Possbility bug

.editorconfig

@@ -0,0 +1,4 @@
+root = true
+
+[*]
+insert_final_newline = true

.gitignore

@@ -234,4 +234,6 @@ _Pvt_Extensions
 
 # Macintosh files
 **/.DS_Store
+/.opencode/
 /AGENTS.md
+/.serena

MetaMorpheus/CMD/CMD.csproj

@@ -24,7 +24,7 @@
     <PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
     <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
-    <PackageReference Include="mzLib" Version="1.0.574" />
+    <PackageReference Include="mzLib" Version="1.0.576" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="SQLite.Interop.dll" Version="1.0.103" />
     <PackageReference Include="System.Data.SQLite" Version="1.0.118" />
@@ -36,4 +36,8 @@
     <ProjectReference Include="..\TaskLayer\TaskLayer.csproj" />
   </ItemGroup>
 
+  <ItemGroup>
+    <Folder Include="Properties\" />
+  </ItemGroup>
+
 </Project>

MetaMorpheus/CMD/Properties/launchSettings.json

@@ -0,0 +1,11 @@
+{
+  "profiles": {
+    "CMD": {
+      "commandName": "Project"
+    },
+    "WSL": {
+      "commandName": "WSL2",
+      "distributionName": ""
+    }
+  }
+}

MetaMorpheus/EngineLayer/ClassicSearch/ClassicSearchEngine.cs

@@ -158,7 +158,7 @@ protected override MetaMorpheusEngineResults RunSpecific()
                                 // check if we've already generated theoretical fragments for this peptide+dissociation type
                                 if (peptideTheorProducts.Count == 0)
                                 {
-                                    specificBioPolymer.Fragment(dissociationType, CommonParameters.DigestionParams.FragmentationTerminus, peptideTheorProducts);
+                                    specificBioPolymer.Fragment(dissociationType, CommonParameters.DigestionParams.FragmentationTerminus, peptideTheorProducts, CommonParameters.FragmentationParameters);
                                 }
 
                                 // match theoretical target ions to spectrum
@@ -205,7 +205,7 @@ private void DecoyScoreForSpectralLibrarySearch(ScanWithIndexAndNotchInfo scan,
 
             if (decoyTheoreticalFragments.Count == 0)
             {
-                reversedOnTheFlyDecoy.Fragment(dissociationType, CommonParameters.DigestionParams.FragmentationTerminus, decoyTheoreticalFragments);
+                reversedOnTheFlyDecoy.Fragment(dissociationType, CommonParameters.DigestionParams.FragmentationTerminus, decoyTheoreticalFragments, CommonParameters.FragmentationParameters);
             }
             Ms2ScanWithSpecificMass theScan = ArrayOfSortedMS2Scans[scan.ScanIndex];
             var decoyMatchedIons = MatchFragmentIons(theScan, decoyTheoreticalFragments, CommonParameters,

MetaMorpheus/EngineLayer/CommonParameters.cs

@@ -7,9 +7,9 @@
 using System.Reflection;
 using Nett;
 using Omics.Digestion;
-using Omics.Fragmentation.Peptide;
 using Transcriptomics.Digestion;
 using EngineLayer.DIA;
+using Transcriptomics;
 
 namespace EngineLayer
 {
@@ -47,7 +47,8 @@ public CommonParameters(
             bool trimMs1Peaks = false,
             bool trimMsMsPeaks = true, 
             Tolerance productMassTolerance = null, 
-            Tolerance precursorMassTolerance = null, 
+            Tolerance precursorMassTolerance = null,
+            Tolerance productMassTolerance_LowRes = null,
             Tolerance deconvolutionMassTolerance = null,
             int maxThreadsToUsePerFile = -1, 
             IDigestionParams digestionParams = null, 
@@ -60,7 +61,8 @@ public CommonParameters(
             DeconvolutionParameters precursorDeconParams = null,
             DeconvolutionParameters productDeconParams = null,
             bool useMostAbundantPrecursorIntensity = true,
-            DIAparameters diaParameters = null)
+            DIAparameters diaParameters = null,
+            IFragmentationParams fragmentationParams = null)
 
         {
             TaskDescriptor = taskDescriptor;
@@ -84,6 +86,7 @@ public CommonParameters(
             MaxThreadsToUsePerFile = maxThreadsToUsePerFile == -1 ? Environment.ProcessorCount > 1 ? Environment.ProcessorCount - 1 : 1 : maxThreadsToUsePerFile;
             ProductMassTolerance = productMassTolerance ?? new PpmTolerance(20);
             PrecursorMassTolerance = precursorMassTolerance ?? new PpmTolerance(5);
+            ProductMassTolerance_LowRes = productMassTolerance_LowRes ?? ProductMassTolerance;
             DeconvolutionMassTolerance = deconvolutionMassTolerance ?? new PpmTolerance(4);
             DigestionParams = digestionParams ?? new DigestionParams();
             DissociationType = dissociationType;
@@ -119,11 +122,13 @@ public CommonParameters(
                 ListOfModsFixed = listOfModsFixed ?? new List<(string, string)>();
                 PrecursorDeconvolutionParameters.AverageResidueModel = new OxyriboAveragine();
                 ProductDeconvolutionParameters.AverageResidueModel = new OxyriboAveragine();
+                FragmentationParameters = fragmentationParams ?? RnaFragmentationParams.Default;
             }
             else
             {
                 ListOfModsVariable = listOfModsVariable ?? new List<(string, string)> { ("Common Variable", "Oxidation on M") };
                 ListOfModsFixed = listOfModsFixed ?? new List<(string, string)> { ("Common Fixed", "Carbamidomethyl on C"), ("Common Fixed", "Carbamidomethyl on U") };
+                FragmentationParameters = fragmentationParams ?? new FragmentationParams();
             }
 
             CustomIons = digestionParams.ProductsFromDissociationType()[DissociationType.Custom];
@@ -157,8 +162,9 @@ public int DeconvolutionMaxAssumedChargeState
         [TomlIgnore] public Tolerance DeconvolutionMassTolerance { get; private set; }
         public int TotalPartitions { get; set; }
         public Tolerance ProductMassTolerance { get; set; } // public setter required for calibration task
+        public Tolerance ProductMassTolerance_LowRes { get; set; }// Wider mass tolerance for lower resolution analyzer (e.g. ion trap). For now, this is a independent parameter, will not be modified by the calibration task.
         public Tolerance PrecursorMassTolerance { get; set; } // public setter required for calibration task
-        public bool AddCompIons { get; private set; }
+        public bool AddCompIons { get; set; }
         /// <summary>
         /// Only peptides/PSMs with Q-Value and Q-Value Notch below this threshold are used for quantification and
         /// spectral library generation. If SearchParameters.WriteHighQValuePsms is set to false, only 
@@ -199,6 +205,7 @@ public int DeconvolutionMaxAssumedChargeState
 
         public bool UseMostAbundantPrecursorIntensity { get; set; }
         public DIAparameters? DIAparameters { get; set; } //only for DIA analysis involving pseudo ms2 scan generation
+        public IFragmentationParams FragmentationParameters { get; set; }
 
         public CommonParameters Clone()
         {
@@ -257,6 +264,7 @@ public CommonParameters CloneWithNewTerminus(FragmentationTerminus? terminus = n
                                 TrimMsMsPeaks,
                                 ProductMassTolerance,
                                 PrecursorMassTolerance,
+                                ProductMassTolerance_LowRes,
                                 DeconvolutionMassTolerance,
                                 MaxThreadsToUsePerFile,
                                 DigestionParams.Clone(terminus),
@@ -267,7 +275,10 @@ public CommonParameters CloneWithNewTerminus(FragmentationTerminus? terminus = n
                                 MinVariantDepth,
                                 AddTruncations,
                                 PrecursorDeconvolutionParameters, 
-                                ProductDeconvolutionParameters);
+                                ProductDeconvolutionParameters,
+                                UseMostAbundantPrecursorIntensity,
+                                DIAparameters,
+                                FragmentationParameters);
         }
 
         public void SetCustomProductTypes()

MetaMorpheus/EngineLayer/EngineLayer.csproj

@@ -29,7 +29,7 @@
     <PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
     <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
-    <PackageReference Include="mzLib" Version="1.0.574" />
+    <PackageReference Include="mzLib" Version="1.0.576" />
     <PackageReference Include="NETStandard.Library" Version="2.0.3" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="Newtonsoft.Json" Version="13.0.3" />

MetaMorpheus/EngineLayer/GlycoSearch/GlycoSearchEngine.cs

@@ -55,7 +55,6 @@ public GlycoSearchEngine(List<GlycoSpectralMatch>[] globalCsms, Ms2ScanWithSpeci
             this.OxoniumIonFilter = oxoniumIonFilter;
             this._oglycanDatabase = oglycanDatabase;
             this._nglycanDatabase = nglycanDatabase;
-
             SecondFragmentIndex = secondFragmentIndex;
             PrecusorSearchMode = commonParameters.PrecursorMassTolerance;
             ProductSearchMode = new SinglePpmAroundZeroSearchMode(20); //For Oxonium ion only
@@ -324,7 +323,8 @@ private GlycoSpectralMatch CreateGsm(Ms2ScanWithSpecificMass theScan, int scanIn
 
             var PeptideScore = score - DiagnosticIonScore;
 
-            var p = theScan.TheScan.MassSpectrum.Size * CommonParameters.ProductMassTolerance.GetRange(1000).Width / theScan.TheScan.MassSpectrum.Range.Width;
+            var parentProductTolerance = IsLowResolutionScan(theScan) ? CommonParameters.ProductMassTolerance_LowRes : CommonParameters.ProductMassTolerance;
+            var p = theScan.TheScan.MassSpectrum.Size * parentProductTolerance.GetRange(1000).Width / theScan.TheScan.MassSpectrum.Range.Width;
 
             int n = fragmentsForEachGlycoPeptide.Where(v => v.ProductType == ProductType.c || v.ProductType == ProductType.zDot).Count();
 
@@ -333,7 +333,6 @@ private GlycoSpectralMatch CreateGsm(Ms2ScanWithSpecificMass theScan, int scanIn
             foreach (var childScan in theScan.ChildScans)
             {
                 var childFragments = GlycoPeptides.OGlyGetTheoreticalFragments(CommonParameters.MS2ChildScanDissociationType, CommonParameters.CustomIons, peptide, peptideWithMod);
-
                 var matchedChildIons = MatchFragmentIons(childScan, childFragments, CommonParameters);
 
                 n += childFragments.Where(v => v.ProductType == ProductType.c || v.ProductType == ProductType.zDot).Count();
@@ -356,7 +355,8 @@ private GlycoSpectralMatch CreateGsm(Ms2ScanWithSpecificMass theScan, int scanIn
                 //TO THINK:may think a different way to use childScore
                 score += childScore;
 
-                p += childScan.TheScan.MassSpectrum.Size * CommonParameters.ProductMassTolerance.GetRange(1000).Width / childScan.TheScan.MassSpectrum.Range.Width;
+                var productTolerance = IsLowResolutionScan(childScan) ? CommonParameters.ProductMassTolerance_LowRes : CommonParameters.ProductMassTolerance;
+                p += childScan.TheScan.MassSpectrum.Size * productTolerance.GetRange(1000).Width / childScan.TheScan.MassSpectrum.Range.Width;
 
             }
 
@@ -439,12 +439,16 @@ private void FindOGlycan(Ms2ScanWithSpecificMass theScan, int scanIndex, int sco
             SortedDictionary<int, string> modPos = GlycoSpectralMatch.GetPossibleModSites(theScanBestPeptide, Motifs); //list all of the possible glycoslation site/postition
 
             var localizationScan = theScan;
+            var toleranceForLocalizationScan = CommonParameters.ProductMassTolerance;
             List<Product> products = new List<Product>(); // product list for the theoretical fragment ions
 
             //For HCD-pd-ETD or CD-pd-EThcD type of data, we generate the different rpoducts.
             if (theScan.ChildScans.Count > 0 && GlycoPeptides.DissociationTypeContainETD(CommonParameters.MS2ChildScanDissociationType, CommonParameters.CustomIons))
             {
                 localizationScan = theScan.ChildScans.First();
+                // For the localization scan, if it is from ion trap, we will use a wider tolerance for the localization.
+                toleranceForLocalizationScan = localizationScan.TheScan.MzAnalyzer == MZAnalyzerType.IonTrap2D ||
+                    localizationScan.TheScan.MzAnalyzer == MZAnalyzerType.IonTrap3D ? CommonParameters.ProductMassTolerance_LowRes : CommonParameters.ProductMassTolerance;
                 theScanBestPeptide.Fragment(DissociationType.ETD, FragmentationTerminus.Both, products);
             }
 
@@ -477,7 +481,7 @@ private void FindOGlycan(Ms2ScanWithSpecificMass theScan, int scanIndex, int sco
                 if (GraphCheck(modPos, GlycanBoxes[iDLow])) // the glycosite number should be larger than the possible glycan number.
                 {
                     LocalizationGraph localizationGraph = new LocalizationGraph(modPos, GlycanBoxes[iDLow], GlycanBoxes[iDLow].ChildGlycanBoxes, iDLow);
-                    LocalizationGraph.LocalizeOGlycan(localizationGraph, localizationScan, CommonParameters.ProductMassTolerance, products); //create the localization graph with the glycan mass and the possible glycosite.
+                    LocalizationGraph.LocalizeOGlycan(localizationGraph, localizationScan, toleranceForLocalizationScan, products); //create the localization graph with the glycan mass and the possible glycosite.
 
                     double currentLocalizationScore = localizationGraph.TotalScore;
                     if (currentLocalizationScore > bestLocalizedScore) //Try to find the best glycanBox with the highest score.

MetaMorpheus/EngineLayer/Gptmd/GptmdEngine.cs

@@ -136,7 +136,7 @@ protected override MetaMorpheusEngineResults RunSpecific()
 
                                 var newPep = pepWithSetMods.Localize(pepSeqIndex, mod.MonoisotopicMass.Value);
                                 peptideTheorProducts.Clear();
-                                newPep.Fragment(dissociationType, CommonParameters.DigestionParams.FragmentationTerminus, peptideTheorProducts);
+                                newPep.Fragment(dissociationType, CommonParameters.DigestionParams.FragmentationTerminus, peptideTheorProducts, CommonParameters.FragmentationParameters);
 
                                 ms2ScanWithSpecificMass ??= new Ms2ScanWithSpecificMass(scan, precursorMass, precursorCharge, fileName, CommonParameters);
                                 var matchedIons = MatchFragmentIons(ms2ScanWithSpecificMass, peptideTheorProducts, CommonParameters, matchAllCharges: false);

MetaMorpheus/EngineLayer/Indexing/IndexingEngine.cs

@@ -160,7 +160,7 @@ protected override MetaMorpheusEngineResults RunSpecific()
 
             for (int peptideId = 0; peptideId < peptides.Count; peptideId++)
             {
-                peptides[peptideId].Fragment(CommonParameters.DissociationType, CommonParameters.DigestionParams.FragmentationTerminus, fragments);
+                peptides[peptideId].Fragment(CommonParameters.DissociationType, CommonParameters.DigestionParams.FragmentationTerminus, fragments, CommonParameters.FragmentationParameters);
 
                 foreach (var theoreticalFragment in fragments)
                 {

MetaMorpheus/EngineLayer/Localization/LocalizationEngine.cs

@@ -65,7 +65,7 @@ protected override MetaMorpheusEngineResults RunSpecific()
                             var peptideWithLocalizedMassDiff = peptide.Localize(r, massDifference);
 
                             // this is the list of theoretical products for this peptide with mass-difference on this residue
-                            peptideWithLocalizedMassDiff.Fragment(CommonParameters.DissociationType, CommonParameters.DigestionParams.FragmentationTerminus, productsWithLocalizedMassDiff);
+                            peptideWithLocalizedMassDiff.Fragment(CommonParameters.DissociationType, CommonParameters.DigestionParams.FragmentationTerminus, productsWithLocalizedMassDiff, CommonParameters.FragmentationParameters);
 
                             var matchedIons = MatchFragmentIons(scanWithSpecificMass, productsWithLocalizedMassDiff, CommonParameters);