#1 - Update Mzlib to 1.0.547 (Omics Update)

MetaMorpheus/CMD/CMD.csproj

@@ -24,7 +24,7 @@
     <PackageReference Include="Microsoft.ML.CpuMath" Version="2.0.0" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="2.0.0" />
     <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
-    <PackageReference Include="mzLib" Version="1.0.542" />
+    <PackageReference Include="mzLib" Version="1.0.546" />
     <PackageReference Include="Nett" Version="0.15.0" />
   </ItemGroup>
 

MetaMorpheus/CMD/Program.cs

@@ -9,6 +9,7 @@
 using System.IO;
 using System.Linq;
 using System.Text.RegularExpressions;
+using Omics.Modifications;
 using TaskLayer;
 
 namespace MetaMorpheusCommandLine

MetaMorpheus/EngineLayer/ClassicSearch/ClassicSearchEngine.cs

@@ -1,12 +1,13 @@
 using MassSpectrometry;
 using MzLibUtil;
 using Proteomics;
-using Proteomics.Fragmentation;
+using Omics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System;
 using System.Collections.Generic;
 using System.Linq;
 using System.Threading.Tasks;
+using Omics.Modifications;
 
 namespace EngineLayer.ClassicSearch
 {

MetaMorpheus/EngineLayer/ClassicSearch/MiniClassicSearchEngine.cs

@@ -1,7 +1,7 @@
 using MassSpectrometry;
 using MassSpectrometry.MzSpectra;
 using MzLibUtil;
-using Proteomics.Fragmentation;
+using Omics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System;
 using System.Collections.Generic;

MetaMorpheus/EngineLayer/CommonParameters.cs

@@ -1,10 +1,11 @@
 using MassSpectrometry;
 using MzLibUtil;
-using Proteomics.Fragmentation;
+using Omics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System;
 using System.Collections.Generic;
 using System.Reflection;
+using Omics.Fragmentation.Peptide;
 
 namespace EngineLayer
 {

MetaMorpheus/EngineLayer/CrosslinkSearch/CrosslinkSearchEngine.cs

@@ -2,13 +2,15 @@
 using MassSpectrometry;
 using MzLibUtil;
 using Proteomics;
-using Proteomics.Fragmentation;
+using Omics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System;
 using System.Collections;
 using System.Collections.Generic;
 using System.Linq;
 using System.Threading.Tasks;
+using Omics.Fragmentation;
+using Omics.Modifications;
 
 namespace EngineLayer.CrosslinkSearch
 {

MetaMorpheus/EngineLayer/CrosslinkSearch/CrosslinkSpectralMatch.cs

@@ -1,5 +1,5 @@
 using Easy.Common.Extensions;
-using Proteomics.Fragmentation;
+using Omics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System;
 using System.Collections.Generic;

MetaMorpheus/EngineLayer/CrosslinkSearch/CrosslinkedPeptides.cs

@@ -1,10 +1,11 @@
 using MassSpectrometry;
 using Proteomics;
-using Proteomics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System;
 using System.Collections.Generic;
 using System.Linq;
+using Omics.Fragmentation;
+using Omics.Modifications;
 
 namespace EngineLayer.CrosslinkSearch
 {

MetaMorpheus/EngineLayer/CrosslinkSearch/Crosslinker.cs

@@ -2,6 +2,7 @@
 using System.IO;
 using MassSpectrometry;
 using System.Globalization;
+using Omics.Modifications;
 using Proteomics;
 
 namespace EngineLayer

MetaMorpheus/EngineLayer/EngineLayer.csproj

@@ -21,7 +21,7 @@
     <PackageReference Include="Microsoft.ML.CpuMath" Version="2.0.0" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="2.0.0" />
     <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
-    <PackageReference Include="mzLib" Version="1.0.542" />
+    <PackageReference Include="mzLib" Version="1.0.546" />
     <PackageReference Include="NETStandard.Library" Version="2.0.3" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="Newtonsoft.Json" Version="13.0.1" />

MetaMorpheus/EngineLayer/FdrAnalysis/PEPValueAnalysisGeneric.cs

@@ -5,7 +5,7 @@
 using Microsoft.ML;
 using Microsoft.ML.Data;
 using Proteomics;
-using Proteomics.Fragmentation;
+using Omics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using Proteomics.RetentionTimePrediction;
 using System;
@@ -15,6 +15,7 @@
 using System.Linq;
 using System.Text;
 using System.Threading.Tasks;
+using Omics.Modifications;
 
 namespace EngineLayer
 {

MetaMorpheus/EngineLayer/GlobalVariables.cs

@@ -11,6 +11,7 @@
 using System.Linq;
 using System.Runtime.InteropServices;
 using System.Text;
+using Omics.Modifications;
 using TopDownProteomics;
 using UsefulProteomicsDatabases;
 

MetaMorpheus/EngineLayer/GlycoSearch/Glycan.cs

@@ -5,6 +5,7 @@
 using System;
 using Proteomics;
 using MassSpectrometry;
+using Omics.Modifications;
 
 namespace EngineLayer
 {

MetaMorpheus/EngineLayer/GlycoSearch/GlycanBox.cs

@@ -5,6 +5,7 @@
 using System;
 using Proteomics;
 using MassSpectrometry;
+using Omics.Modifications;
 
 namespace EngineLayer
 {

MetaMorpheus/EngineLayer/GlycoSearch/GlycoPeptides.cs

@@ -1,11 +1,12 @@
 using MassSpectrometry;
 using Proteomics;
-using Proteomics.Fragmentation;
+using Omics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System;
 using System.Collections.Generic;
 using System.Linq;
 using Chemistry;
+using Omics.Modifications;
 
 namespace EngineLayer.GlycoSearch
 {

MetaMorpheus/EngineLayer/GlycoSearch/GlycoSearchEngine.cs

@@ -1,7 +1,7 @@
 using EngineLayer.ModernSearch;
 using MzLibUtil;
 using Proteomics;
-using Proteomics.Fragmentation;
+using Omics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System;
 using System.Collections.Generic;

MetaMorpheus/EngineLayer/GlycoSearch/GlycoSpectralMatch.cs

@@ -1,9 +1,10 @@
-using Proteomics.Fragmentation;
+using Omics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System;
 using System.Collections.Generic;
 using System.Linq;
 using System.Text;
+using Omics.Modifications;
 using Proteomics;
 
 namespace EngineLayer.GlycoSearch

MetaMorpheus/EngineLayer/GlycoSearch/LocalizationGraph.cs

@@ -1,7 +1,7 @@
 using System;
 using System.Collections.Generic;
 using System.Linq;
-using Proteomics.Fragmentation;
+using Omics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using Proteomics;
 using MzLibUtil;

MetaMorpheus/EngineLayer/Gptmd/GptmdEngine.cs

@@ -4,6 +4,7 @@
 using System;
 using System.Collections.Generic;
 using System.Linq;
+using Omics.Modifications;
 
 namespace EngineLayer.Gptmd
 {

MetaMorpheus/EngineLayer/Gptmd/GptmdResults.cs

@@ -3,6 +3,7 @@
 using System.Collections.Generic;
 using System.Linq;
 using System.Text;
+using Omics.Modifications;
 
 namespace EngineLayer.Gptmd
 {

MetaMorpheus/EngineLayer/HistogramAnalysis/Bin.cs

@@ -4,6 +4,7 @@
 using System.Collections.Generic;
 using System.Globalization;
 using System.Linq;
+using Omics.Modifications;
 
 namespace EngineLayer.HistogramAnalysis
 {

MetaMorpheus/EngineLayer/HistogramAnalysis/BinTreeStructure.cs

@@ -4,7 +4,7 @@
 using System.Collections.Generic;
 using System.Linq;
 using System.Text;
-using Proteomics.Fragmentation;
+using Omics.Fragmentation;
 
 namespace EngineLayer.HistogramAnalysis
 {

MetaMorpheus/EngineLayer/Indexing/IndexingEngine.cs

@@ -1,14 +1,16 @@
 using Chemistry;
 using EngineLayer.NonSpecificEnzymeSearch;
 using Proteomics;
-using Proteomics.Fragmentation;
+using Omics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System;
 using System.Collections.Generic;
 using System.IO;
 using System.Linq;
 using System.Text;
 using System.Threading.Tasks;
+using Omics.Fragmentation.Peptide;
+using Omics.Modifications;
 using UsefulProteomicsDatabases;
 
 namespace EngineLayer.Indexing
@@ -258,9 +260,19 @@ private void AddInteriorTerminalModsToPrecursorIndex(List<int>[] precursorIndex,
             foreach (KeyValuePair<int, List<Modification>> relevantDatabaseMod in databaseAnnotatedMods)
             {
                 int fragmentNumber = relevantDatabaseMod.Key;
-                Product fragmentAtIndex = fragmentMasses.Where(x => x.FragmentNumber == fragmentNumber).FirstOrDefault();
-                double basePrecursorMass = fragmentAtIndex.NeutralMass == default(Product).NeutralMass ? 
-                    peptide.MonoisotopicMass : fragmentAtIndex.NeutralMass - DissociationTypeCollection.GetMassShiftFromProductType(fragmentAtIndex.ProductType) + WaterMonoisotopicMass;
+                Product fragmentAtIndex = fragmentMasses.FirstOrDefault(x => x.FragmentNumber == fragmentNumber);
+
+                double basePrecursorMass;
+                if (fragmentAtIndex is null)
+                {
+                    basePrecursorMass = peptide.MonoisotopicMass;
+                }
+                else
+                {
+                    basePrecursorMass = fragmentAtIndex.NeutralMass -
+                                        DissociationTypeCollection.GetMassShiftFromProductType(fragmentAtIndex.ProductType) +
+                                        WaterMonoisotopicMass;
+                }
 
                 foreach (Modification mod in relevantDatabaseMod.Value)
                 {

MetaMorpheus/EngineLayer/Indexing/IndexingResults.cs

@@ -1,4 +1,4 @@
-using Proteomics.Fragmentation;
+using Omics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System.Collections.Generic;
 using System.Text;

MetaMorpheus/EngineLayer/Localization/LocalizationEngine.cs

@@ -1,5 +1,5 @@
 using MassSpectrometry;
-using Proteomics.Fragmentation;
+using Omics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System.Collections.Concurrent;
 using System.Collections.Generic;

MetaMorpheus/EngineLayer/MetaMorpheusEngine.cs

@@ -2,14 +2,15 @@
 using MassSpectrometry;
 using Microsoft.ML.Trainers.FastTree;
 using MzLibUtil;
-using Proteomics.Fragmentation;
+using Omics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System;
 using System.Collections.Concurrent;
 using System.Collections.Generic;
 using System.Diagnostics;
 using System.Linq;
 using System.Threading.Tasks;
+using Omics.Fragmentation;
 
 namespace EngineLayer
 {
@@ -162,7 +163,7 @@ public static List<MatchedFragmentIon> MatchFragmentIons(Ms2ScanWithSpecificMass
 
                     if (commonParameters.ProductMassTolerance.Within(scan.TheScan.MassSpectrum.XArray[closestMzIndex], theoreticalFragmentMz))
                     {
-                        matchedFragmentIons.Add(new MatchedFragmentIon(ref product, theoreticalFragmentMz, scan.TheScan.MassSpectrum.YArray[closestMzIndex], 1));
+                        matchedFragmentIons.Add(new MatchedFragmentIon(product, theoreticalFragmentMz, scan.TheScan.MassSpectrum.YArray[closestMzIndex], 1));
                     }
                 }
 
@@ -192,7 +193,7 @@ public static List<MatchedFragmentIon> MatchFragmentIons(Ms2ScanWithSpecificMass
                 // is the mass error acceptable?
                 if (closestExperimentalMass != null && commonParameters.ProductMassTolerance.Within(closestExperimentalMass.MonoisotopicMass, product.NeutralMass) && closestExperimentalMass.Charge <= scan.PrecursorCharge)//TODO apply this filter before picking the envelope
                 {
-                    matchedFragmentIons.Add(new MatchedFragmentIon(ref product, closestExperimentalMass.MonoisotopicMass.ToMz(closestExperimentalMass.Charge),
+                    matchedFragmentIons.Add(new MatchedFragmentIon(product, closestExperimentalMass.MonoisotopicMass.ToMz(closestExperimentalMass.Charge),
                         closestExperimentalMass.Peaks.First().intensity, closestExperimentalMass.Charge));
                 }
             }
@@ -222,7 +223,7 @@ public static List<MatchedFragmentIon> MatchFragmentIons(Ms2ScanWithSpecificMass
                             //found the peak, but we don't want to save that m/z because it's the complementary of the observed ion that we "added". Need to create a fake ion instead.
                             double mz = (scan.PrecursorMass + protonMassShift - closestExperimentalMass.MonoisotopicMass).ToMz(closestExperimentalMass.Charge);
 
-                            matchedFragmentIons.Add(new MatchedFragmentIon(ref product, mz, closestExperimentalMass.TotalIntensity, closestExperimentalMass.Charge));
+                            matchedFragmentIons.Add(new MatchedFragmentIon(product, mz, closestExperimentalMass.TotalIntensity, closestExperimentalMass.Charge));
                         }
                     }
                 }
@@ -266,7 +267,7 @@ private static List<MatchedFragmentIon> MatchFragmentIonsOfAllCharges(Ms2ScanWit
                         if (x != null && !ions.Contains(ion) && commonParameters.ProductMassTolerance.Within(x.MonoisotopicMass, product.NeutralMass) && x.Charge <= scan.PrecursorCharge)//TODO apply this filter before picking the envelope
                         {
                             Product temProduct = product;
-                            matchedFragmentIons.Add(new MatchedFragmentIon(ref temProduct, x.MonoisotopicMass.ToMz(x.Charge),
+                            matchedFragmentIons.Add(new MatchedFragmentIon(temProduct, x.MonoisotopicMass.ToMz(x.Charge),
                                 x.Peaks.First().intensity, x.Charge));
 
                             ions.Add(ion);

MetaMorpheus/EngineLayer/ModernSearch/ModernSearchEngine.cs

@@ -1,6 +1,6 @@
 using Chemistry;
 using MassSpectrometry;
-using Proteomics.Fragmentation;
+using Omics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System;
 using System.Collections.Generic;

MetaMorpheus/EngineLayer/NonSpecificEnzymeSearch/NonSpecificEnzymeSearchEngine.cs

@@ -2,14 +2,17 @@
 using EngineLayer.FdrAnalysis;
 using EngineLayer.ModernSearch;
 using Proteomics;
-using Proteomics.Fragmentation;
+using Omics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System;
 using MassSpectrometry;
 using System.Collections.Generic;
 using System.Linq;
 using System.Threading.Tasks;
 using MzLibUtil;
+using Omics.Digestion;
+using Omics.Fragmentation.Peptide;
+using Omics.Modifications;
 
 namespace EngineLayer.NonSpecificEnzymeSearch
 {

MetaMorpheus/EngineLayer/PeptideSpectralMatch.cs

@@ -3,13 +3,15 @@
 using EngineLayer.FdrAnalysis;
 using MassSpectrometry;
 using Proteomics;
-using Proteomics.Fragmentation;
+using Omics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System.Collections.Generic;
 using System.Collections.Immutable;
 using System.Linq;
 using System.Runtime.CompilerServices;
 using Easy.Common.Extensions;
+using Omics;
+using Omics.Modifications;
 using Proteomics.AminoAcidPolymer;
 using ThermoFisher.CommonCore.Data;