Andromeda score

MetaMorpheus/EngineLayer/ClassicSearch/ClassicSearchEngine.cs

@@ -139,8 +139,11 @@ protected override MetaMorpheusEngineResults RunSpecific()
 
  // calculate the peptide's score
  double thisScore = CalculatePeptideScore(scan.TheScan.TheScan, matchedIons, fragmentsCanHaveDifferentCharges: WriteSpectralLibrary);
+
+ double numberOfPeaksPer100Thomsons = scan.TheScan.NumPeaks / ((scan.TheScan.TheScan.ScanWindowRange.Maximum- scan.TheScan.TheScan.ScanWindowRange.Minimum)/100.0);
+ double andromedaScore = AndromedaScore(peptideTheorProducts.Count, matchedIons.Count, numberOfPeaksPer100Thomsons);
 
- AddPeptideCandidateToPsm(scan, myLocks, thisScore, peptide, matchedIons);
+ AddPeptideCandidateToPsm(scan, myLocks, thisScore, peptide, matchedIons, andromedaScore);
 
  if (SpectralLibrary != null)
  {
@@ -186,10 +189,10 @@ private void DecoyScoreForSpectralLibrarySearch(ScanWithIndexAndNotchInfo scan,
  // calculate decoy's score
  var decoyScore = CalculatePeptideScore(scan.TheScan.TheScan, decoyMatchedIons, fragmentsCanHaveDifferentCharges: WriteSpectralLibrary);
 
- AddPeptideCandidateToPsm(scan, myLocks, decoyScore, reversedOnTheFlyDecoy, decoyMatchedIons);
+ AddPeptideCandidateToPsm(scan, myLocks, decoyScore, reversedOnTheFlyDecoy, decoyMatchedIons,0);
  }
 
- private void AddPeptideCandidateToPsm(ScanWithIndexAndNotchInfo scan, object[] myLocks, double thisScore, PeptideWithSetModifications peptide, List<MatchedFragmentIon> matchedIons)
+ private void AddPeptideCandidateToPsm(ScanWithIndexAndNotchInfo scan, object[] myLocks, double thisScore, PeptideWithSetModifications peptide, List<MatchedFragmentIon> matchedIons, double andromedaScore)
  {
  bool meetsScoreCutoff = thisScore >= CommonParameters.ScoreCutoff;
 
@@ -206,11 +209,11 @@ private void AddPeptideCandidateToPsm(ScanWithIndexAndNotchInfo scan, object[] m
  {
  if (PeptideSpectralMatches[scan.ScanIndex] == null)
  {
- PeptideSpectralMatches[scan.ScanIndex] = new PeptideSpectralMatch(peptide, scan.Notch, thisScore, scan.ScanIndex, scan.TheScan, CommonParameters, matchedIons, 0);
+ PeptideSpectralMatches[scan.ScanIndex] = new PeptideSpectralMatch(peptide, scan.Notch, thisScore, scan.ScanIndex, scan.TheScan, CommonParameters, matchedIons, 0, andromedaScore);
  }
  else
  {
- PeptideSpectralMatches[scan.ScanIndex].AddOrReplace(peptide, thisScore, scan.Notch, CommonParameters.ReportAllAmbiguity, matchedIons, 0);
+ PeptideSpectralMatches[scan.ScanIndex].AddOrReplace(peptide, thisScore, scan.Notch, CommonParameters.ReportAllAmbiguity, matchedIons, 0, andromedaScore);
  }
  }
  }

MetaMorpheus/EngineLayer/MetaMorpheusEngine.cs

@@ -10,6 +10,7 @@
 using System.Diagnostics;
 using System.Linq;
 using System.Threading.Tasks;
+using Newtonsoft.Json.Linq;
 
 namespace EngineLayer
 {
@@ -128,9 +129,18 @@ private static double CalculateAllChargesPeptideScore(MsDataScan thisScan, List<
  }
 
  return score;
-
  }
 
+ public static double AndromedaScore(int totalNumberOfTheoreticalIons, int totalNumberOfMatchingIons, double numberOfPeaksPer100Thomsons)
+ {
+ double localSum = 0;
+ for (int j = totalNumberOfMatchingIons; j <= totalNumberOfTheoreticalIons; j++)
+ {
+ localSum += (Math.Pow((numberOfPeaksPer100Thomsons/100),j)*Math.Pow((1-numberOfPeaksPer100Thomsons/100),totalNumberOfTheoreticalIons-j));
+ }
+
+ return -10.0 * Math.Log10(localSum);
+ }
  public static List<MatchedFragmentIon> MatchFragmentIons(Ms2ScanWithSpecificMass scan, List<Product> theoreticalProducts, CommonParameters commonParameters, bool matchAllCharges = false)
  {
  if (matchAllCharges)

MetaMorpheus/EngineLayer/ModernSearch/ModernSearchEngine.cs

@@ -358,7 +358,7 @@ protected PeptideSpectralMatch FineScorePeptide(int id, Ms2ScanWithSpecificMass
  }
  else
  {
- PeptideSpectralMatches[scanIndex].AddOrReplace(peptide, thisScore, notch, CommonParameters.ReportAllAmbiguity, matchedIons, 0);
+ PeptideSpectralMatches[scanIndex].AddOrReplace(peptide, thisScore, notch, CommonParameters.ReportAllAmbiguity, matchedIons, 0,0);
  }
  }
 

MetaMorpheus/EngineLayer/NonSpecificEnzymeSearch/NonSpecificEnzymeSearchEngine.cs

@@ -140,7 +140,7 @@ protected override MetaMorpheusEngineResults RunSpecific()
  }
  else
  {
- localPeptideSpectralMatches[ms2ArrayIndex].AddOrReplace(peptide, thisScore, notch, CommonParameters.ReportAllAmbiguity, matchedIons, 0);
+ localPeptideSpectralMatches[ms2ArrayIndex].AddOrReplace(peptide, thisScore, notch, CommonParameters.ReportAllAmbiguity, matchedIons, 0,0);
  }
  }
  }

MetaMorpheus/EngineLayer/PeptideSpectralMatch.cs

@@ -20,7 +20,7 @@ public class PeptideSpectralMatch
  public const double ToleranceForScoreDifferentiation = 1e-9;
  protected List<(int Notch, PeptideWithSetModifications Pwsm)> _BestMatchingPeptides;
 
- public PeptideSpectralMatch(PeptideWithSetModifications peptide, int notch, double score, int scanIndex, Ms2ScanWithSpecificMass scan, CommonParameters commonParameters, List<MatchedFragmentIon> matchedFragmentIons, double xcorr = 0)
+ public PeptideSpectralMatch(PeptideWithSetModifications peptide, int notch, double score, int scanIndex, Ms2ScanWithSpecificMass scan, CommonParameters commonParameters, List<MatchedFragmentIon> matchedFragmentIons, double xcorr = 0, double andromedaScore = 0)
  {
  _BestMatchingPeptides = new List<(int, PeptideWithSetModifications)>();
  ScanIndex = scanIndex;
@@ -36,12 +36,13 @@ public PeptideSpectralMatch(PeptideWithSetModifications peptide, int notch, doub
  DigestionParams = commonParameters.DigestionParams;
  PeptidesToMatchingFragments = new Dictionary<PeptideWithSetModifications, List<MatchedFragmentIon>>();
  Xcorr = xcorr;
+ AndromedaScore = andromedaScore;
  NativeId = scan.NativeId;
  RunnerUpScore = commonParameters.ScoreCutoff;
  MsDataScan = scan.TheScan;
  SpectralAngle = -1;
 
- AddOrReplace(peptide, score, notch, true, matchedFragmentIons, xcorr);
+ AddOrReplace(peptide, score, notch, true, matchedFragmentIons, xcorr, andromedaScore);
  }
 
  public MsDataScan MsDataScan { get; set; }
@@ -77,6 +78,7 @@ public PeptideSpectralMatch(PeptideWithSetModifications peptide, int notch, doub
 
  public double Score { get; private set; }
  public double Xcorr;
+ public double AndromedaScore { get; private set; }
  public double SpectralAngle { get; set; }
  public string NativeId; // this is a property of the scan. used for mzID writing
 
@@ -108,7 +110,7 @@ public static string GetTabSeparatedHeader()
  return string.Join("\t", DataDictionary(null, null).Keys);
  }
 
- public void AddOrReplace(PeptideWithSetModifications pwsm, double newScore, int notch, bool reportAllAmbiguity, List<MatchedFragmentIon> matchedFragmentIons, double newXcorr)
+ public void AddOrReplace(PeptideWithSetModifications pwsm, double newScore, int notch, bool reportAllAmbiguity, List<MatchedFragmentIon> matchedFragmentIons, double newXcorr, double newAndromedaScore)
  {
  if (newScore - Score > ToleranceForScoreDifferentiation) //if new score beat the old score, overwrite it
  {
@@ -122,6 +124,7 @@ public void AddOrReplace(PeptideWithSetModifications pwsm, double newScore, int
 
  Score = newScore;
  Xcorr = newXcorr;
+ AndromedaScore = newAndromedaScore;
 
  PeptidesToMatchingFragments.Clear();
  PeptidesToMatchingFragments.Add(pwsm, matchedFragmentIons);
@@ -491,6 +494,7 @@ protected PeptideSpectralMatch(PeptideSpectralMatch psm, List<(int Notch, Peptid
  FdrInfo = psm.FdrInfo;
  Score = psm.Score;
  Xcorr = psm.Xcorr;
+ AndromedaScore = psm.AndromedaScore;
  RunnerUpScore = psm.RunnerUpScore;
  IsDecoy = psm.IsDecoy;
  IsContaminant = psm.IsContaminant;

MetaMorpheus/EngineLayer/PsmTsv/PsmTsvHeader.cs

@@ -13,6 +13,7 @@ public static class PsmTsvHeader
  public const string PrecursorMz = "Precursor MZ";
  public const string PrecursorMass = "Precursor Mass";
  public const string Score = "Score";
+ public const string AndromedaScore = "AndromedaScore";
  public const string DeltaScore = "Delta Score";
  public const string Notch = "Notch";
 

MetaMorpheus/EngineLayer/PsmTsv/PsmTsvWriter.cs

@@ -186,6 +186,7 @@ internal static void AddBasicMatchData(Dictionary<string, string> s, PeptideSpec
  s[PsmTsvHeader.PrecursorMz] = psm == null ? " " : psm.ScanPrecursorMonoisotopicPeakMz.ToString("F5", CultureInfo.InvariantCulture);
  s[PsmTsvHeader.PrecursorMass] = psm == null ? " " : psm.ScanPrecursorMass.ToString("F5", CultureInfo.InvariantCulture);
  s[PsmTsvHeader.Score] = psm == null ? " " : psm.Score.ToString("F3", CultureInfo.InvariantCulture);
+ s[PsmTsvHeader.AndromedaScore] = psm == null ? " " : psm.AndromedaScore.ToString("F3", CultureInfo.InvariantCulture);
  s[PsmTsvHeader.DeltaScore] = psm == null ? " " : psm.DeltaScore.ToString("F3", CultureInfo.InvariantCulture);
  s[PsmTsvHeader.Notch] = psm == null ? " " : Resolve(psm.BestMatchingPeptides.Select(p => p.Notch)).ResolvedString;
  }