Ptm stoich

MetaMorpheus/EngineLayer/GlobalVariables.cs

@@ -1,4 +1,4 @@
 global using obo = Omics.Modifications.IO.obo;
 using Chemistry;
 using Easy.Common.Extensions;
 using EngineLayer.GlycoSearch;
@@ -19,6 +19,7 @@
 using Transcriptomics.Digestion;
 using UsefulProteomicsDatabases;
 using System.Security.Cryptography;
+using Omics.Modifications.IO;
 
 namespace EngineLayer
 {

MetaMorpheus/EngineLayer/Ms2ScanWithSpecificMass.cs

@@ -26,6 +26,23 @@
 
             TheScan = mzLibScan;
 
+            // Build the lightweight metadata snapshot
+            ScanMetadata = new ScanMetadata(
+                OneBasedScanNumber: mzLibScan.OneBasedScanNumber,
+                OneBasedPrecursorScanNumber: mzLibScan.OneBasedPrecursorScanNumber,
+                RetentionTime: mzLibScan.RetentionTime,
+                NumPeaks: mzLibScan.MassSpectrum.Size,
+                TotalIonCurrent: mzLibScan.TotalIonCurrent,
+                NativeId: mzLibScan.NativeId,
+                FullFilePath: fullFilePath,
+                PrecursorCharge: precursorCharge,
+                PrecursorMonoisotopicPeakMz: precursorMonoisotopicPeakMz,
+                PrecursorMass: PrecursorMass,
+                PrecursorIntensity: PrecursorIntensity,
+                PrecursorEnvelopePeakCount: PrecursorEnvelopePeakCount,
+                PrecursorFractionalIntensity: PrecursorFractionalIntensity,
+                OneOverK0: mzLibScan is TimsDataScan tims ? tims.OneOverK0 : null);
+
             if (commonParam.DissociationType != DissociationType.LowCID)
             {
                 ExperimentalFragments = neutralExperimentalFragments ?? GetNeutralExperimentalFragments(mzLibScan, commonParam);
@@ -41,6 +58,14 @@
         }
 
         public MsDataScan TheScan { get; }
+
+        /// <summary>
+        /// Lightweight, immutable snapshot of scan and precursor metadata.
+        /// Designed to be passed to SpectralMatch so the heavyweight scan objects
+        /// can be released from memory after scoring.
+        /// </summary>
+        public ScanMetadata ScanMetadata { get; }
+
         public double PrecursorMonoisotopicPeakMz { get; }
         public double PrecursorMass { get; }
         public int PrecursorCharge { get; }
@@ -67,7 +92,7 @@
         /// An array containing the intensities of the reporter ions for isobaric mass tags. 
         /// If multiplex quantification wasn't performed, this will be null
         /// </summary>
         public double[]? IsobaricMassTagReporterIonIntensities { get; private set; }
 
         public static IsotopicEnvelope[] GetNeutralExperimentalFragments(MsDataScan scan, CommonParameters commonParam)
         {

MetaMorpheus/EngineLayer/ProteinScoringAndFdr/ProteinScoringAndFdrEngine.cs

@@ -165,8 +165,8 @@ private List<ProteinGroup> DoProteinFdr(List<ProteinGroup> proteinGroups)
                 }
 
                 pg.BestPeptideScore = pg.AllPsmsBelowOnePercentFDR.Max(psm => psm.Score);
-                pg.BestPeptideQValue = pg.AllPsmsBelowOnePercentFDR.Min(psm => psm.FdrInfo.QValueNotch);
-                pg.BestPeptidePEP = pg.AllPsmsBelowOnePercentFDR.Min(psm => psm.FdrInfo.PEP);
+                pg.BestPeptideQValue = pg.AllPsmsBelowOnePercentFDR.OfType<SpectralMatch>().Min(psm => psm.FdrInfo.QValueNotch);
+                pg.BestPeptidePEP = pg.AllPsmsBelowOnePercentFDR.OfType<SpectralMatch>().Min(psm => psm.FdrInfo.PEP);
             }
 
             // pick the best for each paired accession based on filter type

MetaMorpheus/EngineLayer/Silac/SilacConversions.cs

@@ -8,6 +8,8 @@
 using Omics.Modifications;
 using Omics.Digestion;
 using EngineLayer.SpectrumMatch;
+using Easy.Common.Extensions;
+using MzLibUtil;
 using MassSpectrometry;
 
 namespace EngineLayer
@@ -453,26 +455,30 @@ public static void SilacConversionsPostQuantification(List<SilacLabel> allSilacL
                 flashLfqResults.CalculateProteinResultsMedianPolish(true);
 
                 //update proteingroups to have all files for quantification
+                // Modification occupancy is now computed by BioPolymerGroup.PopulateSampleGroupResults()
                 if (proteinGroups != null)
                 {
                     List<SpectraFileInfo> allInfo = originalToLabeledFileInfoDictionary.SelectMany(x => x.Value).ToList();
                     foreach (ProteinGroup proteinGroup in proteinGroups)
                     {
                         proteinGroup.FilesForQuantification = allInfo;
-                        proteinGroup.IntensitiesByFile = new Dictionary<SpectraFileInfo, double>();
 
+                        // Build the dictionary locally, then assign in one shot.
+                        // The IntensitiesByFile getter returns a copy, so .Add() on it would be lost.
+                        var intensities = new Dictionary<SpectraFileInfo, double>();
                         foreach (var spectraFile in allInfo)
                         {
                             if (flashLfqResults.ProteinGroups.TryGetValue(proteinGroup.ProteinGroupName, out var flashLfqProteinGroup))
                             {
-                                proteinGroup.IntensitiesByFile.Add(spectraFile, flashLfqProteinGroup.GetIntensity(spectraFile));
+                                intensities.Add(spectraFile, flashLfqProteinGroup.GetIntensity(spectraFile));
                             }
                             else
                             {
                                 //needed for decoys/contaminants/proteins that aren't quantified
-                                proteinGroup.IntensitiesByFile.Add(spectraFile, 0);
+                                intensities.Add(spectraFile, 0);
                             }
                         }
+                        proteinGroup.IntensitiesByFile = intensities;
                     }
                 }
 

MetaMorpheus/EngineLayer/SpectralMatch.cs

@@ -7,49 +7,29 @@
 using System.Collections.Generic;
 using System.Linq;
 using Omics;
+using Omics.SpectralMatch;
 using System;
 using Omics.Digestion;
 using EngineLayer.CrosslinkSearch;
 using EngineLayer.SpectrumMatch;
 
 namespace EngineLayer
 {
-    public abstract class SpectralMatch : IComparable<SpectralMatch>
+    public abstract class SpectralMatch : ISpectralMatch, IComparable<SpectralMatch>
     {
         public const double ToleranceForScoreDifferentiation = 1e-9;
 
         protected SpectralMatch(IBioPolymerWithSetMods peptide, int notch, double score, int scanIndex, Ms2ScanWithSpecificMass scan, CommonParameters commonParameters, List<MatchedFragmentIon> matchedFragmentIons)
         {
             _BestMatchingBioPolymersWithSetMods = new List<SpectralMatchHypothesis>();
             ScanIndex = scanIndex;
-            FullFilePath = scan.FullFilePath;
-            ScanNumber = scan.OneBasedScanNumber;
-            PrecursorScanNumber = scan.OneBasedPrecursorScanNumber;
-            ScanRetentionTime = scan.RetentionTime;
-            ScanExperimentalPeaks = scan.NumPeaks;
-            PrecursorScanIntensity = scan.PrecursorIntensity;
-            TotalIonCurrent = scan.TotalIonCurrent;
-            ScanPrecursorCharge = scan.PrecursorCharge;
-            ScanPrecursorMonoisotopicPeakMz = scan.PrecursorMonoisotopicPeakMz;
-            ScanPrecursorMass = scan.PrecursorMass;
-            PrecursorScanEnvelopePeakCount = scan.PrecursorEnvelopePeakCount;
-            PrecursorFractionalIntensity = scan.PrecursorFractionalIntensity;
+            ScanMetadata = scan.ScanMetadata;
             PrecursorScanDeconvolutionScore = scan.PrecursorDeconvolutionScore;
             DigestionParams = commonParameters.DigestionParams;
-            NativeId = scan.NativeId;
             RunnerUpScore = commonParameters.ScoreCutoff;
             SpectralAngle = -1;
             IsobaricMassTagReporterIonIntensities = scan.IsobaricMassTagReporterIonIntensities;
 
-            if (scan.TheScan is TimsDataScan timsScan)
-            {
-                ScanOneOverK0 = timsScan.OneOverK0;
-            }
-            else
-            {
-                ScanOneOverK0 = null; // this is only used for ion mobility data, so it can be null
-            }
-
             AddOrReplace(peptide, score, notch, true, matchedFragmentIons);
         }
 
@@ -69,25 +49,80 @@
         public int PsmCount { get; internal set; }
         public Dictionary<string, int> ModsIdentified { get; private set; } // these should never be null under normal circumstances
         public List<double> LocalizedScores { get; internal set; }
-        public int ScanNumber { get; }
-        public int? PrecursorScanNumber { get; }
-        public double ScanRetentionTime { get; }
-        public int ScanExperimentalPeaks { get; }
-        public double TotalIonCurrent { get; }
-        public int ScanPrecursorCharge { get; }
-        public double ScanPrecursorMonoisotopicPeakMz { get; }
-        public double PrecursorScanIntensity { get; }
-        public int PrecursorScanEnvelopePeakCount { get; }
-        public double PrecursorFractionalIntensity { get; }
+
+        #region Scan metadata — delegated to ScanMetadata record
+
+        /// <summary>
+        /// Lightweight, immutable snapshot of scan and precursor metadata.
+        /// Replaces the individual scan-derived fields that were previously unpacked
+        /// from Ms2ScanWithSpecificMass during construction.
+        /// </summary>
+        public ScanMetadata ScanMetadata { get; }
+
+        // Pass-through properties for backwards compatibility.
+        // Callers can be migrated to ScanMetadata.* over time.
+        public int ScanNumber => ScanMetadata.OneBasedScanNumber;
+        public int? PrecursorScanNumber => ScanMetadata.OneBasedPrecursorScanNumber;
+        public double ScanRetentionTime => ScanMetadata.RetentionTime;
+        public int ScanExperimentalPeaks => ScanMetadata.NumPeaks;
+        public double TotalIonCurrent => ScanMetadata.TotalIonCurrent;
+        public int ScanPrecursorCharge => ScanMetadata.PrecursorCharge;
+        public double ScanPrecursorMonoisotopicPeakMz => ScanMetadata.PrecursorMonoisotopicPeakMz;
+        public double PrecursorScanIntensity => ScanMetadata.PrecursorIntensity;
+        public int PrecursorScanEnvelopePeakCount => ScanMetadata.PrecursorEnvelopePeakCount;
+        public double PrecursorFractionalIntensity => ScanMetadata.PrecursorFractionalIntensity;
+        public double ScanPrecursorMass => ScanMetadata.PrecursorMass;
+        public double? ScanOneOverK0 => ScanMetadata.OneOverK0;
+        public string FullFilePath => ScanMetadata.FullFilePath;
+        public string NativeId => ScanMetadata.NativeId;
+
         /// <summary>
         /// Method-agnostic envelope-quality score in [0, 1] from mzLib's DeconvolutionScorer for
         /// the precursor envelope of this PSM. 0 indicates no envelope was computed or the
         /// envelope is maximally bad; higher = better-shaped Averagine match.
         /// </summary>
         public double PrecursorScanDeconvolutionScore { get; }
-        public double ScanPrecursorMass { get; }
-        public double? ScanOneOverK0 { get; set; } // this is only used for ion mobility data, so it can be null
-        public string FullFilePath { get; private set; }
+
+        #endregion
+
+        #region ISpectralMatch explicit interface implementations
+
+        /// <summary>Maps to <see cref="ScanNumber"/> for ISpectralMatch compatibility.</summary>
+        int ISpectralMatch.OneBasedScanNumber => ScanNumber;
+
+        /// <summary>
+        /// Consolidates quantification intensities for ISpectralMatch compatibility.
+        /// Returns ReporterIonIntensities if available (isobaric), a singleton array of
+        /// PrecursorScanIntensity for LFQ, or null if neither is populated.
+        /// </summary>
+        double[]? ISpectralMatch.Intensities =>
+            IsobaricMassTagReporterIonIntensities ??
+            (PrecursorScanIntensity > 0 ? new[] { PrecursorScanIntensity } : null);
+
+        /// <summary>
+        /// Returns the identified biopolymers (peptides/proteoforms) for ISpectralMatch compatibility.
+        /// Unwraps SpectralMatchHypothesis to the underlying IBioPolymerWithSetMods.
+        /// </summary>
+        public IEnumerable<IBioPolymerWithSetMods> GetIdentifiedBioPolymersWithSetMods() =>
+            BestMatchingBioPolymersWithSetMods.Select(h => h.SpecificBioPolymer);
+
+        public int CompareTo(ISpectralMatch? other)
+        {
+            if (other is null) return 1;
+            if (other is SpectralMatch mm) return CompareTo(mm);
+            // Fallback: compare by score descending
+            return Score.CompareTo(other.Score);
+        }
+
+        public bool Equals(ISpectralMatch? other)
+        {
+            if (other is null) return false;
+            return FullFilePath == other.FullFilePath
+                && ScanNumber == other.OneBasedScanNumber
+                && FullSequence == other.FullSequence;
+        }
+
+        #endregion
         /// <summary>
         /// Refers to the index of the Ms2ScanWithSpecificMass in an array of Ms2ScansWithSpecificMass that is sorted by precursor mass
         /// </summary>
@@ -110,7 +145,6 @@
 
         public double Score { get; private set; }
         public double SpectralAngle { get; set; }
-        public string NativeId; // this is a property of the scan. used for mzID writing
 
         public double DeltaScore { get { return (Score - RunnerUpScore); } }
 
@@ -165,10 +199,11 @@
         protected List<SpectralMatchHypothesis> _BestMatchingBioPolymersWithSetMods;
 
         /// <summary>
-        /// An array containing the intensities of the reporter ions for isobaric mass tags. 
-        /// If multiplex quantification wasn't performed, this will be null
+        /// An array containing the intensities of the reporter ions for isobaric mass tags (TMT, iTRAQ, diLeu, etc.).
+        /// Null if multiplex quantification wasn't performed.
+        /// Array order matches the reporter ion order defined by the mass tag modification.
         /// </summary>
         public double[]? IsobaricMassTagReporterIonIntensities { get; private set; }
 
         public IEnumerable<SpectralMatchHypothesis> BestMatchingBioPolymersWithSetMods
         {
@@ -388,6 +423,12 @@
             BaseSequence = PsmTsvWriter.Resolve(bestMatchingPeptides.Select(b => b.SpecificBioPolymer.BaseSequence)).ResolvedValue;
             FullSequence = PsmTsvWriter.Resolve(bestMatchingPeptides.Select(b => b.SpecificBioPolymer.FullSequence)).ResolvedValue;
 
+            // Scan metadata is an immutable record — safe to share the reference
+            ScanMetadata = psm.ScanMetadata;
+            ScanIndex = psm.ScanIndex;
+            PrecursorScanDeconvolutionScore = psm.PrecursorScanDeconvolutionScore;
+            IsobaricMassTagReporterIonIntensities = psm.IsobaricMassTagReporterIonIntensities;
+
             ModsChemicalFormula = psm.ModsChemicalFormula;
             Notch = psm.Notch;
             BioPolymerWithSetModsLength = psm.BioPolymerWithSetModsLength;
@@ -401,17 +442,8 @@
             PsmCount = psm.PsmCount;
             ModsIdentified = psm.ModsIdentified;
             LocalizedScores = psm.LocalizedScores;
-            ScanNumber = psm.ScanNumber;
-            PrecursorScanNumber = psm.PrecursorScanNumber;
-            ScanRetentionTime = psm.ScanRetentionTime;
-            ScanExperimentalPeaks = psm.ScanExperimentalPeaks;
-            TotalIonCurrent = psm.TotalIonCurrent;
-            ScanPrecursorCharge = psm.ScanPrecursorCharge;
-            ScanPrecursorMonoisotopicPeakMz = psm.ScanPrecursorMonoisotopicPeakMz;
-            ScanPrecursorMass = psm.ScanPrecursorMass;
-            FullFilePath = psm.FullFilePath;
-            ScanIndex = psm.ScanIndex;
             FdrInfo = psm.FdrInfo;
+            PeptideFdrInfo = psm.PeptideFdrInfo;
             Score = psm.Score;
             RunnerUpScore = psm.RunnerUpScore;
             IsDecoy = psm.IsDecoy;
@@ -612,4 +644,4 @@
         }
 
     }
-}
+}

MetaMorpheus/EngineLayer/Util/IsobaricMassTag.cs

@@ -24,7 +24,7 @@
     /// This class contains information about the Isobaric Mass Tag (e.g., TMT), including the theoretical m/z values of the reporter ions
     /// as well as methods designed to retrieve the intensities of those reporter ions from a given MzSpectrum. 
     /// It does not store any intensity information itself. Intensity information is associated with each Ms2ScanWithSpecificMass object or SpectralMatch,
-    /// in the IsobaricMassTagReporterIonIntensities property.
+    /// in the IsobaricMassTagReporterIonIntensities property (Ms2ScanWithSpecificMass) or ReporterIonIntensities property (SpectralMatch).
     /// </summary>
     public class IsobaricMassTag
     {
@@ -103,7 +103,7 @@
         /// Takes in a spectrum, searches for the reporter ions within the specified ppm tolerance,
         /// and returns their intensities. If a reporter ion is not found, its intensity will be zero.
         /// </summary>
         public double[]? GetReporterIonIntensities(MzSpectrum spectrum)
         {
             if (spectrum == null || spectrum.Size < 1) return null;
             double[] reporterIonIntensities = new double[ReporterIonMzs.Length];

MetaMorpheus/GuiFunctions/MetaDraw/FragmentResearching/FragmentationReanalysisViewModel.cs

@@ -6,6 +6,7 @@
 using System.Windows;
 using Easy.Common.Extensions;
 using EngineLayer;
+using GuiFunctions.Util;
 using iText.StyledXmlParser.Jsoup;
 using MassSpectrometry;
 using MzLibUtil;
@@ -26,12 +27,13 @@ public class FragmentationReanalysisViewModel : BaseViewModel
     {
         private readonly bool _isProtein;
         private static readonly object _fragmentationLock = new();
+        private static readonly object _productsLock = new();
 
         public FragmentationReanalysisViewModel(bool isProtein = true)
         {
             _isProtein = isProtein;
             ProductIonMassTolerance = 20;
-            PossibleProducts = [.. GetPossibleProducts()];
+            PossibleProducts = new ThreadSafeObservableCollection<FragmentViewModel>(GetPossibleProducts());
 
             IEnumerable<DissociationType> values;
             CommonParameters common;
@@ -77,15 +79,13 @@ public void LoadFragmentationParameters(CommonParameters common, SearchParameter
             FragmentationParamsViewModel = new(common, search);
         }
 
-        private ObservableCollection<FragmentViewModel> _possibleProducts;
-        public ObservableCollection<FragmentViewModel> PossibleProducts
+        private ThreadSafeObservableCollection<FragmentViewModel> _possibleProducts;
+        public ThreadSafeObservableCollection<FragmentViewModel> PossibleProducts
         {
             get => _possibleProducts;
             set { _possibleProducts = value; OnPropertyChanged(nameof(PossibleProducts)); }
         }
 
-        private IEnumerable<ProductType> _productsToUse => PossibleProducts.Where(p => p.Use).Select(p => p.ProductType);
-
         private bool _persist;
         public bool Persist
         {
@@ -249,7 +249,7 @@ public List<MatchedFragmentIon> MatchIonsWithNewTypes(MsDataScan ms2Scan, Spectr
             List<Product> internalProducts = new List<Product>();
 
             // Snapshot products before acquiring lock to avoid enumerating collection while it may be modified by UI thread
-            var productsSnapshot = _productsToUse.ToList();
+            var productsSnapshot = GetProductsSnapshot();
             // Lock to ensure thread-safe mutation of static DissociationTypeCollection dictionary
             lock (_fragmentationLock)
             {
@@ -298,6 +298,14 @@ public List<MatchedFragmentIon> MatchIonsWithNewTypes(MsDataScan ms2Scan, Spectr
                 .ToList();
         }
 
+        private List<ProductType> GetProductsSnapshot()
+        {
+            lock (_productsLock)
+            {
+                return PossibleProducts.Where(p => p.Use).Select(p => p.ProductType).ToList();
+            }
+        }
+
         public static readonly IEqualityComparer<MatchedFragmentIon> MatchedFragmentIonComparer = new MatchedFragmentIonEqualityComparer();
 
         public class MatchedFragmentIonEqualityComparer : IEqualityComparer<MatchedFragmentIon>