Calibration on peptides with modifications

Stefan branch

Author: stefanks

EngineLayer/CalibrationEngine/CalibrationEngine.cs

@@ -221,17 +221,11 @@ private DataPointAquisitionResults GetDataPoints()
                 // Each identification has an MS2 spectrum attached to it.
                 int ms2spectrumIndex = identification.thisPSM.newPsm.scanNumber;
 
-                //// Get the peptide, don't forget to add the modifications!!!!
-                //var SequenceWithChemicalFormulas = identification.thisPSM.SequenceWithChemicalFormulas;
-                //if (SequenceWithChemicalFormulas == null)
-                //    continue;
-                //Proteomics.Peptide coolPeptide = new Proteomics.Peptide(SequenceWithChemicalFormulas);
-
                 // Get the peptide, don't forget to add the modifications!!!!
-                var seq = identification.thisPSM.FullSequence;
-                if (identification.thisPSM.NumMods > 0)
+                var SequenceWithChemicalFormulas = identification.thisPSM.SequenceWithChemicalFormulas;
+                if (SequenceWithChemicalFormulas == null || identification.thisPSM.peptidesWithSetModifications.First().allModsOneIsNterminus.Any(b => b.Value.neutralLoss != 0))
                     continue;
-                Proteomics.Peptide coolPeptide = new Proteomics.Peptide(seq);
+                Proteomics.Peptide coolPeptide = new Proteomics.Peptide(SequenceWithChemicalFormulas);
 
                 int peptideCharge = identification.thisPSM.newPsm.scanPrecursorCharge;
 

TaskLayer/GPTMDTask/GPTMDTask.cs

@@ -35,7 +35,7 @@ public GptmdTask()
             MaxModificationIsoforms = 4096;
             InitiatorMethionineBehavior = InitiatorMethionineBehavior.Variable;
             ProductMassTolerance = new Tolerance(ToleranceUnit.Absolute, 0.01);
-            PrecursorMassTolerance = new Tolerance(ToleranceUnit.PPM, 5);
+            PrecursorMassTolerance = new Tolerance(ToleranceUnit.PPM, 2);
             BIons = true;
             YIons = true;
             CIons = false;