Increased QValue cutoff for calibrating PSMs to 0.01 (#2392)

smith-chem-wisc · Aug 2, 2024 · 7fd6aee · 7fd6aee
1 parent f48d118
commit 7fd6aee
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Showing 2 changed files with 7 additions and 1 deletion.
diff --git a/MetaMorpheus/TaskLayer/CalibrationTask/CalibrationParameters.cs b/MetaMorpheus/TaskLayer/CalibrationTask/CalibrationParameters.cs
@@ -8,6 +8,7 @@ public CalibrationParameters()
             MinMS1IsotopicPeaksNeededForConfirmedIdentification = 3;
             MinMS2IsotopicPeaksNeededForConfirmedIdentification = 2;
             NumFragmentsNeededForEveryIdentification = 10;
+            QValueCutoffForCalibratingPSMs = 0.01;
             WriteIndexedMzml = true;
         }
 
@@ -17,5 +18,7 @@ public CalibrationParameters()
         public int MinMS1IsotopicPeaksNeededForConfirmedIdentification { get; set; }
         public int MinMS2IsotopicPeaksNeededForConfirmedIdentification { get; set; }
         public int NumFragmentsNeededForEveryIdentification { get; set; }
+
+        public double QValueCutoffForCalibratingPSMs { get; set; }
     }
 }
diff --git a/MetaMorpheus/TaskLayer/CalibrationTask/CalibrationTask.cs b/MetaMorpheus/TaskLayer/CalibrationTask/CalibrationTask.cs
@@ -278,7 +278,10 @@ private DataPointAquisitionResults GetDataAcquisitionResults(MsDataFile myMsData
 
             _ = new FdrAnalysisEngine(allPsms, searchMode.NumNotches, CommonParameters, FileSpecificParameters, new List<string> { taskId, "Individual Spectra Files", fileNameWithoutExtension }, doPEP: false).Run();
 
-            List<SpectralMatch> goodIdentifications = allPsms.Where(b => b.FdrInfo.QValueNotch < 0.001 && !b.IsDecoy && b.FullSequence != null).ToList();
+            List<SpectralMatch> goodIdentifications = allPsms.Where(b => 
+                b.FdrInfo.QValueNotch < CalibrationParameters.QValueCutoffForCalibratingPSMs 
+                && b.FullSequence != null
+                && !b.IsDecoy).ToList();
 
             if (!goodIdentifications.Any())
             {