add hyperscore to PEP calculation

MetaMorpheus/EngineLayer/FdrAnalysis/PEPValueAnalysisGeneric.cs

@@ -683,6 +683,38 @@ private static float GetMobilityZScore(SpectralMatch psm, IBioPolymerWithSetMods
  return (float)mobilityZScore;
  }
 
+ public static float GetFraggerHyperScore(SpectralMatch psm, IBioPolymerWithSetMods selectedPeptide)
+ {
+ var peptideFragmentIons = psm.BioPolymersWithSetModsToMatchingFragments[selectedPeptide];
+ var nIons = peptideFragmentIons.Where(f => f.NeutralTheoreticalProduct.Terminus == FragmentationTerminus.N).ToList();
+ var cIons = peptideFragmentIons.Where(f => f.NeutralTheoreticalProduct.Terminus == FragmentationTerminus.C).ToList();
+ double nIonIntensitySum = nIons.Sum(f => f.Intensity);
+ double cIonIntensitySum = cIons.Sum(f => f.Intensity);
+ float nIon = GetLog10Factorial((int)nIons.Count);
+ float cIon = GetLog10Factorial((int)cIons.Count);
+
+ return (float)((nIon + cIon + Math.Log10(nIonIntensitySum * cIonIntensitySum)));
+ }
+
+ private static ulong GetFactorial(ulong n)
+ {
+ if (n == 0)
+ {
+ return 1;
+ }
+ return n * GetFactorial(n - 1);
+ }
+
+ public static float GetLog10Factorial(int n)
+ {
+ double log10Factorial = 0.0;
+ for (int i = 1; i <= n; i++)
+ {
+ log10Factorial += Math.Log10(i);
+ }
+ return (float)log10Factorial;
+ }
+
  public static IEnumerable<PsmData> CreatePsmData(string searchType, List<(string fileName, CommonParameters fileSpecificParameters)> fileSpecificParameters,
  List<SpectralMatch> psms, List<int> psmIndicies,
  Dictionary<string, Dictionary<int, Tuple<double, double>>> timeDependantHydrophobicityAverageAndDeviation_unmodified,
@@ -790,6 +822,7 @@ public static PsmData CreateOnePsmDataEntry(string searchType, List<(string file
  float peaksInPrecursorEnvelope = 0;
  float mostAbundantPrecursorPeakIntensity = 0;
  float fractionalIntensity = 0;
+ float fraggerHyperScore = 0;
 
  float missedCleavages = 0;
  float longestSeq = 0;
@@ -837,6 +870,7 @@ public static PsmData CreateOnePsmDataEntry(string searchType, List<(string file
  peaksInPrecursorEnvelope = psm.PrecursorScanEnvelopePeakCount;
  mostAbundantPrecursorPeakIntensity = (float)Math.Round((float)psm.PrecursorScanIntensity / normalizationFactor * multiplier, 0);
  fractionalIntensity = (float)psm.PrecursorFractionalIntensity;
+ fraggerHyperScore = GetFraggerHyperScore(psm, selectedPeptide);
 
  if (PsmHasSpectralAngle(psm))
  {
@@ -954,6 +988,7 @@ public static PsmData CreateOnePsmDataEntry(string searchType, List<(string file
  MostAbundantPrecursorPeakIntensity = mostAbundantPrecursorPeakIntensity,
  PrecursorFractionalIntensity = fractionalIntensity,
  InternalIonCount = internalMatchingFragmentCount,
+ FraggerHyperScore = fraggerHyperScore
  };
 
  return psm.PsmData_forPEPandPercolator;

MetaMorpheus/EngineLayer/FdrAnalysis/PsmData.cs

@@ -15,7 +15,7 @@ public class PsmData
  "TotalMatchingFragmentCount", "Intensity", "PrecursorChargeDiffToMode", "DeltaScore",
  "Notch", "ModsCount", "AbsoluteAverageFragmentMassErrorFromMedian", "MissedCleavagesCount", 
  "Ambiguity", "LongestFragmentIonSeries", "ComplementaryIonCount", "HydrophobicityZScore",
- "IsVariantPeptide", "IsDeadEnd", "IsLoop", "SpectralAngle", "HasSpectralAngle", 
+ "IsVariantPeptide", "IsDeadEnd", "IsLoop", "SpectralAngle", "HasSpectralAngle", "FraggerHyperScore"
  }
  },
 
@@ -26,7 +26,7 @@ public class PsmData
  "Notch", "ModsCount", "AbsoluteAverageFragmentMassErrorFromMedian", "Ambiguity", 
  "LongestFragmentIonSeries", "ComplementaryIonCount", "SpectralAngle",
  "HasSpectralAngle", "PeaksInPrecursorEnvelope", "ChimeraCount",
- "MostAbundantPrecursorPeakIntensity", "PrecursorFractionalIntensity", "InternalIonCount"
+ "MostAbundantPrecursorPeakIntensity", "PrecursorFractionalIntensity", "InternalIonCount", "FraggerHyperScore"
  }
  },
 
@@ -75,6 +75,7 @@ public class PsmData
  { "MostAbundantPrecursorPeakIntensity", 1 },
  { "PrecursorFractionalIntensity", 1 },
  { "InternalIonCount", 1},
+ { "FraggerHyperScore", 1},
  }.ToImmutableDictionary();
 
  public string ToString(string searchType)
@@ -179,5 +180,8 @@ public string ToString(string searchType)
 
  [LoadColumn(28)]
  public float InternalIonCount { get; set; }
+
+ [LoadColumn(29)]
+ public float FraggerHyperScore { get; set; }
  }
 }