Added QValueThresholdForPEP to common params

MetaMorpheus/EngineLayer/CommonParameters.cs

@@ -34,6 +34,7 @@ public CommonParameters(
             int totalPartitions = 1, 
             double qValueThreshold = 0.01,
             double pepQValueThreshold = 1.0,
+            double qValueCutoffForPepCalculation = 0.005,
             double scoreCutoff = 5, 
             int? numberOfPeaksToKeepPerWindow = 200, 
             double? minimumAllowedIntensityRatioToBasePeak = 0.01, 
@@ -67,6 +68,7 @@ public CommonParameters(
             TotalPartitions = totalPartitions;
             QValueThreshold = qValueThreshold;
             PepQValueThreshold = pepQValueThreshold;
+            QValueCutoffForPepCalculation = qValueCutoffForPepCalculation;
             ScoreCutoff = scoreCutoff;
             NumberOfPeaksToKeepPerWindow = numberOfPeaksToKeepPerWindow;
             MinimumAllowedIntensityRatioToBasePeak = minimumAllowedIntensityRatioToBasePeak;
@@ -157,6 +159,11 @@ public int DeconvolutionMaxAssumedChargeState
         /// </summary>
         public double PepQValueThreshold { get; private set; }
         public double ScoreCutoff { get; private set; }
+        /// <summary>
+        /// This parameter determines which PSMs/Peptides will be used as postive training examples
+        /// when training the GBDT model for PEP. 
+        /// </summary>
+        public double QValueCutoffForPepCalculation { get; private set; }
         public DigestionParams DigestionParams { get; private set; }
         public bool ReportAllAmbiguity { get; private set; }
         public int? NumberOfPeaksToKeepPerWindow { get; private set; }
@@ -225,6 +232,7 @@ public CommonParameters CloneWithNewTerminus(FragmentationTerminus? terminus = n
                                 TotalPartitions,
                                 QValueThreshold,
                                 PepQValueThreshold,
+                                QValueCutoffForPepCalculation,
                                 ScoreCutoff,
                                 NumberOfPeaksToKeepPerWindow,
                                 MinimumAllowedIntensityRatioToBasePeak,

MetaMorpheus/EngineLayer/FdrAnalysis/PEPValueAnalysisGeneric.cs

@@ -54,36 +54,26 @@ public static string ComputePEPValuesForAllPSMsGeneric(List<SpectralMatch> psms,
                 .Select(b => b.FirstOrDefault()).ToList();
             List<int> countOfPeptidesInEachFile = peptides.GroupBy(b => b.FullFilePath).Select(b => b.Count()).ToList();
             bool allFilesContainPeptides = (countOfPeptidesInEachFile.Count == fileSpecificParameters.Count); //rare condition where each file has psms but some files don't have peptides. probably only happens in unit tests.
+            QValueCutoff = fileSpecificParameters.Select(t => t.fileSpecificParameters.QValueCutoffForPepCalculation).Min();
 
             int chargeStateMode = 0;
-            int numberOfPositiveTrainingExamples = 0;
             Dictionary<string, float> fileSpecificMedianFragmentMassErrors = new Dictionary<string, float>();
-            while (numberOfPositiveTrainingExamples < 10)
+            if (peptides.Count() > 100 && allFilesContainPeptides)
             {
-                if (peptides.Count() > 100 && allFilesContainPeptides)
-                {
-                    foreach (var peptide in peptides)
-                    {
-                        allPeptideIndices.Add(psms.IndexOf(peptide));
-                    }
-                    chargeStateMode = GetChargeStateMode(peptides);
-                    fileSpecificMedianFragmentMassErrors = GetFileSpecificMedianFragmentMassError(peptides);
-                    numberOfPositiveTrainingExamples = peptides.Count(peptide => peptide.GetFdrInfo(UsePeptideLevelQValueForTraining).QValue <= QValueCutoff);
-                }
-                else
+                foreach (var peptide in peptides)
                 {
-                    //there are too few psms to do any meaningful training if we used only peptides. So, we will train using psms instead.
-                    UsePeptideLevelQValueForTraining = false;
-                    numberOfPositiveTrainingExamples = psms.Count(psm => psm.GetFdrInfo(UsePeptideLevelQValueForTraining).QValue <= QValueCutoff);
-                    allPeptideIndices = Enumerable.Range(0, psms.Count).ToList();
-                    chargeStateMode = GetChargeStateMode(psms);
-                    fileSpecificMedianFragmentMassErrors = GetFileSpecificMedianFragmentMassError(psms);
-                }
-
-                if (numberOfPositiveTrainingExamples < 10)
-                {
-                    QValueCutoff = QValueCutoff * 2;
+                    allPeptideIndices.Add(psms.IndexOf(peptide));
                 }
+                chargeStateMode = GetChargeStateMode(peptides);
+                fileSpecificMedianFragmentMassErrors = GetFileSpecificMedianFragmentMassError(peptides);
+            }
+            else
+            {
+                //there are too few psms to do any meaningful training if we used only peptides. So, we will train using psms instead.
+                UsePeptideLevelQValueForTraining = false;
+                allPeptideIndices = Enumerable.Range(0, psms.Count).ToList();
+                chargeStateMode = GetChargeStateMode(psms);
+                fileSpecificMedianFragmentMassErrors = GetFileSpecificMedianFragmentMassError(psms);
             }
 
 

MetaMorpheus/Test/SpectralRecoveryTest.cs

@@ -49,14 +49,16 @@ public void SpectralRecoveryTestSetup()
             string databasePath = Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", @"SpectralRecoveryTest\HumanFastaSlice.fasta");
             proteinList = ProteinDbLoader.LoadProteinFasta(databasePath, true, DecoyType.Reverse, false, out List<string> errors)
                 .Where(protein => protein.AppliedSequenceVariations != null).ToList();
+            CommonParameters commonParameters = new CommonParameters();
+
 
             foreach (PsmFromTsv readPsm in tsvPsms.Where(psm => !psm.FullSequence.Contains('['))) // Modifications break the parser
             {
                 string filePath = Path.Combine(TestContext.CurrentContext.TestDirectory,
                     "TestData", "SpectralRecoveryTest", readPsm.FileNameWithoutExtension + ".mzML");
-                MsDataScan scan = myFileManager.LoadFile(filePath, new CommonParameters()).GetOneBasedScan(readPsm.Ms2ScanNumber);
+                MsDataScan scan = myFileManager.LoadFile(filePath, commonParameters).GetOneBasedScan(readPsm.Ms2ScanNumber);
                 Ms2ScanWithSpecificMass ms2Scan = new Ms2ScanWithSpecificMass(scan, readPsm.PrecursorMz, readPsm.PrecursorCharge,
-                    filePath, new CommonParameters());
+                    filePath, commonParameters);
                 Protein protein = proteinList.First(protein => protein.Accession == readPsm.ProteinAccession);
 
                 //string[] startAndEndResidues = readPsm.StartAndEndResiduesInProtein.Split(" ");
@@ -99,7 +101,7 @@ public void SpectralRecoveryTestSetup()
                     MassDiffAcceptorType = MassDiffAcceptorType.ThreeMM,
                     WriteHighQValuePsms = true
                 },
-                CommonParameters = new CommonParameters()
+                CommonParameters = new CommonParameters(qValueCutoffForPepCalculation: 0.01)
             };
             searchTaskResults = searchTask.RunTask(outputFolder, databaseList, rawSlices, "name");
 
@@ -130,10 +132,10 @@ public void SpectralRecoveryTestSetup()
                         QuantifyPpmTol = 25
                     }
                 },
-                CommonParameters = new CommonParameters(dissociationType: DissociationType.Autodetect),
+                CommonParameters = new CommonParameters(dissociationType: DissociationType.Autodetect, qValueCutoffForPepCalculation: 0.01),
                 FileSpecificParameters = new List<(string FileName, CommonParameters Parameters)> {
-                    (rawSlices[0], new CommonParameters()),
-                    (rawSlices[1], new CommonParameters())
+                    (rawSlices[0], new CommonParameters(qValueCutoffForPepCalculation: 0.01)),
+                    (rawSlices[1], new CommonParameters(qValueCutoffForPepCalculation: 0.01))
                 }
             };