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.STANDARD_RATIO, NullValue = TextUtil.EXCEL_NA)]
+        public double? ProportionTruncated { get { return ChromInfo.TruncatedProportion; } }
         public PeakIdentification Identified { get { return ChromInfo.Identified; } }
         [Format(Formats.STANDARD_RATIO, NullValue = TextUtil.EXCEL_NA)]
         public double? LibraryDotProduct { get { return ChromInfo.LibraryDotProduct; } }

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/Model/Results/DocNodeChromInfo.cs

@@ -172,22 +172,23 @@ public sealed class TransitionGroupChromInfo : ChromInfo
         [Flags]
         private enum Flags
         {
-            HasRetentionTime = 1,
-            HasStartRetentionTime = 2,
-            HasEndRetentionTime = 4,
-            HasFwhm = 8,
-            HasArea = 16,
-            HasAreaMs1 = 32,
-            HasAreaFragment = 64,
-            HasBackgroundArea = 128,
-            HasBackgroundAreaMs1 = 256,
-            HasBackgroundAreaFragment = 512,
-            HasHeight = 1024,
-            HasMassError = 2048,
-            HasLibraryDotProduct = 4096,
-            HasIsotopeDotProduct = 8192,
-            HasQValue = 16384,
-            HasZScore = 32768,
+            HasRetentionTime =          0x00000001,
+            HasStartRetentionTime =     0x00000002,
+            HasEndRetentionTime =       0x00000004,
+            HasFwhm =                   0x00000008,
+            HasArea =                   0x00000010,
+            HasAreaMs1 =                0x00000020,
+            HasAreaFragment =           0x00000040,
+            HasBackgroundArea =         0x00000080,
+            HasBackgroundAreaMs1 =      0x00000100,
+            HasBackgroundAreaFragment = 0x00000200,
+            HasHeight =                 0x00000400,
+            HasMassError =              0x00000800,
+            HasLibraryDotProduct =      0x00001000,
+            HasIsotopeDotProduct =      0x00002000,
+            HasQValue =                 0x00004000,
+            HasZScore =                 0x00008000,
+            HasTruncatedProportion =    0x00010000,
         }
 
         private Flags _flags;
@@ -209,6 +210,7 @@ public TransitionGroupChromInfo(ChromFileInfoId fileId,
                                         float? height,
                                         float? massError,
                                         int? truncated,
+                                        float? truncatedProportion,
                                         PeakIdentification identified,
                                         float? libraryDotProduct,
                                         float? isotopeDotProduct,
@@ -234,6 +236,7 @@ public TransitionGroupChromInfo(ChromFileInfoId fileId,
             Height = height;
             MassError = massError;
             Truncated = truncated;
+            TruncatedProportion = truncatedProportion;
             Identified = identified;
             LibraryDotProduct = libraryDotProduct;
             IsotopeDotProduct = isotopeDotProduct;
@@ -340,6 +343,13 @@ public int? Truncated
             private set { _truncated = value ?? -1; }
         }
 
+        private float _truncatedProportion;
+        public float? TruncatedProportion
+        {
+            get { return GetOptional(_truncatedProportion, Flags.HasTruncatedProportion); }
+            private set { _truncatedProportion = SetOptional(value, Flags.HasTruncatedProportion); }
+        }
+
         public PeakIdentification Identified { get; private set; }
         public bool IsIdentified { get { return Identified != PeakIdentification.FALSE; } }
 
@@ -455,6 +465,7 @@ public bool Equals(TransitionGroupChromInfo other)
                    other.BackgroundAreaFragment.Equals(BackgroundAreaFragment) &&
                    other.Height.Equals(Height) &&
                    other.Truncated.Equals(Truncated) &&
+                   other.TruncatedProportion.Equals(TruncatedProportion) &&
                    other.Identified.Equals(Identified) &&
                    other.LibraryDotProduct.Equals(LibraryDotProduct) &&
                    other.IsotopeDotProduct.Equals(IsotopeDotProduct) &&
@@ -493,6 +504,7 @@ public override int GetHashCode()
                 result = (result*397) ^ (BackgroundAreaFragment.HasValue ? BackgroundAreaFragment.Value.GetHashCode() : 0);
                 result = (result*397) ^ (Height.HasValue ? Height.Value.GetHashCode() : 0);
                 result = (result*397) ^ (Truncated.HasValue ? Truncated.Value.GetHashCode() : 0);
+                result = (result*397) ^ (TruncatedProportion.HasValue ? TruncatedProportion.Value.GetHashCode() : 0);
                 result = (result*397) ^ Identified.GetHashCode();
                 result = (result*397) ^ (LibraryDotProduct.HasValue ? LibraryDotProduct.Value.GetHashCode() : 0);
                 result = (result*397) ^ (IsotopeDotProduct.HasValue ? IsotopeDotProduct.Value.GetHashCode() : 0);

pwiz_tools/Skyline/Model/Serialization/DocumentFormat.cs

@@ -119,7 +119,8 @@ public struct DocumentFormat : IComparable<DocumentFormat>
         public static readonly DocumentFormat VERSION_23_13 = new DocumentFormat(23.13); // Relative abundance formatting
         public static readonly DocumentFormat VERSION_24_1 = new DocumentFormat(24.1); // Release format
         public static readonly DocumentFormat VERSION_24_11 = new DocumentFormat(24.11); // Global spectrum filters
-        public static readonly DocumentFormat CURRENT = VERSION_24_11;
+        public static readonly DocumentFormat VERSION_24_12 = new DocumentFormat(24.12); // truncated_proportion
+        public static readonly DocumentFormat CURRENT = VERSION_24_12;
 
         private readonly double _versionNumber;
         public DocumentFormat(double versionNumber)

pwiz_tools/Skyline/Model/Serialization/DocumentReader.cs

@@ -124,6 +124,10 @@ private TransitionGroupChromInfo ReadTransitionGroupChromInfo(XmlReader reader,
             float? height = reader.GetNullableFloatAttribute(ATTR.height);
             float? massError = reader.GetNullableFloatAttribute(ATTR.mass_error_ppm);
             int? truncated = reader.GetNullableIntAttribute(ATTR.truncated);
+            float? truncatedProportion = reader.GetNullableFloatAttribute(ATTR.truncated_proportion);
+            // When truncated count is zero, truncate proportion is known to be zero
+            if (truncated is 0 && !truncatedProportion.HasValue)
+                truncatedProportion = 0;
             PeakIdentification identified = reader.GetEnumAttribute(ATTR.identified, PeakIdentificationFastLookup.Dict,
                 PeakIdentification.FALSE, XmlUtil.EnumCase.upper);
             float? libraryDotProduct = reader.GetNullableFloatAttribute(ATTR.library_dotp);
@@ -158,6 +162,7 @@ private TransitionGroupChromInfo ReadTransitionGroupChromInfo(XmlReader reader,
                 height,
                 massError,
                 truncated,
+                truncatedProportion,
                 identified,
                 libraryDotProduct,
                 isotopeDotProduct,

pwiz_tools/Skyline/Model/Serialization/DocumentSerializer.cs

@@ -195,6 +195,7 @@ public static class ATTR
             public const string fwhm = "fwhm";
             public const string fwhm_degenerate = "fwhm_degenerate";
             public const string truncated = "truncated";
+            public const string truncated_proportion = "truncated_proportion";
             public const string identified = "identified";
             public const string user_set = "user_set";
             public const string peak_count_ratio = "peak_count_ratio";

pwiz_tools/Skyline/Model/Serialization/DocumentWriter.cs

@@ -670,6 +670,9 @@ private static void WriteTransitionGroupChromInfo(XmlWriter writer, TransitionGr
             writer.WriteAttributeNullable(ATTR.height, chromInfo.Height);
             writer.WriteAttributeNullable(ATTR.mass_error_ppm, chromInfo.MassError);
             writer.WriteAttributeNullable(ATTR.truncated, chromInfo.Truncated);
+            // Writing truncated proportion 0 for peaks with a truncated count of zero is redundant
+            if ((chromInfo.Truncated ?? 0) != 0)
+                writer.WriteAttributeNullable(ATTR.truncated_proportion, chromInfo.TruncatedProportion);
             writer.WriteAttribute(ATTR.identified, chromInfo.Identified.ToString().ToLowerInvariant());
             writer.WriteAttributeNullable(ATTR.library_dotp, chromInfo.LibraryDotProduct);
             writer.WriteAttributeNullable(ATTR.isotope_dotp, chromInfo.IsotopeDotProduct);

pwiz_tools/Skyline/Model/TransitionGroupDocNode.cs

@@ -2566,6 +2566,7 @@ public TransitionGroupChromInfoCalculator(SrmSettings settings,
             private float? BackgroundAreaFragment { get; set; }
             private float? MassError { get; set; }
             private int? Truncated { get; set; }
+            private float? TruncatedProportion { get; set; }
             private PeakIdentification Identified { get; set; }
             private float? LibraryDotProduct { get; set; }
             private float? IsotopeDotProduct { get; set; }
@@ -2625,6 +2626,11 @@ public void AddChromInfo(TransitionDocNode nodeTran, TransitionChromInfo info)
                                 Truncated = 0;
                             if (info.IsTruncated.Value)
                                 Truncated++;
+
+                            // Weighted mean value for truncation
+                            double truncatedProportion = TruncatedProportion ?? 1;
+                            truncatedProportion += ((info.IsTruncated.Value ? 1 : 0) - truncatedProportion) * info.Area / Area.Value;
+                            TruncatedProportion = (float)truncatedProportion;
                         }
                         switch (Settings.GetChromSource(nodeTran))
                         {
@@ -2713,6 +2719,7 @@ public TransitionGroupChromInfo CalcChromInfo()
                                                     (float?) BestRetentionTimes?.Height,
                                                     MassError,
                                                     Truncated,
+                                                    TruncatedProportion,
                                                     Identified,
                                                     LibraryDotProduct,
                                                     IsotopeDotProduct,

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/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(() =>
                 {