Skyline: Raised the peak truncation threshold

pwiz_tools/Skyline/Model/Databinding/Entities/ColumnCaptions.resx

@@ -1158,6 +1158,9 @@
   <data name="ProductNeutralMass">
     <value>Product Neutral Mass</value>
   </data>
+  <data name="ProportionTruncated">
+    <value>Proportion Truncated</value>
+  </data>
   <data name="Protein">
     <value>Protein</value>
   </data>

pwiz_tools/Skyline/Model/Databinding/Entities/ColumnToolTips.resx

@@ -193,7 +193,7 @@ appeared on the heavy transitions.</value>
     <value>If true, then Skyline will automatically add or remove transitions from the precursor depending on the Transition Settings Filter, spectral library, etc.</value>
   </data>
   <data name="AverageMassErrorPPM">
-    <value>Average Mass Error PPM</value>
+    <value>The area weighted mean for all transitions of the difference between the expected and measured m/z values expressed in parts per million (PPM)</value>
   </data>
   <data name="AverageMasses">
     <value>The modified sequence which specifies modifications with their average masses, e.g. "C[+57.05162]".</value>
@@ -319,7 +319,7 @@ specific default collision energy equation within Skyline</value>
   <data name="CountTruncated">
     <value>The number of transitions for a precursor that integrate a peak with a
 boundary at either end of the acquisition time range, where intensity at the end is
-greater than 1% of the entire peak height higher than the other extent.</value>
+greater than 25% of the background-subtracted peak height higher than the other extent.</value>
   </data>
   <data name="Cv">
     <value>Cv</value>
@@ -1246,6 +1246,11 @@ the decoy m/z.</value>
   <data name="ProductNeutralMass">
     <value>Neutral mass of the product ion peptide fragment in Daltons.</value>
   </data>
+  <data name="ProportionTruncated">
+    <value>The area weighted mean (0 to 1.0) of transitions for a precursor that integrate a peak with a
+boundary at either end of the acquisition time range, where intensity at the end is
+greater than 25% of the background-subtracted peak height higher than the other extent.</value>
+  </data>
   <data name="Protein">
     <value>Protein</value>
   </data>
@@ -1651,8 +1656,8 @@ using the Results Grid.</value>
     <value>Transitions</value>
   </data>
   <data name="Truncated">
-    <value>True if the integrated a peak has a boundary at either end of the acquisition
-time range, where intensity at the end is greater than 1% of the entire peak height
+    <value>True if the integrate peak has a boundary at either end of the acquisition
+time range, where intensity at the end is greater than 25% of the background-subtracted peak height
 higher than the other extent.</value>
   </data>
   <data name="TurningPoint">

pwiz_tools/Skyline/Model/Databinding/Entities/PrecursorResult.cs

@@ -116,6 +116,8 @@ public double? RatioDotProduct {
         public double? AverageMassErrorPPM { get { return ChromInfo.MassError; } }
         [Format(NullValue = TextUtil.EXCEL_NA)]
         public int? CountTruncated { get { return ChromInfo.Truncated; } }
+        [Format(Formats.Percent, NullValue = TextUtil.EXCEL_NA)]
+        public double? ProportionTruncated { get { return CalculateProportionTruncated(); } }
         public PeakIdentification Identified { get { return ChromInfo.Identified; } }
         [Format(Formats.STANDARD_RATIO, NullValue = TextUtil.EXCEL_NA)]
         public double? LibraryDotProduct { get { return ChromInfo.LibraryDotProduct; } }
@@ -488,5 +490,48 @@ private LcPeakIonMetrics GetIonMetrics(ResultFileMetaData resultFileMetadata, IL
 
             return lcPeakIonMetrics;
         }
+
+        private double? CalculateProportionTruncated()
+        {
+            double totalArea = 0;
+            double truncatedArea = 0;
+            var srmSettings = DataSchema.Document.Settings;
+            var resultFile = GetResultFile();
+            foreach (var transition in Precursor.DocNode.Transitions)
+            {
+                if (!transition.IsQuantitative(srmSettings))
+                {
+                    continue;
+                }
+
+                foreach (var transitionChromInfo in transition.GetSafeChromInfo(
+                             resultFile.Replicate.ReplicateIndex))
+                {
+                    if (transitionChromInfo.OptimizationStep != resultFile.OptimizationStep ||
+                        !ReferenceEquals(transitionChromInfo.FileId, resultFile.ChromFileInfoId))
+                    {
+                        continue;
+                    }
+
+                    if (!transitionChromInfo.IsTruncated.HasValue || transitionChromInfo.Area <= 0)
+                    {
+                        continue;
+                    }
+
+                    totalArea += transitionChromInfo.Area;
+                    if (transitionChromInfo.IsTruncated.Value)
+                    {
+                        truncatedArea += transitionChromInfo.Area;
+                    }
+                }
+            }
+
+            if (totalArea <= 0)
+            {
+                return null;
+            }
+
+            return truncatedArea / totalArea;
+        }
     }
 }

pwiz_tools/Skyline/Model/Results/ChromHeaderInfo.cs

@@ -1089,7 +1089,7 @@ public ChromPeak(IPeakFinder finder,
             // recorded values, where the intensity is higher than the other extent
             // by more than 1% of the peak height.
             _flagValues |= FlagValues.peak_truncation_known;
-            const double truncationTolerance = 0.01;
+            const double truncationTolerance = 0.25;
             double deltaIntensityExtents = (intensities[peak.EndIndex] - intensities[peak.StartIndex]) / Height;
             if ((peak.StartIndex == 0 && deltaIntensityExtents < -truncationTolerance) ||
                 (peak.EndIndex == times.Count - 1 && deltaIntensityExtents > truncationTolerance))

pwiz_tools/Skyline/Test/MProphetResultsHandlerTest.cs

@@ -113,7 +113,15 @@ public void TestMProphetResultsHandler()
                 AssertEx.FileEquals(mProphetExpected, mProphetActual);
 
                 // 4. Export mProphet -> Import Peak Boundaries leads to same result as reintegrate
-                var resultsHandlerQAll = new MProphetResultsHandler(docOriginal, peakScoringModel) { QValueCutoff = 1.0 };
+
+                // Remove RWSSIPLSQLHLI because its truncation values change between 24.11 and 24.12
+                // That is the ChromPeak.Truncated value stored in the .skyd file is different from
+                // what gets recalculated during peak boundary import.
+                var pepRemovePath = docOriginal.EnumeratePathsAtLevel(IdentityPath.ROOT, SrmDocument.Level.Molecules)
+                    .First(path => path.Child is Peptide { Sequence: @"RWSSIPLSQLHLI" });
+                var docRemoved = (SrmDocument) docOriginal.RemoveChild(pepRemovePath.Parent, docOriginal.FindNode(pepRemovePath));
+
+                var resultsHandlerQAll = new MProphetResultsHandler(docRemoved, peakScoringModel) { QValueCutoff = 1.0 };
                 resultsHandlerQAll.ScoreFeatures();
                 var docNewQAll = resultsHandlerQAll.ChangePeaks();
                 var peakBoundaryImporter = new PeakBoundaryImporter(docNewQAll);

pwiz_tools/Skyline/TestPerf/DiaSwathTutorialTest.cs

@@ -252,9 +252,9 @@ public void TestQeData(bool fullSet)
                         new[] { 2.2, 4.6 },
                         new[] { 1.9, 4.7 },
                     },
-                    DiffPeptideCounts = new[] { 10459, 6387, 2238, 1823 },
-                    UnpolishedProteins = 1647,
-                    PolishedProteins = 1647,
+                    DiffPeptideCounts = new[] { 10467, 6391, 2242, 1823 },
+                    UnpolishedProteins = 1653,
+                    PolishedProteins = 2031,
                 };
             }
             else

pwiz_tools/Skyline/TestTutorial/GroupedStudies1TutorialTest.cs

@@ -368,7 +368,7 @@ private void ExploreTopPeptides()
                 OkDialog(findDlg, findDlg.Close);
 
                 var findView = WaitForOpenForm<FindResultsForm>();
-                int expectedItems = IsFullData ? 454 : 290;
+                int expectedItems = IsFullData ? 228 : 151;
                 try
                 {
                     WaitForConditionUI(1000, () => findView.ItemCount == expectedItems);
@@ -610,9 +610,9 @@ private void AddTruncatedPrecursorsView(DocumentGridForm documentGrid, bool init
             OkDialog(viewEditor, viewEditor.OkDialog);
 
             var pathTruncated = PropertyPath.Parse("Results!*.Value.CountTruncated");
-            int expectedItems = 148;
+            int expectedItems = 86;
             if (IsFullData)
-                expectedItems = 221; // initialTestExecution ? 223 : 221;
+                expectedItems = 129;
             try
             {
                 WaitForConditionUI(1000, () => documentGrid.RowCount == expectedItems &&
@@ -1155,7 +1155,7 @@ private void PrepareForStatistics()
 
                 PauseForScreenShot<DocumentGridForm>("Document Grid with MissingData field");
 
-                int expectedRows = IsFullData ? 222 : 149;
+                int expectedRows = IsFullData ? 133 : 89;
                 const int expectedRowsAbbreviated = 221; // When not all of the tests are run
                 RunUI(() =>
                 {