/pwiz_tools/Shared/CommonMsData/CommonMsData.csproj @@ -9,7 +9,7 @@ Properties pwiz.CommonMsData pwiz.CommonMsData - v4.7.2 + v4.8 512 true win;win-x64 diff --git a/pwiz_tools/Shared/CommonUtil/CommonUtil.csproj b/pwiz_tools/Shared/CommonUtil/CommonUtil.csproj index 1efca2489ec..2005f0460d5 100644 --- a/pwiz_tools/Shared/CommonUtil/CommonUtil.csproj +++ b/pwiz_tools/Shared/CommonUtil/CommonUtil.csproj @@ -10,7 +10,7 @@ Properties pwiz.Common pwiz.CommonUtil - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Shared/Lib/System.Buffers.dll b/pwiz_tools/Shared/Lib/System.Buffers.dll index f2d83c51416..67a31fbae49 100644 Binary files a/pwiz_tools/Shared/Lib/System.Buffers.dll and b/pwiz_tools/Shared/Lib/System.Buffers.dll differ diff --git a/pwiz_tools/Shared/Lib/System.Memory.dll b/pwiz_tools/Shared/Lib/System.Memory.dll index 46171997966..9b4f82402a0 100644 Binary files a/pwiz_tools/Shared/Lib/System.Memory.dll and b/pwiz_tools/Shared/Lib/System.Memory.dll differ diff --git a/pwiz_tools/Shared/Lib/System.Numerics.Vectors.dll b/pwiz_tools/Shared/Lib/System.Numerics.Vectors.dll index 08659724d4f..95a6d990d75 100644 Binary files a/pwiz_tools/Shared/Lib/System.Numerics.Vectors.dll and b/pwiz_tools/Shared/Lib/System.Numerics.Vectors.dll differ diff --git a/pwiz_tools/Shared/Lib/System.Runtime.CompilerServices.Unsafe.dll b/pwiz_tools/Shared/Lib/System.Runtime.CompilerServices.Unsafe.dll index c5ba4e4047a..77956847c34 100644 Binary files a/pwiz_tools/Shared/Lib/System.Runtime.CompilerServices.Unsafe.dll and b/pwiz_tools/Shared/Lib/System.Runtime.CompilerServices.Unsafe.dll differ diff --git a/pwiz_tools/Shared/MSGraph/MSGraph.csproj b/pwiz_tools/Shared/MSGraph/MSGraph.csproj index 0cc43d1abc2..4ba3eace69b 100644 --- a/pwiz_tools/Shared/MSGraph/MSGraph.csproj +++ b/pwiz_tools/Shared/MSGraph/MSGraph.csproj @@ -15,7 +15,7 @@ 3.5 - v4.7.2 + v4.8 diff --git a/pwiz_tools/Shared/PanoramaClient/App.config b/pwiz_tools/Shared/PanoramaClient/App.config index be965e5029b..07ce765697f 100644 --- a/pwiz_tools/Shared/PanoramaClient/App.config +++ b/pwiz_tools/Shared/PanoramaClient/App.config @@ -6,7 +6,7 @@ - + diff --git a/pwiz_tools/Shared/PanoramaClient/PanoramaClient.csproj b/pwiz_tools/Shared/PanoramaClient/PanoramaClient.csproj index 810ee5f9faf..b0851bcd602 100644 --- a/pwiz_tools/Shared/PanoramaClient/PanoramaClient.csproj +++ b/pwiz_tools/Shared/PanoramaClient/PanoramaClient.csproj @@ -8,7 +8,7 @@ Library pwiz.PanoramaClient PanoramaClient - v4.7.2 + v4.8 512 true true diff --git a/pwiz_tools/Shared/ProteomeDb/ProteomeDb.csproj b/pwiz_tools/Shared/ProteomeDb/ProteomeDb.csproj index a7f35564c8a..0760dc62e69 100644 --- a/pwiz_tools/Shared/ProteomeDb/ProteomeDb.csproj +++ b/pwiz_tools/Shared/ProteomeDb/ProteomeDb.csproj @@ -10,7 +10,7 @@ Properties pwiz.ProteomeDatabase ProteomeDb - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Shared/ProteowizardWrapper/ProteowizardWrapper.csproj b/pwiz_tools/Shared/ProteowizardWrapper/ProteowizardWrapper.csproj index 649d01fabb3..6e687672e03 100644 --- a/pwiz_tools/Shared/ProteowizardWrapper/ProteowizardWrapper.csproj +++ b/pwiz_tools/Shared/ProteowizardWrapper/ProteowizardWrapper.csproj @@ -10,7 +10,7 @@ Properties pwiz.ProteowizardWrapper ProteowizardWrapper - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Shared/zedgraph/ZedGraph.csproj b/pwiz_tools/Shared/zedgraph/ZedGraph.csproj index ed4285ad4da..4560df64fd6 100644 --- a/pwiz_tools/Shared/zedgraph/ZedGraph.csproj +++ b/pwiz_tools/Shared/zedgraph/ZedGraph.csproj @@ -17,7 +17,7 @@ true ZedGraph.snk - v4.7.2 + v4.8 diff --git a/pwiz_tools/Skyline/BullseyeSharp/BullseyeSharp.csproj b/pwiz_tools/Skyline/BullseyeSharp/BullseyeSharp.csproj index b425cbdf166..7f92b6bfc03 100644 --- a/pwiz_tools/Skyline/BullseyeSharp/BullseyeSharp.csproj +++ b/pwiz_tools/Skyline/BullseyeSharp/BullseyeSharp.csproj @@ -21,7 +21,7 @@ {4F4C2045-4C86-46F2-A297-C05FC4A48A15} - v4.7.2 + v4.8 diff --git a/pwiz_tools/Skyline/CommonTest/CommonTest.csproj b/pwiz_tools/Skyline/CommonTest/CommonTest.csproj index ec7ec2c447c..b98d472b84f 100644 --- a/pwiz_tools/Skyline/CommonTest/CommonTest.csproj +++ b/pwiz_tools/Skyline/CommonTest/CommonTest.csproj @@ -11,7 +11,7 @@ Properties CommonTest CommonTest - v4.7.2 + v4.8 512 {3AC096D0-A1C2-E12C-1390-A8335801FDAB};{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC} diff --git a/pwiz_tools/Skyline/Executables/AutoQC/AutoQC/AutoQC.csproj b/pwiz_tools/Skyline/Executables/AutoQC/AutoQC/AutoQC.csproj index 62683c8bec6..8389443758d 100644 --- a/pwiz_tools/Skyline/Executables/AutoQC/AutoQC/AutoQC.csproj +++ b/pwiz_tools/Skyline/Executables/AutoQC/AutoQC/AutoQC.csproj @@ -9,7 +9,7 @@ Properties AutoQC AutoQC - v4.7.2 + v4.8 512 true diff --git a/pwiz_tools/Skyline/Executables/AutoQC/AutoQCStarter/App.config b/pwiz_tools/Skyline/Executables/AutoQC/AutoQCStarter/App.config index 20939707c81..033746a4a20 100644 --- a/pwiz_tools/Skyline/Executables/AutoQC/AutoQCStarter/App.config +++ b/pwiz_tools/Skyline/Executables/AutoQC/AutoQCStarter/App.config @@ -1,6 +1,6 @@ - + \ No newline at end of file diff --git a/pwiz_tools/Skyline/Executables/AutoQC/AutoQCStarter/AutoQCStarter.csproj b/pwiz_tools/Skyline/Executables/AutoQC/AutoQCStarter/AutoQCStarter.csproj index f15ad6cbd2e..a4e5c996bc9 100644 --- a/pwiz_tools/Skyline/Executables/AutoQC/AutoQCStarter/AutoQCStarter.csproj +++ b/pwiz_tools/Skyline/Executables/AutoQC/AutoQCStarter/AutoQCStarter.csproj @@ -8,7 +8,7 @@ WinExe AutoQCStarter AutoQCStarter - v4.7.2 + v4.8 512 true true diff --git a/pwiz_tools/Skyline/Executables/AutoQC/AutoQCTest/AutoQCTest.csproj b/pwiz_tools/Skyline/Executables/AutoQC/AutoQCTest/AutoQCTest.csproj index 07dd3d0a1e6..691f483112e 100644 --- a/pwiz_tools/Skyline/Executables/AutoQC/AutoQCTest/AutoQCTest.csproj +++ b/pwiz_tools/Skyline/Executables/AutoQC/AutoQCTest/AutoQCTest.csproj @@ -8,7 +8,7 @@ Properties AutoQCTest AutoQCTest - v4.7.2 + v4.8 512 {3AC096D0-A1C2-E12C-1390-A8335801FDAB};{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC} 10.0 diff --git a/pwiz_tools/Skyline/Executables/BuildMethod/BuildAgilentMH12Method/App.config b/pwiz_tools/Skyline/Executables/BuildMethod/BuildAgilentMH12Method/App.config index ecdcf8a54da..4bfa0056185 100644 --- a/pwiz_tools/Skyline/Executables/BuildMethod/BuildAgilentMH12Method/App.config +++ b/pwiz_tools/Skyline/Executables/BuildMethod/BuildAgilentMH12Method/App.config @@ -1,6 +1,6 @@ - + diff --git a/pwiz_tools/Skyline/Executables/BuildMethod/BuildAgilentMH12Method/BuildAgilentMH12Method.csproj b/pwiz_tools/Skyline/Executables/BuildMethod/BuildAgilentMH12Method/BuildAgilentMH12Method.csproj index a9fa153fea7..ba416141261 100644 --- a/pwiz_tools/Skyline/Executables/BuildMethod/BuildAgilentMH12Method/BuildAgilentMH12Method.csproj +++ b/pwiz_tools/Skyline/Executables/BuildMethod/BuildAgilentMH12Method/BuildAgilentMH12Method.csproj @@ -8,7 +8,7 @@ Exe BuildAgilentMH12Method BuildAgilentMH12Method - v4.7.2 + v4.8 512 true true diff --git a/pwiz_tools/Skyline/Executables/BuildMethod/BuildAgilentMethod/BuildAgilentMethod.csproj b/pwiz_tools/Skyline/Executables/BuildMethod/BuildAgilentMethod/BuildAgilentMethod.csproj index d0efbdf08c1..e6600f9a50b 100644 --- a/pwiz_tools/Skyline/Executables/BuildMethod/BuildAgilentMethod/BuildAgilentMethod.csproj +++ b/pwiz_tools/Skyline/Executables/BuildMethod/BuildAgilentMethod/BuildAgilentMethod.csproj @@ -10,7 +10,7 @@ Properties BuildAgilentMethod BuildAgilentMethod - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Skyline/Executables/BuildMethod/BuildAgilentMethod/app.config b/pwiz_tools/Skyline/Executables/BuildMethod/BuildAgilentMethod/app.config index 312bb3f26fc..3e0e37cfc8c 100644 --- a/pwiz_tools/Skyline/Executables/BuildMethod/BuildAgilentMethod/app.config +++ b/pwiz_tools/Skyline/Executables/BuildMethod/BuildAgilentMethod/app.config @@ -1,3 +1,3 @@ - + diff --git a/pwiz_tools/Skyline/Executables/BuildMethod/BuildAnalystFullScanMethod/BuildAnalystFullScanMethod.csproj b/pwiz_tools/Skyline/Executables/BuildMethod/BuildAnalystFullScanMethod/BuildAnalystFullScanMethod.csproj index bf866900180..d3c0c3e81f0 100644 --- a/pwiz_tools/Skyline/Executables/BuildMethod/BuildAnalystFullScanMethod/BuildAnalystFullScanMethod.csproj +++ b/pwiz_tools/Skyline/Executables/BuildMethod/BuildAnalystFullScanMethod/BuildAnalystFullScanMethod.csproj @@ -10,7 +10,7 @@ Properties BuildAnalystFullScanMethod BuildAnalystFullScanMethod - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Skyline/Executables/BuildMethod/BuildAnalystFullScanMethod/app.config b/pwiz_tools/Skyline/Executables/BuildMethod/BuildAnalystFullScanMethod/app.config index 312bb3f26fc..3e0e37cfc8c 100644 --- a/pwiz_tools/Skyline/Executables/BuildMethod/BuildAnalystFullScanMethod/app.config +++ b/pwiz_tools/Skyline/Executables/BuildMethod/BuildAnalystFullScanMethod/app.config @@ -1,3 +1,3 @@ - + diff --git a/pwiz_tools/Skyline/Executables/BuildMethod/BuildAnalystMethod/BuildAnalystMethod.csproj b/pwiz_tools/Skyline/Executables/BuildMethod/BuildAnalystMethod/BuildAnalystMethod.csproj index d1b08682d2e..50a13d3b93f 100644 --- a/pwiz_tools/Skyline/Executables/BuildMethod/BuildAnalystMethod/BuildAnalystMethod.csproj +++ b/pwiz_tools/Skyline/Executables/BuildMethod/BuildAnalystMethod/BuildAnalystMethod.csproj @@ -10,7 +10,7 @@ Properties BuildAnalystMethod BuildAnalystMethod - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Skyline/Executables/BuildMethod/BuildBrukerMethod/BuildBrukerMethod.csproj b/pwiz_tools/Skyline/Executables/BuildMethod/BuildBrukerMethod/BuildBrukerMethod.csproj index bdfafd826b9..fa35d4a0b33 100644 --- a/pwiz_tools/Skyline/Executables/BuildMethod/BuildBrukerMethod/BuildBrukerMethod.csproj +++ b/pwiz_tools/Skyline/Executables/BuildMethod/BuildBrukerMethod/BuildBrukerMethod.csproj @@ -10,7 +10,7 @@ Properties BuildBrukerMethod BuildBrukerMethod - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Skyline/Executables/BuildMethod/BuildBrukerMethod/app.config b/pwiz_tools/Skyline/Executables/BuildMethod/BuildBrukerMethod/app.config index 9d151822aa0..99dca7597b1 100644 --- a/pwiz_tools/Skyline/Executables/BuildMethod/BuildBrukerMethod/app.config +++ b/pwiz_tools/Skyline/Executables/BuildMethod/BuildBrukerMethod/app.config @@ -1,3 +1,3 @@ - + diff --git a/pwiz_tools/Skyline/Executables/BuildMethod/BuildQTRAPMethod/BuildQTRAPMethod.csproj b/pwiz_tools/Skyline/Executables/BuildMethod/BuildQTRAPMethod/BuildQTRAPMethod.csproj index f80783be48d..3fa8a82cce0 100644 --- a/pwiz_tools/Skyline/Executables/BuildMethod/BuildQTRAPMethod/BuildQTRAPMethod.csproj +++ b/pwiz_tools/Skyline/Executables/BuildMethod/BuildQTRAPMethod/BuildQTRAPMethod.csproj @@ -10,7 +10,7 @@ Properties BuildQTRAPMethod BuildQTRAPMethod - v4.7.2 + v4.8 512 publish\ true diff --git a/pwiz_tools/Skyline/Executables/BuildMethod/BuildQTRAPMethod/app.config b/pwiz_tools/Skyline/Executables/BuildMethod/BuildQTRAPMethod/app.config index 312bb3f26fc..3e0e37cfc8c 100644 --- a/pwiz_tools/Skyline/Executables/BuildMethod/BuildQTRAPMethod/app.config +++ b/pwiz_tools/Skyline/Executables/BuildMethod/BuildQTRAPMethod/app.config @@ -1,3 +1,3 @@ - + diff --git a/pwiz_tools/Skyline/Executables/BuildMethod/BuildSciexMethod/App.config b/pwiz_tools/Skyline/Executables/BuildMethod/BuildSciexMethod/App.config index 20939707c81..033746a4a20 100644 --- a/pwiz_tools/Skyline/Executables/BuildMethod/BuildSciexMethod/App.config +++ b/pwiz_tools/Skyline/Executables/BuildMethod/BuildSciexMethod/App.config @@ -1,6 +1,6 @@ - + \ No newline at end of file diff --git a/pwiz_tools/Skyline/Executables/BuildMethod/BuildSciexMethod/BuildSciexMethod.csproj b/pwiz_tools/Skyline/Executables/BuildMethod/BuildSciexMethod/BuildSciexMethod.csproj index 5a9da513f20..53f569ffff6 100644 --- a/pwiz_tools/Skyline/Executables/BuildMethod/BuildSciexMethod/BuildSciexMethod.csproj +++ b/pwiz_tools/Skyline/Executables/BuildMethod/BuildSciexMethod/BuildSciexMethod.csproj @@ -8,7 +8,7 @@ Exe BuildSciexMethod BuildSciexMethod - v4.7.2 + v4.8 512 true true diff --git a/pwiz_tools/Skyline/Executables/BuildMethod/BuildThermoMethod/BuildThermoMethod.csproj b/pwiz_tools/Skyline/Executables/BuildMethod/BuildThermoMethod/BuildThermoMethod.csproj index 69bbeeac258..b117ab49327 100644 --- a/pwiz_tools/Skyline/Executables/BuildMethod/BuildThermoMethod/BuildThermoMethod.csproj +++ b/pwiz_tools/Skyline/Executables/BuildMethod/BuildThermoMethod/BuildThermoMethod.csproj @@ -10,7 +10,7 @@ Properties BuildThermoMethod BuildThermoMethod - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Skyline/Executables/BuildMethod/BuildThermoMethod/app.config b/pwiz_tools/Skyline/Executables/BuildMethod/BuildThermoMethod/app.config index 312bb3f26fc..3e0e37cfc8c 100644 --- a/pwiz_tools/Skyline/Executables/BuildMethod/BuildThermoMethod/app.config +++ b/pwiz_tools/Skyline/Executables/BuildMethod/BuildThermoMethod/app.config @@ -1,3 +1,3 @@ - + diff --git a/pwiz_tools/Skyline/Executables/DevTools/AssortResources/App.config b/pwiz_tools/Skyline/Executables/DevTools/AssortResources/App.config index 20939707c81..033746a4a20 100644 --- a/pwiz_tools/Skyline/Executables/DevTools/AssortResources/App.config +++ b/pwiz_tools/Skyline/Executables/DevTools/AssortResources/App.config @@ -1,6 +1,6 @@ - + \ No newline at end of file diff --git a/pwiz_tools/Skyline/Executables/DevTools/AssortResources/AssortResources.csproj b/pwiz_tools/Skyline/Executables/DevTools/AssortResources/AssortResources.csproj index 3d3515c4a4d..dc484a59569 100644 --- a/pwiz_tools/Skyline/Executables/DevTools/AssortResources/AssortResources.csproj +++ b/pwiz_tools/Skyline/Executables/DevTools/AssortResources/AssortResources.csproj @@ -8,7 +8,7 @@ Exe AssortResources AssortResources - v4.7.2 + v4.8 512 true true diff --git a/pwiz_tools/Skyline/Executables/DevTools/ImageComparer/App.config b/pwiz_tools/Skyline/Executables/DevTools/ImageComparer/App.config index 5e138d807ce..707c2896e53 100644 --- a/pwiz_tools/Skyline/Executables/DevTools/ImageComparer/App.config +++ b/pwiz_tools/Skyline/Executables/DevTools/ImageComparer/App.config @@ -6,7 +6,7 @@ - + diff --git a/pwiz_tools/Skyline/Executables/DevTools/ImageComparer/ImageComparer.csproj b/pwiz_tools/Skyline/Executables/DevTools/ImageComparer/ImageComparer.csproj index 83a1c68218e..74d6500e0ba 100644 --- a/pwiz_tools/Skyline/Executables/DevTools/ImageComparer/ImageComparer.csproj +++ b/pwiz_tools/Skyline/Executables/DevTools/ImageComparer/ImageComparer.csproj @@ -8,7 +8,7 @@ WinExe ImageComparer ImageComparer - v4.7.2 + v4.8 512 true true diff --git a/pwiz_tools/Skyline/Executables/DevTools/SortRESX/SortRESX/SortRESX.csproj b/pwiz_tools/Skyline/Executables/DevTools/SortRESX/SortRESX/SortRESX.csproj index a1302dfe7fb..47b7e33412d 100644 --- a/pwiz_tools/Skyline/Executables/DevTools/SortRESX/SortRESX/SortRESX.csproj +++ b/pwiz_tools/Skyline/Executables/DevTools/SortRESX/SortRESX/SortRESX.csproj @@ -10,7 +10,7 @@ Properties SortRESX SortRESX - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Skyline/Executables/DevTools/SortRESX/SortRESX/app.config b/pwiz_tools/Skyline/Executables/DevTools/SortRESX/SortRESX/app.config index 312bb3f26fc..3e0e37cfc8c 100644 --- a/pwiz_tools/Skyline/Executables/DevTools/SortRESX/SortRESX/app.config +++ b/pwiz_tools/Skyline/Executables/DevTools/SortRESX/SortRESX/app.config @@ -1,3 +1,3 @@ - + diff --git a/pwiz_tools/Skyline/Executables/DevTools/TutorialLocalization/TutorialLocalization/App.config b/pwiz_tools/Skyline/Executables/DevTools/TutorialLocalization/TutorialLocalization/App.config index 20939707c81..033746a4a20 100644 --- a/pwiz_tools/Skyline/Executables/DevTools/TutorialLocalization/TutorialLocalization/App.config +++ b/pwiz_tools/Skyline/Executables/DevTools/TutorialLocalization/TutorialLocalization/App.config @@ -1,6 +1,6 @@ - + \ No newline at end of file diff --git a/pwiz_tools/Skyline/Executables/DevTools/TutorialLocalization/TutorialLocalization/TutorialLocalization.csproj b/pwiz_tools/Skyline/Executables/DevTools/TutorialLocalization/TutorialLocalization/TutorialLocalization.csproj index 9a39013f194..9a3971a933f 100644 --- a/pwiz_tools/Skyline/Executables/DevTools/TutorialLocalization/TutorialLocalization/TutorialLocalization.csproj +++ b/pwiz_tools/Skyline/Executables/DevTools/TutorialLocalization/TutorialLocalization/TutorialLocalization.csproj @@ -8,7 +8,7 @@ Exe TutorialLocalization TutorialLocalization - v4.7.2 + v4.8 512 true true diff --git a/pwiz_tools/Skyline/Executables/DevTools/UniModCompiler/UniModCompiler.csproj b/pwiz_tools/Skyline/Executables/DevTools/UniModCompiler/UniModCompiler.csproj index a58be596930..2e0821b1430 100644 --- a/pwiz_tools/Skyline/Executables/DevTools/UniModCompiler/UniModCompiler.csproj +++ b/pwiz_tools/Skyline/Executables/DevTools/UniModCompiler/UniModCompiler.csproj @@ -10,7 +10,7 @@ Properties UniModCompiler UniModCompiler - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Skyline/Executables/DevTools/UniModCompiler/app.config b/pwiz_tools/Skyline/Executables/DevTools/UniModCompiler/app.config index 05d8b241fde..2c0f5590f09 100644 --- a/pwiz_tools/Skyline/Executables/DevTools/UniModCompiler/app.config +++ b/pwiz_tools/Skyline/Executables/DevTools/UniModCompiler/app.config @@ -1,3 +1,3 @@ - + diff --git a/pwiz_tools/Skyline/Executables/Installer/SetupDeployProject.csproj b/pwiz_tools/Skyline/Executables/Installer/SetupDeployProject.csproj index dfdf85493fe..449d562cca4 100644 --- a/pwiz_tools/Skyline/Executables/Installer/SetupDeployProject.csproj +++ b/pwiz_tools/Skyline/Executables/Installer/SetupDeployProject.csproj @@ -10,7 +10,7 @@ Properties SetupDeployProject SetupDeployProject - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Skyline/Executables/SharedBatch/LaunchBatch/App.config b/pwiz_tools/Skyline/Executables/SharedBatch/LaunchBatch/App.config index de277144ee4..5ffd8f8ee21 100644 --- a/pwiz_tools/Skyline/Executables/SharedBatch/LaunchBatch/App.config +++ b/pwiz_tools/Skyline/Executables/SharedBatch/LaunchBatch/App.config @@ -1,6 +1,6 @@ - + diff --git a/pwiz_tools/Skyline/Executables/SharedBatch/LaunchBatch/LaunchBatch.csproj b/pwiz_tools/Skyline/Executables/SharedBatch/LaunchBatch/LaunchBatch.csproj index 0b268a72299..402e91329a8 100644 --- a/pwiz_tools/Skyline/Executables/SharedBatch/LaunchBatch/LaunchBatch.csproj +++ b/pwiz_tools/Skyline/Executables/SharedBatch/LaunchBatch/LaunchBatch.csproj @@ -8,7 +8,7 @@ WinExe LaunchBatch LaunchBatch - v4.7.2 + v4.8 512 true true diff --git a/pwiz_tools/Skyline/Executables/SharedBatch/SharedBatch/SharedBatch.csproj b/pwiz_tools/Skyline/Executables/SharedBatch/SharedBatch/SharedBatch.csproj index a572f114d6b..e3e3401d379 100644 --- a/pwiz_tools/Skyline/Executables/SharedBatch/SharedBatch/SharedBatch.csproj +++ b/pwiz_tools/Skyline/Executables/SharedBatch/SharedBatch/SharedBatch.csproj @@ -9,7 +9,7 @@ Properties SharedBatch SharedBatch - v4.7.2 + v4.8 512 true diff --git a/pwiz_tools/Skyline/Executables/SharedBatch/SharedBatch/app.config b/pwiz_tools/Skyline/Executables/SharedBatch/SharedBatch/app.config index 4260ffef9ef..ff9914c685f 100644 --- a/pwiz_tools/Skyline/Executables/SharedBatch/SharedBatch/app.config +++ b/pwiz_tools/Skyline/Executables/SharedBatch/SharedBatch/app.config @@ -30,4 +30,4 @@ - + diff --git a/pwiz_tools/Skyline/Executables/SharedBatch/SharedBatchTest/SharedBatchTest.csproj b/pwiz_tools/Skyline/Executables/SharedBatch/SharedBatchTest/SharedBatchTest.csproj index a669b2b2afb..9da07b21be2 100644 --- a/pwiz_tools/Skyline/Executables/SharedBatch/SharedBatchTest/SharedBatchTest.csproj +++ b/pwiz_tools/Skyline/Executables/SharedBatch/SharedBatchTest/SharedBatchTest.csproj @@ -8,7 +8,7 @@ Properties SharedBatchTest SharedBatchTest - v4.7.2 + v4.8 512 {3AC096D0-A1C2-E12C-1390-A8335801FDAB};{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC} 10.0 diff --git a/pwiz_tools/Skyline/Executables/SkylineBatch/SkylineBatch/SkylineBatch.csproj b/pwiz_tools/Skyline/Executables/SkylineBatch/SkylineBatch/SkylineBatch.csproj index 8a47aa2feda..3f8ff897132 100644 --- a/pwiz_tools/Skyline/Executables/SkylineBatch/SkylineBatch/SkylineBatch.csproj +++ b/pwiz_tools/Skyline/Executables/SkylineBatch/SkylineBatch/SkylineBatch.csproj @@ -9,7 +9,7 @@ Properties SkylineBatch SkylineBatch - v4.7.2 + v4.8 512 true diff --git a/pwiz_tools/Skyline/Executables/SkylineBatch/SkylineBatchTest/SkylineBatchTest.csproj b/pwiz_tools/Skyline/Executables/SkylineBatch/SkylineBatchTest/SkylineBatchTest.csproj index ae502c4ddfc..cf67e537519 100644 --- a/pwiz_tools/Skyline/Executables/SkylineBatch/SkylineBatchTest/SkylineBatchTest.csproj +++ b/pwiz_tools/Skyline/Executables/SkylineBatch/SkylineBatchTest/SkylineBatchTest.csproj @@ -8,7 +8,7 @@ Properties SkylineBatchTest SkylineBatchTest - v4.7.2 + v4.8 512 {3AC096D0-A1C2-E12C-1390-A8335801FDAB};{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC} 10.0 diff --git a/pwiz_tools/Skyline/Executables/SkylineRunner/SkylineRunner.csproj b/pwiz_tools/Skyline/Executables/SkylineRunner/SkylineRunner.csproj index dbd54a6018c..b7343b0e335 100644 --- a/pwiz_tools/Skyline/Executables/SkylineRunner/SkylineRunner.csproj +++ b/pwiz_tools/Skyline/Executables/SkylineRunner/SkylineRunner.csproj @@ -10,7 +10,7 @@ Properties pwiz.SkylineRunner SkylineDailyRunner - v4.7.2 + v4.8 512 B226686C5D57EC6D3C850F6DD0334C32C39A5AAC SkylineRunner_TemporaryKey.pfx diff --git a/pwiz_tools/Skyline/Executables/SkylineRunner/app.config b/pwiz_tools/Skyline/Executables/SkylineRunner/app.config index 312bb3f26fc..3e0e37cfc8c 100644 --- a/pwiz_tools/Skyline/Executables/SkylineRunner/app.config +++ b/pwiz_tools/Skyline/Executables/SkylineRunner/app.config @@ -1,3 +1,3 @@ - + diff --git a/pwiz_tools/Skyline/Executables/Tools/ExampleInteractiveTool/ExampleInteractiveTool.csproj b/pwiz_tools/Skyline/Executables/Tools/ExampleInteractiveTool/ExampleInteractiveTool.csproj index ad894fb4316..371aab69c92 100644 --- a/pwiz_tools/Skyline/Executables/Tools/ExampleInteractiveTool/ExampleInteractiveTool.csproj +++ b/pwiz_tools/Skyline/Executables/Tools/ExampleInteractiveTool/ExampleInteractiveTool.csproj @@ -10,7 +10,7 @@ Properties ExampleInteractiveTool ExampleInteractiveTool - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Skyline/Executables/Tools/MPPExport/src/MPP Export.csproj b/pwiz_tools/Skyline/Executables/Tools/MPPExport/src/MPP Export.csproj index bf7dff8d059..3f1c8ab066a 100644 --- a/pwiz_tools/Skyline/Executables/Tools/MPPExport/src/MPP Export.csproj +++ b/pwiz_tools/Skyline/Executables/Tools/MPPExport/src/MPP Export.csproj @@ -10,7 +10,7 @@ Properties MPP_Export MPPExport - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Skyline/Executables/Tools/MPPExport/src/app.config b/pwiz_tools/Skyline/Executables/Tools/MPPExport/src/app.config index 312bb3f26fc..3e0e37cfc8c 100644 --- a/pwiz_tools/Skyline/Executables/Tools/MPPExport/src/app.config +++ b/pwiz_tools/Skyline/Executables/Tools/MPPExport/src/app.config @@ -1,3 +1,3 @@ - + diff --git a/pwiz_tools/Skyline/Executables/Tools/MSstats/ArgsCollectors/MSStatGroupComparisonUI/MSStatArgCollectors.csproj b/pwiz_tools/Skyline/Executables/Tools/MSstats/ArgsCollectors/MSStatGroupComparisonUI/MSStatArgCollectors.csproj index 6734c25fd77..85e2f1c770f 100644 --- a/pwiz_tools/Skyline/Executables/Tools/MSstats/ArgsCollectors/MSStatGroupComparisonUI/MSStatArgCollectors.csproj +++ b/pwiz_tools/Skyline/Executables/Tools/MSstats/ArgsCollectors/MSStatGroupComparisonUI/MSStatArgCollectors.csproj @@ -10,7 +10,7 @@ Properties MSStatArgsCollector MSStatArgsCollector - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Skyline/Executables/Tools/MSstats/ArgsCollectors/TestHarness/App.config b/pwiz_tools/Skyline/Executables/Tools/MSstats/ArgsCollectors/TestHarness/App.config index 20939707c81..033746a4a20 100644 --- a/pwiz_tools/Skyline/Executables/Tools/MSstats/ArgsCollectors/TestHarness/App.config +++ b/pwiz_tools/Skyline/Executables/Tools/MSstats/ArgsCollectors/TestHarness/App.config @@ -1,6 +1,6 @@ - + \ No newline at end of file diff --git a/pwiz_tools/Skyline/Executables/Tools/MSstats/ArgsCollectors/TestHarness/TestHarness.csproj b/pwiz_tools/Skyline/Executables/Tools/MSstats/ArgsCollectors/TestHarness/TestHarness.csproj index 538fa6dfe35..5d398a3fde0 100644 --- a/pwiz_tools/Skyline/Executables/Tools/MSstats/ArgsCollectors/TestHarness/TestHarness.csproj +++ b/pwiz_tools/Skyline/Executables/Tools/MSstats/ArgsCollectors/TestHarness/TestHarness.csproj @@ -8,7 +8,7 @@ WinExe TestHarness TestHarness - v4.7.2 + v4.8 512 true true diff --git a/pwiz_tools/Skyline/Executables/Tools/SkylineMcp/SkylineAiConnector/SkylineAiConnector.csproj b/pwiz_tools/Skyline/Executables/Tools/SkylineMcp/SkylineAiConnector/SkylineAiConnector.csproj index 45ce98c01cd..5f1d91bf456 100644 --- a/pwiz_tools/Skyline/Executables/Tools/SkylineMcp/SkylineAiConnector/SkylineAiConnector.csproj +++ b/pwiz_tools/Skyline/Executables/Tools/SkylineMcp/SkylineAiConnector/SkylineAiConnector.csproj @@ -2,7 +2,7 @@ WinExe - net472 + net48 SkylineAiConnector SkylineAiConnector latest diff --git a/pwiz_tools/Skyline/Executables/Tools/TFExport/TFExportTool/TFExportTool/TFExportTool.csproj b/pwiz_tools/Skyline/Executables/Tools/TFExport/TFExportTool/TFExportTool/TFExportTool.csproj index bc1bf869865..69fb60a251e 100644 --- a/pwiz_tools/Skyline/Executables/Tools/TFExport/TFExportTool/TFExportTool/TFExportTool.csproj +++ b/pwiz_tools/Skyline/Executables/Tools/TFExport/TFExportTool/TFExportTool/TFExportTool.csproj @@ -9,7 +9,7 @@ Properties TFExportTool TFExportTool - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Skyline/Executables/Tools/TestCommandLineInteractiveTool/App.config b/pwiz_tools/Skyline/Executables/Tools/TestCommandLineInteractiveTool/App.config index 20939707c81..033746a4a20 100644 --- a/pwiz_tools/Skyline/Executables/Tools/TestCommandLineInteractiveTool/App.config +++ b/pwiz_tools/Skyline/Executables/Tools/TestCommandLineInteractiveTool/App.config @@ -1,6 +1,6 @@ - + \ No newline at end of file diff --git a/pwiz_tools/Skyline/Executables/Tools/TestCommandLineInteractiveTool/TestCommandLineInteractiveTool.csproj b/pwiz_tools/Skyline/Executables/Tools/TestCommandLineInteractiveTool/TestCommandLineInteractiveTool.csproj index a70cde354df..66c853cf98b 100644 --- a/pwiz_tools/Skyline/Executables/Tools/TestCommandLineInteractiveTool/TestCommandLineInteractiveTool.csproj +++ b/pwiz_tools/Skyline/Executables/Tools/TestCommandLineInteractiveTool/TestCommandLineInteractiveTool.csproj @@ -8,7 +8,7 @@ Exe TestCommandLineInteractiveTool TestCommandLineInteractiveTool - v4.7.2 + v4.8 512 true true diff --git a/pwiz_tools/Skyline/Executables/Tools/TestInteractiveTool/TestInteractiveTool.csproj b/pwiz_tools/Skyline/Executables/Tools/TestInteractiveTool/TestInteractiveTool.csproj index 1151500ab15..1ecf6592718 100644 --- a/pwiz_tools/Skyline/Executables/Tools/TestInteractiveTool/TestInteractiveTool.csproj +++ b/pwiz_tools/Skyline/Executables/Tools/TestInteractiveTool/TestInteractiveTool.csproj @@ -10,7 +10,7 @@ Properties TestInteractiveTool TestInteractiveTool - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Skyline/Executables/Tools/XLTCalc/c#/SkylineIntegration/SkylineIntegration.csproj b/pwiz_tools/Skyline/Executables/Tools/XLTCalc/c#/SkylineIntegration/SkylineIntegration.csproj index 6f59d4b54a5..f0c0fc3caef 100644 --- a/pwiz_tools/Skyline/Executables/Tools/XLTCalc/c#/SkylineIntegration/SkylineIntegration.csproj +++ b/pwiz_tools/Skyline/Executables/Tools/XLTCalc/c#/SkylineIntegration/SkylineIntegration.csproj @@ -9,7 +9,7 @@ Properties SkylineIntegration SkylineIntegration - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Skyline/Method/AbSciex/SciexOS/BuildSciexMethod.exe.config b/pwiz_tools/Skyline/Method/AbSciex/SciexOS/BuildSciexMethod.exe.config index 20939707c81..033746a4a20 100644 --- a/pwiz_tools/Skyline/Method/AbSciex/SciexOS/BuildSciexMethod.exe.config +++ b/pwiz_tools/Skyline/Method/AbSciex/SciexOS/BuildSciexMethod.exe.config @@ -1,6 +1,6 @@ - + \ No newline at end of file diff --git a/pwiz_tools/Skyline/Method/AbSciex/TOF/BuildAnalystFullScanMethod.exe.config b/pwiz_tools/Skyline/Method/AbSciex/TOF/BuildAnalystFullScanMethod.exe.config index 312bb3f26fc..3e0e37cfc8c 100644 --- a/pwiz_tools/Skyline/Method/AbSciex/TOF/BuildAnalystFullScanMethod.exe.config +++ b/pwiz_tools/Skyline/Method/AbSciex/TOF/BuildAnalystFullScanMethod.exe.config @@ -1,3 +1,3 @@ - + diff --git a/pwiz_tools/Skyline/Method/AbSciex/TQ/BuildQTRAPMethod.exe.config b/pwiz_tools/Skyline/Method/AbSciex/TQ/BuildQTRAPMethod.exe.config index 05d8b241fde..2c0f5590f09 100644 --- a/pwiz_tools/Skyline/Method/AbSciex/TQ/BuildQTRAPMethod.exe.config +++ b/pwiz_tools/Skyline/Method/AbSciex/TQ/BuildQTRAPMethod.exe.config @@ -1,3 +1,3 @@ - + diff --git a/pwiz_tools/Skyline/Method/Agilent/6400/BuildAgilentMethod.exe.config b/pwiz_tools/Skyline/Method/Agilent/6400/BuildAgilentMethod.exe.config index 312bb3f26fc..3e0e37cfc8c 100644 --- a/pwiz_tools/Skyline/Method/Agilent/6400/BuildAgilentMethod.exe.config +++ b/pwiz_tools/Skyline/Method/Agilent/6400/BuildAgilentMethod.exe.config @@ -1,3 +1,3 @@ - + diff --git a/pwiz_tools/Skyline/Method/Agilent/MH12/BuildAgilentMH12Method.exe.config b/pwiz_tools/Skyline/Method/Agilent/MH12/BuildAgilentMH12Method.exe.config index ecdcf8a54da..4bfa0056185 100644 --- a/pwiz_tools/Skyline/Method/Agilent/MH12/BuildAgilentMH12Method.exe.config +++ b/pwiz_tools/Skyline/Method/Agilent/MH12/BuildAgilentMH12Method.exe.config @@ -1,6 +1,6 @@ - + diff --git a/pwiz_tools/Skyline/Method/Bruker/BuildBrukerMethod.exe.config b/pwiz_tools/Skyline/Method/Bruker/BuildBrukerMethod.exe.config index 5c22b42e59f..786a845b30b 100644 --- a/pwiz_tools/Skyline/Method/Bruker/BuildBrukerMethod.exe.config +++ b/pwiz_tools/Skyline/Method/Bruker/BuildBrukerMethod.exe.config @@ -1,3 +1,3 @@ - + diff --git a/pwiz_tools/Skyline/Method/Thermo/BuildThermoMethod.exe.config b/pwiz_tools/Skyline/Method/Thermo/BuildThermoMethod.exe.config index 312bb3f26fc..3e0e37cfc8c 100644 --- a/pwiz_tools/Skyline/Method/Thermo/BuildThermoMethod.exe.config +++ b/pwiz_tools/Skyline/Method/Thermo/BuildThermoMethod.exe.config @@ -1,3 +1,3 @@ - + diff --git a/pwiz_tools/Skyline/Skyline.csproj b/pwiz_tools/Skyline/Skyline.csproj index 087d810197c..8498425f0bb 100644 --- a/pwiz_tools/Skyline/Skyline.csproj +++ b/pwiz_tools/Skyline/Skyline.csproj @@ -10,7 +10,7 @@ Properties pwiz.Skyline Skyline-daily - v4.7.2 + v4.8 512 Skyline.ico true @@ -7485,6 +7485,20 @@ 1.0.2420.47 + + + 4.6.3 + + + 4.6.1 + + + 4.6.1 + + + 6.1.2 + diff --git a/pwiz_tools/Skyline/SkylineCmd.exe.config b/pwiz_tools/Skyline/SkylineCmd.exe.config index f7034c6830d..398a9075882 100644 --- a/pwiz_tools/Skyline/SkylineCmd.exe.config +++ b/pwiz_tools/Skyline/SkylineCmd.exe.config @@ -1,7 +1,7 @@ - + diff --git a/pwiz_tools/Skyline/SkylineCmd/SkylineCmd.csproj b/pwiz_tools/Skyline/SkylineCmd/SkylineCmd.csproj index 1034fff3ca9..4a637314681 100644 --- a/pwiz_tools/Skyline/SkylineCmd/SkylineCmd.csproj +++ b/pwiz_tools/Skyline/SkylineCmd/SkylineCmd.csproj @@ -8,7 +8,7 @@ Properties pwiz.SkylineCmd SkylineCmd - v4.7.2 + v4.8 512 false diff --git a/pwiz_tools/Skyline/SkylineNightly/SkylineNightly.csproj b/pwiz_tools/Skyline/SkylineNightly/SkylineNightly.csproj index 5bc82155d99..d95aeb05f64 100644 --- a/pwiz_tools/Skyline/SkylineNightly/SkylineNightly.csproj +++ b/pwiz_tools/Skyline/SkylineNightly/SkylineNightly.csproj @@ -10,7 +10,7 @@ Properties SkylineNightly SkylineNightly - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Skyline/SkylineNightly/app.config b/pwiz_tools/Skyline/SkylineNightly/app.config index 22e8e6f6b44..96910aa31d3 100644 --- a/pwiz_tools/Skyline/SkylineNightly/app.config +++ b/pwiz_tools/Skyline/SkylineNightly/app.config @@ -24,7 +24,7 @@ - + diff --git a/pwiz_tools/Skyline/SkylineNightlyShim/SkylineNightlyShim.csproj b/pwiz_tools/Skyline/SkylineNightlyShim/SkylineNightlyShim.csproj index f833955d508..5e6e64bed67 100644 --- a/pwiz_tools/Skyline/SkylineNightlyShim/SkylineNightlyShim.csproj +++ b/pwiz_tools/Skyline/SkylineNightlyShim/SkylineNightlyShim.csproj @@ -8,7 +8,7 @@ Properties SkylineNightlyShim SkylineNightlyShim - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Skyline/SkylineTester/SkylineTester.csproj b/pwiz_tools/Skyline/SkylineTester/SkylineTester.csproj index 0a9d8760502..c8fca518041 100644 --- a/pwiz_tools/Skyline/SkylineTester/SkylineTester.csproj +++ b/pwiz_tools/Skyline/SkylineTester/SkylineTester.csproj @@ -10,7 +10,7 @@ Properties SkylineTester SkylineTester - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Skyline/SkylineTester/app.config b/pwiz_tools/Skyline/SkylineTester/app.config index 672fb7a5e46..8d40b0823d9 100644 --- a/pwiz_tools/Skyline/SkylineTester/app.config +++ b/pwiz_tools/Skyline/SkylineTester/app.config @@ -5,7 +5,7 @@
- + 0, 0 diff --git a/pwiz_tools/Skyline/SkylineTool/SkylineTool.csproj b/pwiz_tools/Skyline/SkylineTool/SkylineTool.csproj index c72a3d42079..4dd5eaf8e6e 100644 --- a/pwiz_tools/Skyline/SkylineTool/SkylineTool.csproj +++ b/pwiz_tools/Skyline/SkylineTool/SkylineTool.csproj @@ -10,7 +10,7 @@ Properties SkylineTool SkylineTool - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Skyline/Test/Test.csproj b/pwiz_tools/Skyline/Test/Test.csproj index d1e47e2523c..f5cb77c90d3 100644 --- a/pwiz_tools/Skyline/Test/Test.csproj +++ b/pwiz_tools/Skyline/Test/Test.csproj @@ -10,7 +10,7 @@ Properties pwiz.SkylineTest Test - v4.7.2 + v4.8 512 {3AC096D0-A1C2-E12C-1390-A8335801FDAB};{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC} diff --git a/pwiz_tools/Skyline/TestConnected/TestConnected.csproj b/pwiz_tools/Skyline/TestConnected/TestConnected.csproj index e2f542b57a1..04ecbabed38 100644 --- a/pwiz_tools/Skyline/TestConnected/TestConnected.csproj +++ b/pwiz_tools/Skyline/TestConnected/TestConnected.csproj @@ -10,7 +10,7 @@ Properties pwiz.SkylineTestConnected TestConnected - v4.7.2 + v4.8 512 {3AC096D0-A1C2-E12C-1390-A8335801FDAB};{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC} diff --git a/pwiz_tools/Skyline/TestConnected/app.config b/pwiz_tools/Skyline/TestConnected/app.config index 476eedc2b81..19f166813bf 100644 --- a/pwiz_tools/Skyline/TestConnected/app.config +++ b/pwiz_tools/Skyline/TestConnected/app.config @@ -6,13 +6,13 @@ - + - + diff --git a/pwiz_tools/Skyline/TestData/TestData.csproj b/pwiz_tools/Skyline/TestData/TestData.csproj index 6fca9a8f4b6..eadcb37a90f 100644 --- a/pwiz_tools/Skyline/TestData/TestData.csproj +++ b/pwiz_tools/Skyline/TestData/TestData.csproj @@ -10,7 +10,7 @@ Properties pwiz.SkylineTestData TestData - v4.7.2 + v4.8 512 {3AC096D0-A1C2-E12C-1390-A8335801FDAB};{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC} diff --git a/pwiz_tools/Skyline/TestFunctional/App.config b/pwiz_tools/Skyline/TestFunctional/App.config index 629c3f18d68..41b18e4351a 100644 --- a/pwiz_tools/Skyline/TestFunctional/App.config +++ b/pwiz_tools/Skyline/TestFunctional/App.config @@ -1,7 +1,7 @@ - + @@ -15,19 +15,19 @@ - + - + - + - + diff --git a/pwiz_tools/Skyline/TestFunctional/TestFunctional.csproj b/pwiz_tools/Skyline/TestFunctional/TestFunctional.csproj index bff5396435a..d5adb0772dc 100644 --- a/pwiz_tools/Skyline/TestFunctional/TestFunctional.csproj +++ b/pwiz_tools/Skyline/TestFunctional/TestFunctional.csproj @@ -10,7 +10,7 @@ Properties pwiz.SkylineTestFunctional TestFunctional - v4.7.2 + v4.8 512 {3AC096D0-A1C2-E12C-1390-A8335801FDAB};{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC} diff --git a/pwiz_tools/Skyline/TestPerf/TestPerf.csproj b/pwiz_tools/Skyline/TestPerf/TestPerf.csproj index 75dffd3da4e..2da32627deb 100644 --- a/pwiz_tools/Skyline/TestPerf/TestPerf.csproj +++ b/pwiz_tools/Skyline/TestPerf/TestPerf.csproj @@ -10,7 +10,7 @@ Properties TestPerf TestPerf - v4.7.2 + v4.8 512 {3AC096D0-A1C2-E12C-1390-A8335801FDAB};{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC} diff --git a/pwiz_tools/Skyline/TestRunner/TestRunner.csproj b/pwiz_tools/Skyline/TestRunner/TestRunner.csproj index 3d505bfb6c2..ea19e2f96f5 100644 --- a/pwiz_tools/Skyline/TestRunner/TestRunner.csproj +++ b/pwiz_tools/Skyline/TestRunner/TestRunner.csproj @@ -10,7 +10,7 @@ Properties TestRunner TestRunner - v4.7.2 + v4.8 None diff --git a/pwiz_tools/Skyline/TestRunner/app.config b/pwiz_tools/Skyline/TestRunner/app.config index 7dee0576991..7e609410f74 100644 --- a/pwiz_tools/Skyline/TestRunner/app.config +++ b/pwiz_tools/Skyline/TestRunner/app.config @@ -1,7 +1,7 @@ - + @@ -11,7 +11,7 @@ - + @@ -27,15 +27,15 @@ - + - + - + diff --git a/pwiz_tools/Skyline/TestRunnerLib/TestRunnerLib.csproj b/pwiz_tools/Skyline/TestRunnerLib/TestRunnerLib.csproj index f4cf5163581..15968fe19ec 100644 --- a/pwiz_tools/Skyline/TestRunnerLib/TestRunnerLib.csproj +++ b/pwiz_tools/Skyline/TestRunnerLib/TestRunnerLib.csproj @@ -10,7 +10,7 @@ Properties TestRunnerLib TestRunnerLib - v4.7.2 + v4.8 512 None diff --git a/pwiz_tools/Skyline/TestTutorial/TestTutorial.csproj b/pwiz_tools/Skyline/TestTutorial/TestTutorial.csproj index b32e75cbb55..a2371706c39 100644 --- a/pwiz_tools/Skyline/TestTutorial/TestTutorial.csproj +++ b/pwiz_tools/Skyline/TestTutorial/TestTutorial.csproj @@ -10,7 +10,7 @@ Properties pwiz.SkylineTestTutorial TestTutorial - v4.7.2 + v4.8 512 {3AC096D0-A1C2-E12C-1390-A8335801FDAB};{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC} diff --git a/pwiz_tools/Skyline/TestUtil/TestUtil.csproj b/pwiz_tools/Skyline/TestUtil/TestUtil.csproj index fb3fbdb2f36..5c569cb8b7a 100644 --- a/pwiz_tools/Skyline/TestUtil/TestUtil.csproj +++ b/pwiz_tools/Skyline/TestUtil/TestUtil.csproj @@ -10,7 +10,7 @@ Properties pwiz.SkylineTestUtil TestUtil - v4.7.2 + v4.8 512 diff --git a/pwiz_tools/Skyline/app.config b/pwiz_tools/Skyline/app.config index 68760a98192..511612feef1 100644 --- a/pwiz_tools/Skyline/app.config +++ b/pwiz_tools/Skyline/app.config @@ -961,7 +961,7 @@ - + @@ -983,19 +983,19 @@ - + - + - + - +