#3 -Spectral Match Generalization

MetaMorpheus/EngineLayer/Calibration/DataPointAcquisitionEngine.cs

@@ -14,15 +14,15 @@ public class DataPointAcquisitionEngine : MetaMorpheusEngine
     {
         private const double FineResolutionForIsotopeDistCalculation = 0.1;
 
-        private readonly List<PeptideSpectralMatch> GoodIdentifications;
+        private readonly List<SpectralMatch> GoodIdentifications;
         private readonly List<Ms2ScanWithSpecificMass> GoodScans;
         private readonly MsDataFile MyMsDataFile;
         private readonly Tolerance PrecursorMassTolerance;
         private readonly Tolerance ProductMassTolerance;
         private readonly int MinMS1isotopicPeaksNeededForConfirmedIdentification;
 
         public DataPointAcquisitionEngine(
-            List<PeptideSpectralMatch> goodIdentifications,
+            List<SpectralMatch> goodIdentifications,
             List<Ms2ScanWithSpecificMass> goodScans,
             MsDataFile myMsDataFile,
             Tolerance precursorMassTolerance,
@@ -65,16 +65,16 @@ protected override MetaMorpheusEngineResults RunSpecific()
                     // Stop loop if canceled
                     if (GlobalVariables.StopLoops) { return; }
 
-                    PeptideSpectralMatch identification = GoodIdentifications[matchIndex];
+                    SpectralMatch identification = GoodIdentifications[matchIndex];
 
                     // Each identification has an MS2 spectrum attached to it.
                     int ms2scanNumber = identification.ScanNumber;
                     int peptideCharge = identification.ScanPrecursorCharge;
                     //skip if ambiguous
-                    if (identification.FullSequence == null || identification.BestMatchingPeptides.Any(p => p.Peptide.AllModsOneIsNterminus.Any(m => m.Value.ChemicalFormula == null)))
+                    if (identification.FullSequence == null || identification.BestMatchingBioPolymersWithSetMods.Any(p => p.Peptide.AllModsOneIsNterminus.Any(m => m.Value.ChemicalFormula == null)))
                         continue;
 
-                    var representativeSinglePeptide = identification.BestMatchingPeptides.First().Peptide;
+                    var representativeSinglePeptide = identification.BestMatchingBioPolymersWithSetMods.First().Peptide;
 
                     // Get the peptide, don't forget to add the modifications!!!!
                     var SequenceWithChemicalFormulas = representativeSinglePeptide.SequenceWithChemicalFormulas;
@@ -126,7 +126,7 @@ protected override MetaMorpheusEngineResults RunSpecific()
             );
         }
 
-        private (List<LabeledDataPoint>, int, int) SearchMS1Spectra(double[] theoreticalMasses, double[] theoreticalIntensities, int ms2spectrumIndex, int direction, int peptideCharge, PeptideSpectralMatch identification)
+        private (List<LabeledDataPoint>, int, int) SearchMS1Spectra(double[] theoreticalMasses, double[] theoreticalIntensities, int ms2spectrumIndex, int direction, int peptideCharge, SpectralMatch identification)
         {
             List<LabeledDataPoint> result = new List<LabeledDataPoint>();
             int numMs1MassChargeCombinationsConsidered = 0;
@@ -220,7 +220,7 @@ protected override MetaMorpheusEngineResults RunSpecific()
             return (result, numMs1MassChargeCombinationsConsidered, numMs1MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks);
         }
 
-        private static List<LabeledDataPoint> SearchMS2Spectrum(Ms2ScanWithSpecificMass ms2DataScan, PeptideSpectralMatch identification, Tolerance ms2Tolerance)
+        private static List<LabeledDataPoint> SearchMS2Spectrum(Ms2ScanWithSpecificMass ms2DataScan, SpectralMatch identification, Tolerance ms2Tolerance)
         {
             List<LabeledDataPoint> result = new List<LabeledDataPoint>();
 

MetaMorpheus/EngineLayer/Calibration/DataPointAquisitionResults.cs

@@ -11,7 +11,7 @@ public class DataPointAquisitionResults : MetaMorpheusEngineResults
     {
         public DataPointAquisitionResults(
             MetaMorpheusEngine dataPointAcquisitionEngine,
-            List<PeptideSpectralMatch> psms,
+            List<SpectralMatch> psms,
             List<LabeledDataPoint> ms1List,
             List<LabeledDataPoint> ms2List,
             int numMs1MassChargeCombinationsConsidered,
@@ -41,7 +41,7 @@ public DataPointAquisitionResults(
             NumMs2MassChargeCombinationsConsidered = numMs2MassChargeCombinationsConsidered;
             NumMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks = numMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks;
 
-            var precursorErrors = psms.Select(p => (p.ScanPrecursorMass - p.PeptideMonisotopicMass.Value) / p.PeptideMonisotopicMass.Value * 1e6).ToList();
+            var precursorErrors = psms.Select(p => (p.ScanPrecursorMass - p.BioPolymerWithSetModsMonoisotopicMass.Value) / p.BioPolymerWithSetModsMonoisotopicMass.Value * 1e6).ToList();
             PsmPrecursorIqrPpmError = precursorErrors.InterquartileRange();
             PsmPrecursorMedianPpmError = precursorErrors.Median();
 
@@ -67,7 +67,7 @@ public DataPointAquisitionResults(
         public readonly double PsmProductMedianPpmError;
         public readonly double PsmPrecursorIqrPpmError;
         public readonly double PsmProductIqrPpmError;
-        public readonly List<PeptideSpectralMatch> Psms;
+        public readonly List<SpectralMatch> Psms;
 
         public int Count { get { return Ms1List.Count + Ms2List.Count; } }
 

MetaMorpheus/EngineLayer/Calibration/LabeledDataPoint.cs

@@ -9,9 +9,9 @@ public class LabeledDataPoint
         public readonly double LogIntensity;
         public readonly double TheoreticalMz;
         public readonly double RelativeMzError;
-        public readonly PeptideSpectralMatch Identification;
+        public readonly SpectralMatch Identification;
 
-        public LabeledDataPoint(double experimentalMz, int scanNumber, double logTotalIonCurrent, double logInjectionTime, double logIntensity, double theoreticalMz, PeptideSpectralMatch identification)
+        public LabeledDataPoint(double experimentalMz, int scanNumber, double logTotalIonCurrent, double logInjectionTime, double logIntensity, double theoreticalMz, SpectralMatch identification)
         {
             this.ExperimentalMz = experimentalMz;
             this.ScanNumber = scanNumber;

MetaMorpheus/EngineLayer/ClassicSearch/ClassicSearchEngine.cs

@@ -20,12 +20,12 @@ public class ClassicSearchEngine : MetaMorpheusEngine
         private readonly List<Modification> VariableModifications;
         private readonly List<SilacLabel> SilacLabels;
         private readonly (SilacLabel StartLabel, SilacLabel EndLabel)? TurnoverLabels;
-        private readonly PeptideSpectralMatch[] PeptideSpectralMatches;
+        private readonly SpectralMatch[] PeptideSpectralMatches;
         private readonly Ms2ScanWithSpecificMass[] ArrayOfSortedMS2Scans;
         private readonly double[] MyScanPrecursorMasses;
         private readonly bool WriteSpectralLibrary;
 
-        public ClassicSearchEngine(PeptideSpectralMatch[] globalPsms, Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans,
+        public ClassicSearchEngine(SpectralMatch[] globalPsms, Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans,
             List<Modification> variableModifications, List<Modification> fixedModifications, List<SilacLabel> silacLabels, SilacLabel startLabel, SilacLabel endLabel,
             List<Protein> proteinList, MassDiffAcceptor searchMode, CommonParameters commonParameters, List<(string FileName, CommonParameters Parameters)> fileSpecificParameters,
             SpectralLibrary spectralLibrary, List<string> nestedIds, bool writeSpectralLibrary)
@@ -163,7 +163,7 @@ protected override MetaMorpheusEngineResults RunSpecific()
                 });
             }
 
-            foreach (PeptideSpectralMatch psm in PeptideSpectralMatches.Where(p => p != null))
+            foreach (SpectralMatch psm in PeptideSpectralMatches.Where(p => p != null))
             {
                 psm.ResolveAllAmbiguities();
             }
@@ -201,7 +201,7 @@ private void AddPeptideCandidateToPsm(ScanWithIndexAndNotchInfo scan, object[] m
                 // valid hit (met the cutoff score); lock the scan to prevent other threads from accessing it
                 lock (myLocks[scan.ScanIndex])
                 {
-                    bool scoreImprovement = PeptideSpectralMatches[scan.ScanIndex] == null || (thisScore - PeptideSpectralMatches[scan.ScanIndex].RunnerUpScore) > -PeptideSpectralMatch.ToleranceForScoreDifferentiation;
+                    bool scoreImprovement = PeptideSpectralMatches[scan.ScanIndex] == null || (thisScore - PeptideSpectralMatches[scan.ScanIndex].RunnerUpScore) > -SpectralMatch.ToleranceForScoreDifferentiation;
 
                     if (scoreImprovement)
                     {

MetaMorpheus/EngineLayer/ClassicSearch/MiniClassicSearchEngine.cs

@@ -1,6 +1,7 @@
 using MassSpectrometry;
 using MassSpectrometry.MzSpectra;
 using MzLibUtil;
+using Omics;
 using Omics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System;
@@ -42,7 +43,7 @@ public MiniClassicSearchEngine(
         /// <param name="donorPwsm"> Ms2 scans in window are searched for matches to this donor peptide</param>
         /// <param name="peakApexRT"> The center of the 2 minute window where the search occurs</param>
         /// <returns></returns>
-        public IEnumerable<PeptideSpectralMatch> SearchAroundPeak(PeptideWithSetModifications donorPwsm, double peakApexRT)
+        public IEnumerable<SpectralMatch> SearchAroundPeak(IBioPolymerWithSetMods donorPwsm, double peakApexRT)
         {
             var targetFragmentsForEachDissociationType = new Dictionary<DissociationType, List<Product>>();
 
@@ -66,7 +67,7 @@ public IEnumerable<PeptideSpectralMatch> SearchAroundPeak(PeptideWithSetModifica
                 return null;
             }
 
-            List<PeptideSpectralMatch> acceptablePsms = new();
+            List<SpectralMatch> acceptablePsms = new();
             foreach (ScanWithIndexAndNotchInfo scan in acceptableScans)
             {
                 var dissociationType = FileSpecificParameters.DissociationType == DissociationType.Autodetect ?
@@ -95,8 +96,8 @@ public IEnumerable<PeptideSpectralMatch> SearchAroundPeak(PeptideWithSetModifica
                 acceptablePsms.Add(new PeptideSpectralMatch(donorPwsm, scan.Notch, thisScore, scan.ScanIndex, scan.TheScan, FileSpecificParameters, matchedIons, 0));
             }
 
-            IEnumerable<PeptideSpectralMatch> matchedSpectra = acceptablePsms.Where(p => p != null);
-            foreach (PeptideSpectralMatch psm in matchedSpectra)
+            IEnumerable<SpectralMatch> matchedSpectra = acceptablePsms.Where(p => p != null);
+            foreach (SpectralMatch psm in matchedSpectra)
             {
                 psm.ResolveAllAmbiguities();
             }
@@ -106,7 +107,7 @@ public IEnumerable<PeptideSpectralMatch> SearchAroundPeak(PeptideWithSetModifica
             return matchedSpectra;
         }
 
-        public static void CalculateSpectralAngles(SpectralLibrary spectralLibrary, PeptideSpectralMatch[] psms,
+        public static void CalculateSpectralAngles(SpectralLibrary spectralLibrary, SpectralMatch[] psms,
             Ms2ScanWithSpecificMass[] arrayOfSortedMs2Scans, CommonParameters commonParameters, CommonParameters fileSpecificParameters)
         {
             if (spectralLibrary != null)
@@ -128,12 +129,12 @@ public static void CalculateSpectralAngles(SpectralLibrary spectralLibrary, Pept
                         if (psms[i] != null)
                         {
                             Ms2ScanWithSpecificMass scan = arrayOfSortedMs2Scans[psms[i].ScanIndex];
-                            List<(int, PeptideWithSetModifications)> pwsms = new();
+                            List<(int, IBioPolymerWithSetMods)> pwsms = new();
                             List<double> pwsmSpectralAngles = new();
-                            foreach (var (Notch, Peptide) in psms[i].BestMatchingPeptides)
+                            foreach (var (Notch, Peptide) in psms[i].BestMatchingBioPolymersWithSetMods)
                             {
                                 //if peptide is target, directly look for the target's spectrum in the spectral library
-                                if (!Peptide.Protein.IsDecoy && spectralLibrary.TryGetSpectrum(Peptide.FullSequence, scan.PrecursorCharge, out var librarySpectrum))
+                                if (!Peptide.Parent.IsDecoy && spectralLibrary.TryGetSpectrum(Peptide.FullSequence, scan.PrecursorCharge, out var librarySpectrum))
                                 {
                                     SpectralSimilarity s = new SpectralSimilarity(scan.TheScan.MassSpectrum, librarySpectrum.XArray, librarySpectrum.YArray,
                                         SpectralSimilarity.SpectrumNormalizationScheme.squareRootSpectrumSum, fileSpecificParameters.ProductMassTolerance.Value, false);

MetaMorpheus/EngineLayer/CrosslinkSearch/CrosslinkSearchEngine.cs

@@ -734,7 +734,7 @@ private List<MatchedFragmentIon> ScoreChildScan(Ms2ScanWithSpecificMass parentSc
                 }
 
                 var peptideWithMod = new PeptideWithSetModifications(mainPeptide.Protein, mainPeptide.DigestionParams,
-                    mainPeptide.OneBasedStartResidueInProtein, mainPeptide.OneBasedEndResidueInProtein,
+                    mainPeptide.OneBasedStartResidue, mainPeptide.OneBasedEndResidue,
                     mainPeptide.CleavageSpecificityForFdrCategory, mainPeptide.PeptideDescription,
                     mainPeptide.MissedCleavages, mod, mainPeptide.NumFixedMods);
 
@@ -784,8 +784,8 @@ private CrosslinkSpectralMatch LocalizeDeadEndSite(PeptideWithSetModifications o
 
                 mods.Add(location + 1, deadEndMod);
 
-                var localizedPeptide = new PeptideWithSetModifications(originalPeptide.Protein, originalPeptide.DigestionParams, originalPeptide.OneBasedStartResidueInProtein,
-                    originalPeptide.OneBasedEndResidueInProtein, originalPeptide.CleavageSpecificityForFdrCategory, originalPeptide.PeptideDescription, originalPeptide.MissedCleavages, mods, originalPeptide.NumFixedMods);
+                var localizedPeptide = new PeptideWithSetModifications(originalPeptide.Protein, originalPeptide.DigestionParams, originalPeptide.OneBasedStartResidue,
+                    originalPeptide.OneBasedEndResidue, originalPeptide.CleavageSpecificityForFdrCategory, originalPeptide.PeptideDescription, originalPeptide.MissedCleavages, mods, originalPeptide.NumFixedMods);
 
                 localizedPeptide.Fragment(commonParameters.DissociationType, FragmentationTerminus.Both, products);
                 var matchedFragmentIons = MatchFragmentIons(theScan, products, commonParameters);