skyline: Stop skipping spectra that have empty m/z intensity arrays

pwiz_tools/Skyline/Controls/Graphs/GraphFullScan.cs

@@ -2169,6 +2169,29 @@ private void GetMaxMzIntensity(out double maxMz, out double maxIntensity)
                 double intensity = SumIntensities(fullScans, minMz, indices, minIonMobilityVal, maxIonMobilityVal);
                 maxIntensity = Math.Max(maxIntensity, intensity);
             }
+
+            if (maxMz <= 0)
+            {
+                // None of the scans have any peaks in them because they measured no ions. Show the
+                // m/z range that the instrument was scanning so that the axes still get drawn.
+                maxMz = GetMaxScanWindow(fullScans);
+            }
+        }
+
+        /// <summary>
+        /// The highest scan window upper limit declared by any of the spectra, or zero if none of
+        /// them says what m/z range it was measuring.
+        /// </summary>
+        private static double GetMaxScanWindow(IEnumerable<MsDataSpectrum> spectra)
+        {
+            double maxScanWindow = 0;
+            foreach (var spectrum in spectra)
+            {
+                var upperLimit = spectrum.Metadata?.ScanWindowUpperLimit;
+                if (upperLimit.HasValue)
+                    maxScanWindow = Math.Max(maxScanWindow, upperLimit.Value);
+            }
+            return maxScanWindow;
         }
 
         private void GetIonMobilityRange(out double minIonMobility, out double maxIonMobility)
@@ -2271,21 +2294,28 @@ private void ZoomXAxis()
         private void ApplyXZoomToPane(GraphPane pane)
         {
             var xScale = pane.XAxis.Scale;
-            xScale.MinAuto = xScale.MaxAuto = false;
 
             if (magnifyBtn.Checked)
             {
                 double mz = _msDataFileScanHelper.Source == ChromSource.ms1
                     ? _msDataFileScanHelper.ScanProvider.Transitions[_msDataFileScanHelper.TransitionIndex].PrecursorMz
                     : _msDataFileScanHelper.ScanProvider.Transitions[_msDataFileScanHelper.TransitionIndex].ProductMz;
+                xScale.MinAuto = xScale.MaxAuto = false;
                 xScale.Min = mz - 1.5;
                 xScale.Max = mz + 3.5;
             }
-            else if (_requestedRange != null)
+            else if (_requestedRange != null && _requestedRange.Max > _requestedRange.Min)
             {
+                xScale.MinAuto = xScale.MaxAuto = false;
                 xScale.Min = _requestedRange.Min;
                 xScale.Max = _requestedRange.Max;
             }
+            else
+            {
+                // There is no m/z range to show. Leave the axis auto-scaled, since collapsing it to
+                // a single value makes ZedGraph skip drawing the axis entirely.
+                xScale.MinAuto = xScale.MaxAuto = true;
+            }
         }
 
         public void SetMzScale(MzRange range)
@@ -2458,6 +2488,13 @@ public bool ShowPropertiesSheet
 
         public bool HasChromatogramData => false;
 
+        /// <summary>
+        /// The maximum for an intensity axis, which is never zero. ZedGraph draws nothing at all --
+        /// not even the axes -- when the minimum of any of a pane's axis scales equals its maximum,
+        /// so a scan which measured no ions would otherwise produce a completely blank graph.
+        /// </summary>
+        private double IntensityAxisMax => _maxIntensity > 0 ? _maxIntensity * 1.1 : 1;
+
         private void ZoomYAxis()
         {
             if (_msDataFileScanHelper.ScanProvider == null || _msDataFileScanHelper.ScanProvider.Transitions.Length == 0)
@@ -2479,7 +2516,7 @@ private void ZoomYAxis()
             if (isSpectrum)
             {
                 yScale.Min = 0;
-                yScale.Max = _maxIntensity * 1.1;
+                yScale.Max = IntensityAxisMax;
                 if (magnifyBtn.Checked)
                 {
                     yScale.MaxAuto = true;
@@ -2540,11 +2577,11 @@ private void ZoomStickYAxis()
                             maxY = pt.Y;
                     }
                 }
-                yScale.Max = maxY > 0 ? maxY * 1.1 : _maxIntensity * 1.1;
+                yScale.Max = maxY > 0 ? maxY * 1.1 : IntensityAxisMax;
             }
             else
             {
-                yScale.Max = _maxIntensity * 1.1;
+                yScale.Max = IntensityAxisMax;
             }
             _stickSpectrumPane.AxisChange();
         }
@@ -2566,7 +2603,7 @@ private void ResetStickYAxis()
             yScale.MinAuto = false;
             _heatMapPane.LockYAxisMinAtZero = true;
             yScale.Min = 0;
-            yScale.Max = _maxIntensity * 1.1;
+            yScale.Max = IntensityAxisMax;
             // Magnify on → auto-fit Y to data in the zoomed X range during next paint.
             yScale.MaxAuto = magnifyBtn.Checked;
         }

pwiz_tools/Skyline/Model/Results/SpectraChromDataProvider.cs

@@ -839,6 +839,20 @@ public static bool HasSpectrumData(MsDataFileImpl dataFile)
             return dataFile.SpectrumCount > 0;
         }
 
+        /// <summary>
+        /// Returns true if a spectrum has no m/z values and should be ignored.
+        /// A spectrum which measured no ions is a valid measurement of zero intensity, but only if
+        /// we know which m/z values it was measuring. That range comes from the scan window limits,
+        /// so a spectrum which declares them is not considered empty.
+        /// </summary>
+        public static bool IsEmptySpectrum(MsDataSpectrum spectrum)
+        {
+            if (spectrum.Mzs != null && spectrum.Mzs.Length != 0)
+                return false;
+            return spectrum.Metadata?.ScanWindowLowerLimit == null &&
+                   spectrum.Metadata?.ScanWindowUpperLimit == null;
+        }
+
         private class Spectra : IDisposable
         {
             private bool _runningAsync;
@@ -1218,7 +1232,7 @@ private SpectrumInfo ReadSpectrum(ref int i)
                             // Assertion for testing ID to spectrum index support
                             //                        int iFromId = dataFile.GetSpectrumIndex(dataSpectrum.Id);
                             //                        Assume.IsTrue(i == iFromId);
-                            if (nextSpectrum.Mzs.Length == 0)
+                            if (IsEmptySpectrum(nextSpectrum))
                                 continue;
 
                             double? rt = nextSpectrum.RetentionTime;
@@ -1574,7 +1588,7 @@ public MsDataSpectrum[] Lookahead(MsDataSpectrum dataSpectrum, out double? rt)
                     while (_lookAheadIndex++ < _lenSpectra)
                     {
                         _rt = dataSpectrum.RetentionTime;
-                        if (_rt.HasValue && dataSpectrum.Mzs.Length != 0)
+                        if (_rt.HasValue && !IsEmptySpectrum(dataSpectrum))
                         {
                             spectrumList.Add(dataSpectrum);
                             if (!rtReported.HasValue)
@@ -1630,7 +1644,7 @@ public MsDataSpectrum[] Lookahead(MsDataSpectrum dataSpectrum, out double? rt)
                     while (_lookAheadIndex++ < _lenSpectra)
                     {
                         _rt = dataSpectrum.RetentionTime;
-                        if (_rt.HasValue && dataSpectrum.Mzs.Length != 0)
+                        if (_rt.HasValue && !IsEmptySpectrum(dataSpectrum))
                         {
                             spectrumList.Add(dataSpectrum);
                             rtTotal += dataSpectrum.RetentionTime.Value;
@@ -1649,7 +1663,7 @@ public MsDataSpectrum[] Lookahead(MsDataSpectrum dataSpectrum, out double? rt)
                 {
                     // No need to search forward, this isn't IMS or Agilent ramped-CE data
                     rtReported = dataSpectrum.RetentionTime;
-                    if (rtReported.HasValue && dataSpectrum.Mzs.Length != 0)
+                    if (rtReported.HasValue && !IsEmptySpectrum(dataSpectrum))
                     {
                         spectrumList.Add(dataSpectrum);
                     }

pwiz_tools/Skyline/Model/Results/SpectrumFilterPair.cs

@@ -344,7 +344,11 @@ private ExtractedSpectrum FilterSpectrumList(MsDataSpectrum[] spectra,
                                 iPeak = ~iPeak;
                         }
                         if (iPeak >= mzArray.Length)
+                        {
+                            // The extracted intensities for the remaining targets will be zero so we can stop extracting
+                            // Consider: we probably still need to keep checking "hasScanWindowCoverage"
                             break; // No further overlap
+                        }
                     }
 
                     // TODO:(bspratt) for full frame diaPASEF MS2, try not sorting - make IM the initial binary search range (and deal with mz that rolls over)

pwiz_tools/Skyline/TestFunctional/SettingsChangeReimportTest.cs

@@ -57,7 +57,7 @@ protected override void DoTest()
             Assert.AreEqual(1, transitionGroup.Results.Count);
             var transitionGroupChromInfo = transitionGroup.Results[0].First();
             // Verify the peak area is what we expect
-            Assert.AreEqual(1.460189E+08f, transitionGroupChromInfo.Area.Value);
+            Assert.AreEqual(147639168f, transitionGroupChromInfo.Area.Value);
 
             // Reimport the file with "UseSelectiveExtraction" set to "true"
             RunUI(() => SkylineWindow.ModifyDocument("Change selective extraction",
@@ -87,7 +87,7 @@ protected override void DoTest()
             Assert.AreEqual(1, transitionGroup.Results.Count);
             transitionGroupChromInfo = transitionGroup.Results[0].First();
             // Verify that the peak area is a smaller number because the chromatogram extraction was more selective
-            Assert.AreEqual(119880880f, transitionGroupChromInfo.Area.Value);
+            Assert.AreEqual(121269248f, transitionGroupChromInfo.Area.Value);
         }
     }
 }

pwiz_tools/Skyline/TestFunctional/TestFunctional.csproj

@@ -560,6 +560,7 @@
     <Compile Include="UpdateGlobalStandardTest.cs" />
     <Compile Include="UpgradeTest.cs" />
     <Compile Include="VolcanoPlotFormattingTest.cs" />
+    <Compile Include="ZeroLengthSpectraTest.cs" />
     <Compile Include="ZeroLengthSrmChromatogramTest.cs" />
   </ItemGroup>
   <ItemGroup>

pwiz_tools/Skyline/TestFunctional/ZeroLengthSpectraTest.cs

@@ -0,0 +1,100 @@
+/*
+ * Original author: Nicholas Shulman <nicksh .at. u.washington.edu>,
+ *                  MacCoss Lab, Department of Genome Sciences, UW
+ *
+ * Copyright 2026 University of Washington - Seattle, WA
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+using Microsoft.VisualStudio.TestTools.UnitTesting;
+using pwiz.CommonMsData;
+using pwiz.Skyline.Controls.Graphs;
+using pwiz.Skyline.Model;
+using pwiz.Skyline.Model.Results;
+using pwiz.SkylineTestUtil;
+using System.Linq;
+using ZedGraph;
+
+namespace pwiz.SkylineTestFunctional
+{
+    /// <summary>
+    /// Verifies that spectra with no m/z's and intensities are still included in the extracted chromatogram.
+    /// </summary>
+    [TestClass]
+    public class ZeroLengthSpectraTest : AbstractFunctionalTestEx
+    {
+        [TestMethod]
+        public void TestZeroLengthSpectra()
+        {
+            TestFilesZip = @"TestFunctional\ZeroLengthSpectraTest.zip";
+            RunFunctionalTest();
+        }
+
+        protected override void DoTest()
+        {
+            RunUI(()=>SkylineWindow.OpenFile(TestFilesDir.GetTestPath("ZeroLengthSpectraTest.sky")));
+            var msDataFilePath = new MsDataFilePath(TestFilesDir.GetTestPath("S_1.mzML"));
+            ImportResultsFile(msDataFilePath.FilePath);
+            using var dataFile = msDataFilePath.OpenMsDataFile(new OpenMsDataFileParams());
+            var ms1Spectra = Enumerable.Range(0, dataFile.SpectrumCount).Select(dataFile.GetSpectrum)
+                .Where(spectrum => spectrum.Level == 1).ToList();
+            var emptyMs1Spectra = ms1Spectra.Where(spectrum => spectrum.Mzs.Length == 0).ToList();
+            Assert.AreNotEqual(0, emptyMs1Spectra.Count);
+            Assert.AreNotEqual(emptyMs1Spectra.Count, ms1Spectra.Count);
+            var document = SkylineWindow.Document;
+            var peptideDocNode = document.Molecules.First();
+            Assert.IsTrue(document.MeasuredResults.TryLoadChromatogram(0, peptideDocNode, peptideDocNode.TransitionGroups.First(), (float) document.Settings.TransitionSettings.Instrument.MzMatchTolerance, out var chromatogramGroupInfos));
+            Assert.AreEqual(1, chromatogramGroupInfos.Length);
+            var chromatogramInfo = chromatogramGroupInfos[0].GetRawTransitionInfo(0);
+            Assert.IsNotNull(chromatogramInfo);
+            Assert.AreEqual(ms1Spectra.Count, chromatogramInfo.Times.Count);
+            RunUI(() =>
+            {
+                SkylineWindow.SelectedPath =
+                    SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.TransitionGroups, 0);
+                SkylineWindow.SetTransformChrom(TransformChrom.raw);
+            });
+
+            // Click on a point in the chromatogram which came from one of the empty spectra
+            ClickChromatogram(22.3, 1e4);
+            var graphFullScan = WaitForOpenForm<GraphFullScan>();
+            RunUI(() =>
+            {
+                graphFullScan.SetZoom(false);
+                AssertAxesNotDegenerate(graphFullScan.ZedGraphControl.GraphPane);
+
+                // The empty spectrum still says which m/z values it was measuring, and the x-axis
+                // is supposed to show that range instead of collapsing to nothing
+                var scanWindowUpperLimit = emptyMs1Spectra.Max(spectrum => spectrum.Metadata.ScanWindowUpperLimit);
+                Assert.IsNotNull(scanWindowUpperLimit);
+                AssertEx.IsGreaterThanOrEqual(graphFullScan.ZedGraphControl.GraphPane.XAxis.Scale.Max,
+                    scanWindowUpperLimit.Value);
+            });
+        }
+
+        /// <summary>
+        /// Asserts that the graph will actually be drawn. ZedGraph skips the axes, the grid and the
+        /// curves when the minimum of any of a pane's axis scales is not less than its maximum,
+        /// which leaves nothing but the title, so a degenerate range means a blank graph.
+        /// </summary>
+        private static void AssertAxesNotDegenerate(GraphPane graphPane)
+        {
+            AssertEx.IsGreaterThan(graphPane.XAxis.Scale.Max, graphPane.XAxis.Scale.Min);
+            AssertEx.IsGreaterThan(graphPane.X2Axis.Scale.Max, graphPane.X2Axis.Scale.Min);
+            foreach (var yAxis in graphPane.YAxisList)
+                AssertEx.IsGreaterThan(yAxis.Scale.Max, yAxis.Scale.Min);
+            foreach (var y2Axis in graphPane.Y2AxisList)
+                AssertEx.IsGreaterThan(y2Axis.Scale.Max, y2Axis.Scale.Min);
+        }
+    }
+}

pwiz_tools/Skyline/TestPerf/DiaSwathTutorialTest.data/TestQeDataDiaNN.json

@@ -18,24 +18,24 @@
       3.01
     ],
     [
-      1.77,
-      3.02
+      1.76,
+      2.99
     ],
     [
-      2.05,
+      2.04,
       3.16
     ],
     [
-      2.06,
-      3.66
+      2.08,
+      3.68
     ],
     [
-      1.94,
+      1.95,
       3.17
     ],
     [
-      1.63,
-      3.36
+      1.64,
+      3.38
     ]
   ],
   "DiffPeptideCounts": [

pwiz_tools/Skyline/TestPerf/DiaSwathTutorialTest.data/TestTtofData.json

@@ -11,30 +11,30 @@
   "MassErrorStats": [
     [
       3.03,
-      4.37
+      4.38
     ],
     [
-      2.78,
-      4.1
+      2.79,
+      4.12
     ],
     [
-      3.88,
+      3.89,
       4.25
     ],
     [
       5.87,
-      3.58
+      3.55
     ],
     [
       4.69,
       4.17
     ],
     [
-      -0.07,
-      3.42
+      -0.08,
+      3.43
     ],
     [
-      1.01,
+      1.02,
       3.63
     ]
   ],
@@ -47,13 +47,13 @@
   "UnpolishedProteins": 9,
   "PolishedProteins": 11,
   "ScoringModelCoefficients": [
-    0.2332,
-    -0.667,
-    3.4044,
-    -0.0138,
-    -0.4653,
-    0.9273,
-    0.112,
-    -0.0497
+    0.2442,
+    -0.6843,
+    3.403,
+    0.0632,
+    -0.4762,
+    0.9162,
+    0.0914,
+    -0.0489
   ]
 }