Allow changes to molecule name (or anything that doesn't change its mass) without losing the association to any existing chromatograms.

pwiz_tools/Skyline/Controls/Graphs/GraphChromatogram.cs

@@ -2379,7 +2379,7 @@ private class DisplayPeptide
 
                         if (nodePep != null && nodeTranGroup != null)
                         {
-                            var libKey = new LibKey(nodePep.ModifiedTarget, nodeTranGroup.PrecursorAdduct);
+                            var libKey = new LibKey(nodePep.ChromatogramTarget, nodeTranGroup.PrecursorAdduct);
                             chromGraphPrimary.MidasRetentionMsMs = settings.PeptideSettings.Libraries.MidasLibraries
                                 .SelectMany(lib => lib.GetSpectraByPeptide(chromGraphPrimary.Chromatogram.FilePath, libKey))
                                 .Select(s => s.RetentionTime).ToArray();

pwiz_tools/Skyline/Controls/Graphs/GraphSpectrum.cs

@@ -1358,7 +1358,7 @@ private void DoUpdate()
 
                         _graphHelper.ZoomSpectrumToSettings(DocumentUI, selection.NodeTranGroup);
 
-                        if (GraphItem.PeptideDocNode != null && GraphItem.TransitionGroupNode != null && spectrum?.SpectrumInfo is SpectrumInfoLibrary libInfo)
+                        if (GraphItem != null && GraphItem.PeptideDocNode != null && GraphItem.TransitionGroupNode != null && spectrum?.SpectrumInfo is SpectrumInfoLibrary libInfo)
                         {
                             var pepInfo = new ViewLibraryPepInfo(
                                 GraphItem.PeptideDocNode.ModifiedTarget.GetLibKey(GraphItem.TransitionGroupNode.PrecursorAdduct), 

pwiz_tools/Skyline/Model/Peptide.cs

@@ -56,11 +56,16 @@ public Peptide(FastaSequence fastaSequence, string sequence, int? begin, int? en
             Validate();
         }
 
-        public Peptide(CustomMolecule customMolecule)
+        public Peptide(CustomMolecule customMolecule, Target originalMoleculeDescription = null)
         {
             Target = new Target(customMolecule);
 
             Validate();
+            if (originalMoleculeDescription != null)
+            {
+                // As when user changes molecule name, CAS etc, but not mass or formula, so we still want to associate chromatograms
+                OriginalMoleculeTarget = originalMoleculeDescription;
+            }
         }
 
         public Peptide(Target pepOrMol)
@@ -84,6 +89,9 @@ public Peptide(Target pepOrMol)
         public int Length { get { return Target.IsProteomic ? Target.Sequence.Length : 0; }}
         public string TextId { get { return IsCustomMolecule ? Target.Molecule.InvariantName : Target.Sequence; } }
 
+        // For robust chromatogram association in the event of user tweaking molecule details like name, CAS etc (but not mass!)
+        public Target OriginalMoleculeTarget;
+
         public SmallMoleculeLibraryAttributes GetSmallMoleculeLibraryAttributes()
         {
             return IsCustomMolecule ? CustomMolecule.GetSmallMoleculeLibraryAttributes() : SmallMoleculeLibraryAttributes.EMPTY;
@@ -340,6 +348,7 @@ private void Validate()
                 Assume.IsNull(_fastaSequence);
                 Assume.IsNull(Sequence);
                 CustomMolecule.Validate();
+                OriginalMoleculeTarget = Target;
             }
             else if (_fastaSequence == null)
             {
@@ -380,6 +389,7 @@ public bool Equals(Peptide obj)
             if (ReferenceEquals(this, obj)) return true;
             var equal = Equals(obj._fastaSequence, _fastaSequence) &&
                 Equals(obj.Target, Target) &&
+                Equals(obj.OriginalMoleculeTarget, OriginalMoleculeTarget) &&
                 obj.Begin.Equals(Begin) &&
                 obj.End.Equals(End) &&
                 obj.MissedCleavages == MissedCleavages &&
@@ -400,7 +410,8 @@ public override int GetHashCode()
             unchecked
             {
                 int result = (_fastaSequence != null ? _fastaSequence.GetHashCode() : 0);
-                result = (result*397) ^ (Target != null ? Target.GetHashCode() : 0);
+                result = (result * 397) ^ (Target != null ? Target.GetHashCode() : 0);
+                result = (result * 397) ^ (OriginalMoleculeTarget != null ? OriginalMoleculeTarget.GetHashCode() : 0);
                 result = (result*397) ^ (Begin.HasValue ? Begin.Value : 0);
                 result = (result*397) ^ (End.HasValue ? End.Value : 0);
                 result = (result*397) ^ MissedCleavages;

pwiz_tools/Skyline/Model/PeptideDocNode.cs

@@ -227,6 +227,9 @@ public string GetCrosslinkedSequence()
         public Color Color { get; private set; }
         public static readonly Color UNKNOWN_COLOR = Color.FromArgb(170, 170, 170);
 
+        // For robust chromatogram association in the event of user tweaking molecule details like name, CAS etc (but not mass!)
+        public Target ChromatogramTarget => Peptide.OriginalMoleculeTarget ?? ModifiedTarget;
+
         public Target Target { get { return Peptide.Target; }}
         public string TextId { get { return CustomInvariantNameOrText(Peptide.Sequence); } }
         public string RawTextId { get { return CustomInvariantNameOrText(ModifiedTarget.Sequence); } }
@@ -682,7 +685,10 @@ public PeptideDocNode ChangeExplicitRetentionTime(double? prop)
         // Note: this potentially returns a node with a different ID, which has to be Inserted rather than Replaced
         public PeptideDocNode ChangeCustomIonValues(SrmSettings settings, CustomMolecule customMolecule, ExplicitRetentionTimeInfo explicitRetentionTime)
         {
-            var newPeptide = new Peptide(customMolecule);
+            // Make note of original description for chromatogram association, if nothing has changed to affect the chromatogram, so we can keep the association
+            var sameMass = Equals(customMolecule.AverageMass, Peptide.CustomMolecule.AverageMass) && 
+                           Equals(customMolecule.Formula, Peptide.CustomMolecule.Formula);
+            var newPeptide = new Peptide(customMolecule, sameMass ? Peptide.Target : null);
             Helpers.AssignIfEquals(ref newPeptide, Peptide);
             if (Equals(Peptide, newPeptide))
             {

pwiz_tools/Skyline/Model/Results/ChromDataSet.cs

@@ -194,7 +194,7 @@ public Target ModifiedSequence
                     var peptideDocNode = NodeGroups.FirstOrDefault()?.Item1;
                     if (peptideDocNode != null)
                     {
-                        return peptideDocNode.ModifiedTarget;
+                        return peptideDocNode.ChromatogramTarget;
                     }
                 }
                 return _listChromData.Count > 0 ? BestChromatogram.Key.Target : null;

pwiz_tools/Skyline/Model/Results/ChromatogramCache.cs

@@ -395,7 +395,7 @@ private bool TextIdEqual(ChromGroupHeaderInfo entry, PeptideDocNode nodePep)
             int textIdLen = entry.TextIdLen;
             if (nodePep.Peptide.IsCustomMolecule)
             {
-                if (EqualTextIdBytes(nodePep.CustomMolecule.ToSerializableString(), textIdIndex, textIdLen))
+                if (EqualTextIdBytes(nodePep.ChromatogramTarget.ToSerializableString(), textIdIndex, textIdLen))
                 {
                     return true;
                 }

pwiz_tools/Skyline/Model/Results/OnDemandFeatureCalculator.cs

@@ -357,7 +357,7 @@ internal PeptideChromDataSets MakePeptideChromDataSets()
                         continue;
                     }
                     var rawTimeIntensities = chromatogramInfo.TimeIntensities;
-                    var chromKey = new ChromKey(PeptideDocNode.ModifiedTarget, transitionGroup.PrecursorMz, null,
+                    var chromKey = new ChromKey(PeptideDocNode.ChromatogramTarget, transitionGroup.PrecursorMz, null,
                         transition.Mz, 0, 0, 0, transition.IsMs1 ? ChromSource.ms1 : ChromSource.fragment,
                         ChromExtractor.summed, true, false);
                     chromDatas.Add(new ChromData(chromKey, transition, rawTimeIntensities, rawTimeIntensities));

pwiz_tools/Skyline/Model/Results/PeptideChromData.cs

@@ -144,7 +144,7 @@ public bool Load(ChromDataProvider provider)
             foreach (var set in _dataSets.ToArray())
             {
                 Color peptideColor = NodePep != null ? NodePep.Color : PeptideDocNode.UNKNOWN_COLOR;
-                if (!set.Load(provider, NodePep != null ? NodePep.ModifiedTarget : null, peptideColor))
+                if (!set.Load(provider, NodePep != null ? NodePep.ChromatogramTarget : null, peptideColor))
                     _dataSets.Remove(set);
             }
             //Console.Out.WriteLine("Ending {0} {1} {2}", NodePep, _dataSets.Count, RuntimeHelpers.GetHashCode(this));

pwiz_tools/Skyline/Model/Results/SpectraChromDataProvider.cs

@@ -306,7 +306,7 @@ private void ExtractChromatogramsLocked()
                     var peptideNode = peptideFinder != null ? peptideFinder.FindPeptide(precursorMz) : null;
                     ProcessSrmSpectrum(
                         (float) dataSpectrum.RetentionTime.Value,
-                        peptideNode != null ? peptideNode.ModifiedTarget : null,
+                        peptideNode != null ? peptideNode.ChromatogramTarget : null,
                         peptideNode != null ? peptideNode.Color : PeptideDocNode.UNKNOWN_COLOR,
                         precursorMz,
                         filterIndex,

pwiz_tools/Skyline/Model/Results/SpectrumFilter.cs

@@ -281,7 +281,7 @@ public sealed class SpectrumFilter : IFilterInstrumentInfo
                             var ce = step.HasValue
                                 ? document.GetCollisionEnergy(nodePep, nodeGroup, null, step.Value)
                                 : (double?)null;
-                            var key = new PrecursorTextId(mz, step, ce, ionMobilityFilter, nodePep.ModifiedTarget, ChromExtractor.summed);
+                            var key = new PrecursorTextId(mz, step, ce, ionMobilityFilter, nodePep.ChromatogramTarget, ChromExtractor.summed);
 
                             if (!dictPrecursorMzToFilter.TryGetValue(key, out var filter))
                             {

pwiz_tools/Skyline/Model/Serialization/DocumentReader.cs

@@ -1013,6 +1013,7 @@ private PeptideDocNode ReadPeptideXml(XmlReader reader, PeptideGroup group, bool
             TransitionGroupDocNode[] children = null;
             Adduct adduct = Adduct.EMPTY;
             var customMolecule = isCustomMolecule ? CustomMolecule.Deserialize(reader, out adduct) : null; // This Deserialize only reads attributes, doesn't advance the reader
+            Target chromatogramTarget = null;
             if (customMolecule != null)
             {
                 if (DocumentMayContainMoleculesWithEmbeddedIons && customMolecule.ParsedMolecule.IsMassOnly && customMolecule.MonoisotopicMass.IsMassH())
@@ -1023,10 +1024,16 @@ private PeptideDocNode ReadPeptideXml(XmlReader reader, PeptideGroup group, bool
                         customMolecule.AverageMass.ChangeIsMassH(false),
                         customMolecule.Name);
                 }
+                // If user changed any molecule details (other than formula or mass) after chromatogram extraction, this info continues the target->chromatogram association
+                var encodedChromatogramTarget = reader.GetAttribute(ATTR.chromatogram_target);
+                if (!string.IsNullOrEmpty(encodedChromatogramTarget))
+                {
+                    chromatogramTarget = Target.FromSerializableString(encodedChromatogramTarget);
+                }
             }
             Assume.IsTrue(DocumentMayContainMoleculesWithEmbeddedIons || adduct.IsEmpty); // Shouldn't be any charge info at the peptide/molecule level
             var peptide = isCustomMolecule ?
-                new Peptide(customMolecule) :
+                new Peptide(customMolecule, chromatogramTarget) :
                 new Peptide(group as FastaSequence, sequence, start, end, missedCleavages, isDecoy);
             if (reader.IsEmptyElement)
                 reader.Read();

pwiz_tools/Skyline/Model/Serialization/DocumentSerializer.cs

@@ -178,6 +178,7 @@ public static class ATTR
             public const string precursor_concentration = "precursor_concentration";
             public const string attribute_group_id = "attribute_group_id";
             public const string peptide_index = "peptide_index";
+            public const string chromatogram_target = "chromatogram_target";
 
             // Results
             public const string replicate = "replicate";

pwiz_tools/Skyline/Model/Serialization/DocumentWriter.cs

@@ -264,6 +264,11 @@ private void WritePeptideXml(XmlWriter writer, PeptideDocNode node)
             if (isCustomIon)
             {
                 peptide.CustomMolecule.WriteXml(writer, Adduct.EMPTY);
+                // If user changed any molecule details (other than formula or mass) after chromatogram extraction, this info continues the target->chromatogram association
+                if (!Equals(peptide.Target, peptide.OriginalMoleculeTarget))
+                {
+                    writer.WriteAttributeString(ATTR.chromatogram_target, peptide.OriginalMoleculeTarget.ToSerializableString());
+                }
             }
             else
             {

pwiz_tools/Skyline/TestFunctional/AgilentGCEITest.cs

@@ -18,6 +18,7 @@
  */
 
 using Microsoft.VisualStudio.TestTools.UnitTesting;
+using pwiz.Skyline.SettingsUI;
 using pwiz.SkylineTestUtil;
 
 namespace pwiz.SkylineTestFunctional
@@ -51,6 +52,16 @@ protected override void DoTest()
             // Extract chromatograms from an Agilent file describing GC EI data as MS1
             ImportResults(new[] { TestFilesDir.GetTestPath(@"cmsptc_00000_20230106_SCFA_1.mzML") });
 
+            // Now tinker with molecule details that don't change the molecule mass - should still be able to associate chromatograms
+            RunUI(() => { SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].FirstNode; });
+            var doc = SkylineWindow.Document;
+            var editMoleculeDlg = ShowDialog<EditCustomMoleculeDlg>(SkylineWindow.ModifyPeptide);
+            RunUI(() => { editMoleculeDlg.NameText = editMoleculeDlg.NameText + "_renamed"; }); // Change the name - will not break the molecule/chromatogram association
+            // RunUI(() => { editMoleculeDlg.FormulaBox.Formula += "N2"; }); This would break the molecule/chromatogram association
+            OkDialog(editMoleculeDlg, editMoleculeDlg.OkDialog);
+            WaitForDocumentChangeLoaded(doc);
+            VerifyAllTransitionsHaveChromatograms(); // Verify that name change did not break the molecule/chromatogram association
+
             // If data has not been properly understood as GC EI all-ions, some peaks won't be found
             var nPeaksFound = 0;
             foreach (var tg in SkylineWindow.Document.MoleculeTransitions)

pwiz_tools/Skyline/TestFunctional/SrmSmMolChromTest.cs

@@ -17,8 +17,8 @@
  * limitations under the License.
  */
 using Microsoft.VisualStudio.TestTools.UnitTesting;
-using pwiz.Skyline.Model;
 using pwiz.Skyline.Model.Results;
+using pwiz.Skyline.SettingsUI;
 using pwiz.SkylineTestUtil;
 
 namespace pwiz.SkylineTestFunctional
@@ -39,36 +39,30 @@ public void TestSrmSmallMoleculeChromatograms()
 
         protected override void DoTest()
         {
-            RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("SrmSmMolChromTest.sky")));
+            var testPath = TestFilesDir.GetTestPath("SrmSmMolChromTest.sky");
+            RunUI(() => SkylineWindow.OpenFile(testPath));
             ImportResultsFiles(new[]
             {
                 new MsDataFilePath(TestFilesDir.GetTestPath("ID36310_01_WAA263_3771_030118" + ExtensionTestContext.ExtMz5)),
                 new MsDataFilePath(TestFilesDir.GetTestPath("ID36311_01_WAA263_3771_030118" + ExtensionTestContext.ExtMz5))
             });
-            VerifyAllTransitionsHaveChromatograms(SkylineWindow.Document);
-        }
+            VerifyAllTransitionsHaveChromatograms();
 
-        private void VerifyAllTransitionsHaveChromatograms(SrmDocument doc)
-        {
-            var tolerance = (float) doc.Settings.TransitionSettings.Instrument.MzMatchTolerance;
-            foreach (var molecule in doc.Molecules)
-            {
-                foreach (var precursor in molecule.TransitionGroups)
-                {
-                    foreach (var chromatogramSet in doc.MeasuredResults.Chromatograms)
-                    {
-                        ChromatogramGroupInfo[] chromatogramGroups;
-                        Assert.IsTrue(doc.MeasuredResults.TryLoadChromatogram(chromatogramSet, molecule, precursor, tolerance, out chromatogramGroups));
-                        Assert.AreEqual(1, chromatogramGroups.Length);
-                        foreach (var transition in precursor.Transitions)
-                        {
-                            var chromatogram = chromatogramGroups[0].GetTransitionInfo(transition, tolerance);
-                            Assert.IsNotNull(chromatogram);
-                        }
-                    }
-                }
-            }
-
+            // Now tinker with molecule details that don't change the molecule mass - should still be able to associate chromatograms
+            RunUI(() => { SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].FirstNode; });
+            var doc = SkylineWindow.Document;
+            var editMoleculeDlg = ShowDialog<EditCustomMoleculeDlg>(SkylineWindow.ModifyPeptide);
+            RunUI(() => { editMoleculeDlg.NameText = editMoleculeDlg.NameText + "_renamed"; }); // Change the name
+            OkDialog(editMoleculeDlg, editMoleculeDlg.OkDialog);
+            WaitForDocumentChangeLoaded(doc);
+            VerifyAllTransitionsHaveChromatograms();
+
+            // That info should survive serialization round trip
+            RunUI(() => SkylineWindow.SaveDocument(testPath));
+            RunUI(() => SkylineWindow.NewDocument());
+            RunUI(() => SkylineWindow.OpenFile(testPath));
+            VerifyAllTransitionsHaveChromatograms();
         }
+
     }
 }

pwiz_tools/Skyline/TestUtil/Schemas/Skyline_Current.xsd

@@ -921,6 +921,8 @@
         <xs:attribute name="custom_ion_name" type="xs:string" use="optional"/>
         <!--Any or all of InChiKey, CAS, HMDB etc tab separated -->
         <xs:attribute name="id" type="xs:string" use="optional"/>
+        <!-- Encodes the molecule description used in chromatogram extraction if user changed the name etc afterwards -->
+        <xs:attribute name="chromatogram_target" type="xs:string" use="optional"/>
       </xs:extension>
     </xs:complexContent>
   </xs:complexType>

pwiz_tools/Skyline/TestUtil/TestFunctional.cs

@@ -2521,6 +2521,29 @@ public void ImportResultsFiles(string dirPath, string ext, string filter, bool?
             WaitForDocumentChange(doc);
         }
 
+        public void VerifyAllTransitionsHaveChromatograms()
+        {
+            var doc = WaitForDocumentLoaded();
+            var tolerance = (float)doc.Settings.TransitionSettings.Instrument.MzMatchTolerance;
+            foreach (var molecule in doc.Molecules)
+            {
+                foreach (var precursor in molecule.TransitionGroups)
+                {
+                    foreach (var chromatogramSet in doc.MeasuredResults.Chromatograms)
+                    {
+                        ChromatogramGroupInfo[] chromatogramGroups;
+                        Assert.IsTrue(doc.MeasuredResults.TryLoadChromatogram(chromatogramSet, molecule, precursor, tolerance, out chromatogramGroups));
+                        Assert.AreEqual(1, chromatogramGroups.Length);
+                        foreach (var transition in precursor.Transitions)
+                        {
+                            var chromatogram = chromatogramGroups[0].GetTransitionInfo(transition, tolerance);
+                            Assert.IsNotNull(chromatogram);
+                        }
+                    }
+                }
+            }
+        }
+
         #endregion
 
         #region Spectral library test helpers