Changes to MBR within FlashLFQ

mzLib/FlashLFQ/ChromatographicPeak.cs

@@ -1,9 +1,9 @@
-using MzLibUtil;
-using System;
+using System;
 using System.Collections.Generic;
 using System.Linq;
 using System.Text;
 using ClassExtensions = Chemistry.ClassExtensions;
+using FlashLFQ.PEP;
 
 namespace FlashLFQ
 {
@@ -16,20 +16,23 @@ public class ChromatographicPeak
  public int ScanCount => IsotopicEnvelopes.Count;
  public double SplitRT;
  public readonly bool IsMbrPeak;
- public double PredictedRetentionTime { get; init; }
-
+ public double MbrScore;
+ public double PpmScore { get; set; }
+ public double IntensityScore { get; set; }
+ public double RtScore { get; set; }
+ public double ScanCountScore { get; set; }
+ public double IsotopicDistributionScore { get; set; }
  /// <summary>
- /// A score bounded by 100 and 0, with more confident MBR-detections receiving higher scores
+ /// Stores the pearson correlation between the apex isotopic envelope and the theoretical isotopic distribution
  /// </summary>
- public double MbrScore { get; private set; }
-
- /// The four scores below are bounded by 0 and 1, with higher scores being better
- public double PpmScore { get; private set; }
- public double IntensityScore { get; private set; }
- public double RtScore { get; private set; }
- public double ScanCountScore { get; private set; }
-
- public ChromatographicPeak(Identification id, bool isMbrPeak, SpectraFileInfo fileInfo)
+ public double IsotopicPearsonCorrelation => Apex?.PearsonCorrelation ?? -1;
+ public double RtPredictionError { get; set; }
+ public List<int> ChargeList { get; set; }
+ internal double MbrQValue { get; set; }
+ public ChromatographicPeakData PepPeakData { get; set; }
+ public double? MbrPep { get; set; }
+
+ public ChromatographicPeak(Identification id, bool isMbrPeak, SpectraFileInfo fileInfo, bool randomRt = false)
  {
  SplitRT = 0;
  NumChargeStatesObserved = 0;
@@ -40,12 +43,14 @@ public ChromatographicPeak(Identification id, bool isMbrPeak, SpectraFileInfo fi
  IsotopicEnvelopes = new List<IsotopicEnvelope>();
  IsMbrPeak = isMbrPeak;
  SpectraFileInfo = fileInfo;
+ RandomRt = randomRt;
  }
 
- public ChromatographicPeak(Identification id, bool isMbrPeak, SpectraFileInfo fileInfo, double predictedRetentionTime) :
- this(id, isMbrPeak, fileInfo)
+ public bool Equals(ChromatographicPeak peak)
  {
- PredictedRetentionTime = predictedRetentionTime;
+ return SpectraFileInfo.Equals(peak.SpectraFileInfo) 
+ && Identifications.First().ModifiedSequence.Equals(peak.Identifications.First().ModifiedSequence)
+ && ApexRetentionTime == peak.ApexRetentionTime;
  }
 
  public IsotopicEnvelope Apex { get; private set; }
@@ -54,13 +59,18 @@ public ChromatographicPeak(Identification id, bool isMbrPeak, SpectraFileInfo fi
  public int NumIdentificationsByBaseSeq { get; private set; }
  public int NumIdentificationsByFullSeq { get; private set; }
  public double MassError { get; private set; }
+ /// <summary>
+ /// Bool that describes whether the retention time of this peak was randomized
+ /// If true, implies that this peak is a decoy peak identified by the MBR algorithm
+ /// </summary>
+ public bool RandomRt { get; }
+ public bool DecoyPeptide => Identifications.First().IsDecoy;
 
  public void CalculateIntensityForThisFeature(bool integrate)
  {
  if (IsotopicEnvelopes.Any())
  {
- double maxIntensity = IsotopicEnvelopes.Max(p => p.Intensity);
- Apex = IsotopicEnvelopes.First(p => p.Intensity == maxIntensity);
+ Apex = IsotopicEnvelopes.MaxBy(p => p.Intensity);
 
  if (integrate)
  {
@@ -123,25 +133,6 @@ public void ResolveIdentifications()
  this.NumIdentificationsByBaseSeq = Identifications.Select(v => v.BaseSequence).Distinct().Count();
  this.NumIdentificationsByFullSeq = Identifications.Select(v => v.ModifiedSequence).Distinct().Count();
  }
-
- /// <summary>
- /// Calculates four component scores and one overarching Mbr score for an MBR peak.
- /// MBR Score is equal to 100 * the geometric mean of the four component scores.
- /// </summary>
- /// <param name="scorer"> An MbrScorer specific to the file where this peak was found </param>
- /// <param name="donorPeak"> The donor peak used as the basis for the MBR identification. </param>
- internal void CalculateMbrScore(MbrScorer scorer, ChromatographicPeak donorPeak)
- {
- if (SpectraFileInfo != scorer.AcceptorFile) throw new MzLibException("Error when performing match-between-runs: Mismatch between scorer and peak.");
-
- IntensityScore = scorer.CalculateIntensityScore(this, donorPeak);
- RtScore = scorer.CalculateRetentionTimeScore(this, donorPeak);
- PpmScore = scorer.CalculatePpmErrorScore(this);
- ScanCountScore = scorer.CalculateScanCountScore(this);
-
- MbrScore = 100 * Math.Pow(IntensityScore * RtScore * PpmScore * ScanCountScore, 0.25);
- }
-
  public static string TabSeparatedHeader
  {
  get
@@ -164,20 +155,18 @@ public static string TabSeparatedHeader
  sb.Append("Peak Charge" + "\t");
  sb.Append("Num Charge States Observed" + "\t");
  sb.Append("Peak Detection Type" + "\t");
- sb.Append("MBR Score" + "\t");
- sb.Append("Ppm Score" + "\t");
- sb.Append("Intensity Score" + "\t");
- sb.Append("Rt Score" + "\t");
- sb.Append("Scan Count Score" + "\t");
+ sb.Append("PIP Q-Value" + "\t");
+ sb.Append("PIP PEP" + "\t");
  sb.Append("PSMs Mapped" + "\t");
  sb.Append("Base Sequences Mapped" + "\t");
  sb.Append("Full Sequences Mapped" + "\t");
  sb.Append("Peak Split Valley RT" + "\t");
- sb.Append("Peak Apex Mass Error (ppm)");
+ sb.Append("Peak Apex Mass Error (ppm)" + "\t");
+ sb.Append("Decoy Peptide" + "\t");
+ sb.Append("Random RT");
  return sb.ToString();
  }
  }
-
  public override string ToString()
  {
  StringBuilder sb = new StringBuilder();
@@ -260,17 +249,16 @@ public override string ToString()
  sb.Append("" + "MSMS" + "\t");
  }
 
- sb.Append("" + (IsMbrPeak ? MbrScore.ToString() : "") + "\t");
- sb.Append("" + (IsMbrPeak ? PpmScore.ToString() : "") + "\t");
- sb.Append("" + (IsMbrPeak ? IntensityScore.ToString() : "") + "\t");
- sb.Append("" + (IsMbrPeak ? RtScore.ToString() : "") + "\t");
- sb.Append("" + (IsMbrPeak ? ScanCountScore.ToString() : "") + "\t");
+ sb.Append("" + (IsMbrPeak ? MbrQValue.ToString() : "") + "\t");
+ sb.Append("" + (IsMbrPeak ? MbrPep.ToString() : "") + "\t");
 
  sb.Append("" + Identifications.Count + "\t");
  sb.Append("" + NumIdentificationsByBaseSeq + "\t");
  sb.Append("" + NumIdentificationsByFullSeq + "\t");
  sb.Append("" + SplitRT + "\t");
  sb.Append("" + MassError);
+ sb.Append("\t" + DecoyPeptide);
+ sb.Append("\t" + RandomRt);
 
  return sb.ToString();
  }

mzLib/FlashLFQ/FlashLFQ.csproj

@@ -13,6 +13,8 @@
  <ItemGroup>
  <PackageReference Include="CsvHelper" Version="32.0.3" />
  <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
+ <PackageReference Include="Microsoft.ML" Version="3.0.1" />
+ <PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
  <PackageReference Include="NetSerializer" Version="4.1.2" />
  <PackageReference Include="SharpLearning.Optimization" Version="[0.28.0]" />
  </ItemGroup>

mzLib/FlashLFQ/FlashLFQResults.cs

@@ -15,27 +15,26 @@ public class FlashLfqResults
  public readonly Dictionary<string, ProteinGroup> ProteinGroups;
  public readonly Dictionary<SpectraFileInfo, List<ChromatographicPeak>> Peaks;
  private readonly HashSet<string> _peptideModifiedSequencesToQuantify;
+ public string PepResultString { get; set; }
+ public double MbrQValueThreshold { get; set; }
 
- public FlashLfqResults(List<SpectraFileInfo> spectraFiles, List<Identification> identifications, HashSet<string> peptides = null)
+ public FlashLfqResults(List<SpectraFileInfo> spectraFiles, List<Identification> identifications, double mbrQValueThreshold = 0.05,
+ HashSet<string> peptideModifiedSequencesToQuantify = null)
  {
  SpectraFiles = spectraFiles;
  PeptideModifiedSequences = new Dictionary<string, Peptide>();
  ProteinGroups = new Dictionary<string, ProteinGroup>();
  Peaks = new Dictionary<SpectraFileInfo, List<ChromatographicPeak>>();
- if(peptides == null || !peptides.Any())
- {
- peptides = identifications.Select(id => id.ModifiedSequence).ToHashSet();
- }
- _peptideModifiedSequencesToQuantify = peptides;
+ MbrQValueThreshold = mbrQValueThreshold;
+ _peptideModifiedSequencesToQuantify = peptideModifiedSequencesToQuantify ?? identifications.Where(id => !id.IsDecoy).Select(id => id.ModifiedSequence).ToHashSet();
 
  foreach (SpectraFileInfo file in spectraFiles)
  {
  Peaks.Add(file, new List<ChromatographicPeak>());
  }
 
-
  // Only quantify peptides within the set of valid peptide modified (full) sequences. This is done to enable pepitde-level FDR control of reported results
- foreach (Identification id in identifications.Where(id => peptides.Contains(id.ModifiedSequence)))
+ foreach (Identification id in identifications.Where(id => !id.IsDecoy & _peptideModifiedSequencesToQuantify.Contains(id.ModifiedSequence)))
  {
  if (!PeptideModifiedSequences.TryGetValue(id.ModifiedSequence, out Peptide peptide))
  {
@@ -59,6 +58,17 @@ public FlashLfqResults(List<SpectraFileInfo> spectraFiles, List<Identification>
  }
  }
 
+ public void ReNormalizeResults(bool integrate = false, int maxThreads = 10, bool useSharedPeptides = false)
+ {
+ foreach(var peak in Peaks.SelectMany(p => p.Value))
+ {
+ peak.CalculateIntensityForThisFeature(integrate);
+ }
+ new IntensityNormalizationEngine(this, integrate, silent: true, maxThreads).NormalizeResults();
+ CalculatePeptideResults(quantifyAmbiguousPeptides: false);
+ CalculateProteinResultsMedianPolish(useSharedPeptides: useSharedPeptides);
+ }
+
  public void MergeResultsWith(FlashLfqResults mergeFrom)
  {
  this.SpectraFiles.AddRange(mergeFrom.SpectraFiles);
@@ -128,6 +138,8 @@ public void CalculatePeptideResults(bool quantifyAmbiguousPeptides)
  {
  var groupedPeaks = filePeaks.Value
  .Where(p => p.NumIdentificationsByFullSeq == 1)
+ .Where(p => !p.Identifications.First().IsDecoy)
+ .Where(p => !p.IsMbrPeak || (p.MbrQValue < MbrQValueThreshold && !p.RandomRt))
  .GroupBy(p => p.Identifications.First().ModifiedSequence)
  .Where(group => _peptideModifiedSequencesToQuantify.Contains(group.Key))
  .ToList();
@@ -163,11 +175,15 @@ public void CalculatePeptideResults(bool quantifyAmbiguousPeptides)
  // report ambiguous quantification
  var ambiguousPeaks = filePeaks.Value
  .Where(p => p.NumIdentificationsByFullSeq > 1)
+ .Where(p => !p.Identifications.First().IsDecoy)
+ .Where(p => !p.IsMbrPeak || (p.MbrQValue < MbrQValueThreshold && !p.RandomRt))
  .ToList();
  foreach (ChromatographicPeak ambiguousPeak in ambiguousPeaks)
  {
- foreach (Identification id in ambiguousPeak.Identifications)
+ foreach (Identification id in ambiguousPeak.Identifications.Where(id => !id.IsDecoy))
  {
+ if (!_peptideModifiedSequencesToQuantify.Contains(id.ModifiedSequence)) continue; // Ignore the ids/sequences we don't want to quantify
+
  string sequence = id.ModifiedSequence;
 
  double alreadyRecordedIntensity = PeptideModifiedSequences[sequence].GetIntensity(filePeaks.Key);
@@ -224,7 +240,7 @@ private void HandleAmbiguityInFractions()
 
  foreach (SpectraFileInfo file in sample)
  {
- foreach (ChromatographicPeak peak in Peaks[file])
+ foreach (ChromatographicPeak peak in Peaks[file].Where(p => !p.IsMbrPeak || p.MbrQValue < MbrQValueThreshold))
  {
  foreach (Identification id in peak.Identifications)
  {
@@ -549,7 +565,7 @@ public void CalculateProteinResultsMedianPolish(bool useSharedPeptides)
  }
  }
 
- public void WriteResults(string peaksOutputPath, string modPeptideOutputPath, string proteinOutputPath, string bayesianProteinQuantOutput, bool silent = true)
+ public void WriteResults(string peaksOutputPath, string modPeptideOutputPath, string proteinOutputPath, string bayesianProteinQuantOutput, bool silent)
  {
  if (!silent)
  {