Max quant reader

MetaMorpheus/Bootstrapper/Bootstrapper - Backup.wixproj

@@ -0,0 +1,24 @@
+<Project Sdk="WixToolset.Sdk/4.0.0-rc.2">
+  <PropertyGroup>
+    <OutputName>MetaMorpheusInstaller</OutputName>
+    <OutputType>Bundle</OutputType>
+    <Platforms>x64;ARM64</Platforms>
+  </PropertyGroup>
+  <ItemGroup>
+    <PackageReference Include="WixToolset.Util.wixext" Version="4.0.0-rc.2" />
+    <PackageReference Include="WixToolset.Bal.wixext" Version="4.0.0-rc.2" />
+  </ItemGroup>
+  <ItemGroup>
+    <ProjectReference Include="..\MetaMorpheusSetup\MetaMorpheusSetup.wixproj">
+      <Name>MetaMorpheusSetup</Name>
+      <Project>{be72541a-66a4-4958-9d19-56acc7d3876b}</Project>
+      <Private>True</Private>
+      <DoNotHarvest>True</DoNotHarvest>
+      <RefProjectOutputGroups>Binaries;Content;Satellites</RefProjectOutputGroups>
+      <RefTargetDir>INSTALLFOLDER</RefTargetDir>
+    </ProjectReference>
+  </ItemGroup>
+  <ItemGroup>
+    <Content Include="theme.xml" />
+  </ItemGroup>
+</Project>

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="1.0.537" />
+    <PackageReference Include="mzLib" Version="5.1.538" />
     <PackageReference Include="Nett" Version="0.15.0" />
   </ItemGroup>
 

MetaMorpheus/EngineLayer/ClassicSearch/MiniClassicSearchEngine.cs

@@ -8,6 +8,8 @@
 using System.Collections.Generic;
 using System.Linq;
 using System.Threading.Tasks;
+using Easy.Common.Extensions;
+using ThermoFisher.CommonCore.Data;
 
 namespace EngineLayer.ClassicSearch
 {
@@ -19,20 +21,23 @@ public class MiniClassicSearchEngine
         private readonly double[] ArrayOfRTs;
         private CommonParameters myCommonParameters;
         private CommonParameters FileSpecificParameters;
+        private bool _maxQuantAnalysis;
 
         public MiniClassicSearchEngine(
             Ms2ScanWithSpecificMass[] arrayOfRTSortedMS2Scans,
             MassDiffAcceptor searchMode,
             CommonParameters commonParameters,
             SpectralLibrary spectralLibrary,
-            CommonParameters fileSpecificParameters)
+            CommonParameters fileSpecificParameters,
+            bool maxQuantAnalysis = false)
         {
             MS2ByRetentionTime = arrayOfRTSortedMS2Scans;
             ArrayOfRTs = MS2ByRetentionTime.Select(p => p.RetentionTime).ToArray();
             SearchMode = searchMode;
             SpectralLibrary = spectralLibrary;
             myCommonParameters = commonParameters;
             FileSpecificParameters = fileSpecificParameters ?? commonParameters;
+            _maxQuantAnalysis = maxQuantAnalysis;
             // Each instance of MCSE will be specific to one file.
         }
 
@@ -72,7 +77,7 @@ public IEnumerable<PeptideSpectralMatch> SearchAroundPeak(PeptideWithSetModifica
             foreach (ScanWithIndexAndNotchInfo scan in acceptableScans)
             {
                 var dissociationType = FileSpecificParameters.DissociationType == DissociationType.Autodetect ?
-                    scan.TheScan.TheScan.DissociationType.Value : FileSpecificParameters.DissociationType;
+                        scan.TheScan.TheScan.DissociationType.Value : FileSpecificParameters.DissociationType;
 
                 if (!targetFragmentsForEachDissociationType.TryGetValue(dissociationType, out var peptideTheorProducts))
                 {
@@ -98,17 +103,14 @@ public IEnumerable<PeptideSpectralMatch> SearchAroundPeak(PeptideWithSetModifica
             }
 
             IEnumerable<PeptideSpectralMatch> matchedSpectra = acceptablePsms.Where(p => p != null);
-            foreach (PeptideSpectralMatch psm in matchedSpectra)
-            {
-                psm.ResolveAllAmbiguities();
-            }
+            if (!_maxQuantAnalysis) foreach (PeptideSpectralMatch psm in matchedSpectra) psm.ResolveAllAmbiguities();
 
             CalculateSpectralAngles(SpectralLibrary, acceptablePsms.ToArray(), GetScansInWindow(peakApexRT), myCommonParameters, FileSpecificParameters);
 
             return matchedSpectra;
         }
 
-        public static void CalculateSpectralAngles(SpectralLibrary spectralLibrary, PeptideSpectralMatch[] psms,
+        public void CalculateSpectralAngles(SpectralLibrary spectralLibrary, PeptideSpectralMatch[] psms,
             Ms2ScanWithSpecificMass[] arrayOfSortedMs2Scans, CommonParameters commonParameters, CommonParameters fileSpecificParameters)
         {
             if (spectralLibrary != null)
@@ -124,7 +126,6 @@ public static void CalculateSpectralAngles(SpectralLibrary spectralLibrary, Pept
                 int[] threads = Enumerable.Range(0, maxThreadsPerFile).ToArray();
                 for (int i = 0; i < psms.Length; i++)
                 {
-
                     lock (myLocks[i])
                     {
                         if (psms[i] != null)
@@ -134,11 +135,14 @@ public static void CalculateSpectralAngles(SpectralLibrary spectralLibrary, Pept
                             List<double> pwsmSpectralAngles = new();
                             foreach (var (Notch, Peptide) in psms[i].BestMatchingPeptides)
                             {
+                                bool decoy = _maxQuantAnalysis ? false : Peptide.Protein.IsDecoy;
                                 //if peptide is target, directly look for the target's spectrum in the spectral library
-                                if (!Peptide.Protein.IsDecoy && spectralLibrary.TryGetSpectrum(Peptide.FullSequence, scan.PrecursorCharge, out var librarySpectrum))
+                                if (!decoy && spectralLibrary.TryGetSpectrum(Peptide.FullSequence, scan.PrecursorCharge, out var librarySpectrum))
                                 {
-                                    SpectralSimilarity s = new SpectralSimilarity(scan.TheScan.MassSpectrum, librarySpectrum.XArray, librarySpectrum.YArray,
-                                        SpectralSimilarity.SpectrumNormalizationScheme.squareRootSpectrumSum, fileSpecificParameters.ProductMassTolerance.Value, false);
+                                    SpectralSimilarity s = new SpectralSimilarity(scan.TheScan.MassSpectrum,
+                                        librarySpectrum.XArray, librarySpectrum.YArray,
+                                        SpectralSimilarity.SpectrumNormalizationScheme.squareRootSpectrumSum,
+                                        fileSpecificParameters.ProductMassTolerance.Value, false);
                                     if (s.SpectralContrastAngle().HasValue)
                                     {
                                         pwsms.Add((Notch, Peptide));

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="1.0.537" />
+    <PackageReference Include="mzLib" Version="5.1.538" />
     <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/PeptideSpectralMatch.cs

@@ -97,7 +97,9 @@ public PeptideSpectralMatch(PeptideWithSetModifications peptide, int notch, doub
         {
             get
             {
-                return _BestMatchingPeptides.OrderBy(p => p.Pwsm.FullSequence)
+                var sequenceOrderedPeptides = _BestMatchingPeptides.OrderBy(p => p.Pwsm.FullSequence);
+                if (sequenceOrderedPeptides.Any(p => p.Pwsm.Protein == null)) return sequenceOrderedPeptides;
+                return sequenceOrderedPeptides
                     .ThenBy(p => p.Pwsm.Protein.Accession)
                     .ThenBy(p => p.Pwsm.OneBasedStartResidueInProtein);
             }
@@ -194,6 +196,17 @@ public void SetFdrValues(double cumulativeTarget, double cumulativeDecoy, double
         /// </summary>
         public void ResolveAllAmbiguities()
         {
+            // Ad-hoc error handling for MaxQuant PsmFromTsv
+            if (_BestMatchingPeptides.Any(p => p.Pwsm.Protein == null))
+            {
+                FullSequence = PsmTsvWriter.Resolve(_BestMatchingPeptides.Select(b => b.Pwsm.FullSequence)).ResolvedValue;
+                BaseSequence = PsmTsvWriter.Resolve(_BestMatchingPeptides.Select(b => b.Pwsm.BaseSequence)).ResolvedValue;
+                PeptideLength = PsmTsvWriter.Resolve(_BestMatchingPeptides.Select(b => b.Pwsm.Length)).ResolvedValue;
+                PeptideMonisotopicMass = PsmTsvWriter.Resolve(_BestMatchingPeptides.Select(b => b.Pwsm.MonoisotopicMass)).ResolvedValue;
+                ModsIdentified = PsmTsvWriter.Resolve(_BestMatchingPeptides.Select(b => b.Pwsm.AllModsOneIsNterminus)).ResolvedValue;
+                ModsChemicalFormula = PsmTsvWriter.Resolve(_BestMatchingPeptides.Select(b => b.Pwsm.AllModsOneIsNterminus.Select(c => (c.Value)))).ResolvedValue;
+                return;
+            }
             IsDecoy = _BestMatchingPeptides.Any(p => p.Pwsm.Protein.IsDecoy);
             IsContaminant = _BestMatchingPeptides.Any(p => p.Pwsm.Protein.IsContaminant);
             FullSequence = PsmTsvWriter.Resolve(_BestMatchingPeptides.Select(b => b.Pwsm.FullSequence)).ResolvedValue;

MetaMorpheus/EngineLayer/PsmTsv/MaxQuantMsmsHeader.cs

@@ -0,0 +1,76 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace EngineLayer
+{
+    public class MaxQuantMsmsHeader
+    {
+        // File and scan information
+        public const string FileName = "Raw file";
+        public const string Ms2ScanNumber = "Scan number";
+        public const string Ms2ScanRetentionTime = "Retention time";
+        //public const string NumExperimentalPeaks = "Number of Matches";
+        //public const string TotalIonCurrent = "Total Ion Current";
+        public const string PrecursorScanNum = "Precursor full scan number";
+        public const string PrecursorCharge = "Charge";
+        public const string PrecursorMz = "m/z";
+        public const string PrecursorMass = "Mass";
+        public const string Score = "Score";
+        public const string DeltaScore = "Delta score";
+        //public const string Notch = "Notch";
+
+        // Sequence information
+        public const string BaseSequence = "Sequence";
+        public const string FullSequence = "Modified sequence";
+        //public const string EssentialSequence = "Essential Sequence";
+        //public const string AmbiguityLevel = "Ambiguity Level";
+        //public const string PsmCount = "PSM Count (unambiguous, <0.01 q-value)";
+        public const string Mods = "Modifications";
+        //public const string ModsChemicalFormulas = "Mods Chemical Formulas";
+        //public const string ModsCombinedChemicalFormula = "Mods Combined Chemical Formula";
+        //public const string NumVariableMods = "Num Variable Mods";
+        //public const string MissedCleavages = "Missed Cleavages";
+        //public const string PeptideMonoMass = "Peptide Monoisotopic Mass";
+        public const string MassDiffDa = "Mass error [Da]";
+        public const string MassDiffPpm = "Mass error [ppm]";
+        public const string ProteinAccession = "Proteins";
+        public const string ProteinName = "Protein Names";
+        public const string GeneName = "Gene Names";
+        //public const string OrganismName = "Organism Name";
+        //public const string IntersectingSequenceVariations = "Intersecting Sequence Variations";
+        //public const string IdentifiedSequenceVariations = "Identified Sequence Variations";
+        //public const string SpliceSites = "Splice Sites";
+        //public const string Contaminant = "Contaminant";
+        public const string Decoy = "Reverse";
+        //public const string PeptideDesicription = "Peptide Description";
+        //public const string StartAndEndResiduesInProtein = "Start and End Residues In Protein";
+        //public const string PreviousAminoAcid = "Previous Amino Acid";
+        //public const string NextAminoAcid = "Next Amino Acid";
+        //public const string TheoreticalsSearched = "Theoreticals Searched";
+        //public const string DecoyContaminantTarget = "Decoy/Contaminant/Target";
+        public const string MatchedIonSeries = "Matches";
+        public const string MatchedIonMzRatios = "Masses";
+        public const string MatchedIonMassDiffDa = "Mass deviations [Da]";
+        public const string MatchedIonMassDiffPpm = "Mass deviations [ppm]";
+        public const string MatchedIonIntensities = "Intensities";
+        public const string MatchedIonCounts = "Number of matches";
+
+        // Scoring
+        public const string PEP = "PEP";
+        //public const string LocalizedScores = "Localized Scores";
+        //public const string ImprovementPossible = "Improvement Possible";
+        //public const string CumulativeTarget = "Cumulative Target";
+        //public const string CumulativeDecoy = "Cumulative Decoy";
+        //public const string CumulativeTargetNotch = "Cumulative Target Notch";
+        //public const string CumulativeDecoyNotch = "Cumulative Decoy Notch";
+        //public const string QValue = "QValue";
+        //public const string QValueNotch = "QValue Notch";
+        //public const string PEP_QValue = "PEP_QValue";
+        //public const string SpectralAngle = "Normalized Spectral Angle";
+
+
+    }
+}