PTM Stoichiometry

.github/workflows/dotnet.yml

@@ -38,3 +38,65 @@ jobs:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         verbose: true
         files: mzLib/Test*/TestResults/*/coverage.cobertura.xml
+  integration:
+    runs-on: windows-latest
+    timeout-minutes: 15
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up .NET
+      uses: actions/setup-dotnet@v1
+      with:
+        dotnet-version: 8.0.x
+    - name: Restore dependencies
+      run: cd mzLib && dotnet restore
+    - name: Build
+      run: cd mzLib && dotnet build --no-restore --configuration Release
+    - name: Change mzLib version, pack, add source
+      run: |
+        cd mzLib;
+        (Get-Content mzLib.nuspec) -replace "\<version\>(.*)\</version\>", "<version>9.9.9</version>" | Set-Content mzLib.nuspec; 
+        $mzlibMatch = Select-String -Path mzLib.nuspec -Pattern "(?<=\<version\>)(.*)(?=\</version)";
+        $mzlibVersion = $mzlibMatch.Matches[0].Value;
+        echo "mzLib version number changed to: $mzlibVersion";
+        nuget pack;
+        $currentFolder = pwd;
+        dotnet nuget add source $currentFolder;
+        dotnet nuget list source;
+    - name: Clone MetaMorpheus
+      uses: actions/checkout@master
+      with:
+        path: ./MetaMorpheus
+        repository: smith-chem-wisc/MetaMorpheus 
+        ref: master
+    - name: Change MetaMorpheus mzLib version and restore
+      run: |
+        cd ./MetaMorpheus/MetaMorpheus;
+        dotnet remove CMD package mzLib;
+        dotnet add CMD package mzLib -v 9.9.9;
+        dotnet remove GUI package mzLib;
+        dotnet add GUI package mzLib -v 9.9.9;
+        dotnet remove GuiFunctions package mzLib;
+        dotnet add GuiFunctions package mzLib -v 9.9.9;
+        dotnet remove EngineLayer package mzLib;
+        dotnet add EngineLayer package mzLib -v 9.9.9;
+        dotnet remove Test package mzLib;
+        dotnet add Test package mzLib -v 9.9.9;
+        dotnet remove TaskLayer package mzLib;
+        dotnet add TaskLayer package mzLib -v 9.9.9;
+        dotnet restore;
+    - name: Build MetaMorpheus
+      run: cd ./MetaMorpheus/MetaMorpheus && dotnet build --no-restore
+    - name: Test
+      run: cd ./MetaMorpheus/MetaMorpheus && dotnet test --no-build --verbosity normal
+    - name: Upload artifact (installer)
+      uses: actions/upload-artifact@v4
+      with:
+        name: MetaMorpheusInstaller
+        path: ./MetaMorpheus/MetaMorpheus/MetaMorpheusSetup/bin/Debug/MetaMorpheusInstaller.msi
+        compression-level: 0
+    - name: Upload artifact (GUI)
+      uses: actions/upload-artifact@v4
+      with:
+        name: MetaMorpheusGUI
+        path: ./MetaMorpheus/MetaMorpheus/GUI/bin/Debug/net8.0-windows/
+

mzLib/Chemistry/ClassExtensions.cs

@@ -48,6 +48,7 @@ public static double ToMass(this double massToChargeRatio, int charge)
             return Math.Abs(charge) * massToChargeRatio - charge * Constants.ProtonMass;
         }
 
+        public static double? RoundedDouble(this double myNumber, int places = 9) => RoundedDouble(myNumber as double?, places);
         public static double? RoundedDouble(this double? myNumber, int places = 9)
         {
             if (myNumber != null)

mzLib/Development/Deconvolution/TestCases/SinglePeakDeconvolutionTestCase.cs → mzLib/Development/DeconvolutionDevelopment/TestCases/SinglePeakDeconvolutionTestCase.cs

@@ -23,7 +23,7 @@ public class SinglePeakDeconvolutionTestCase
         public SinglePeakDeconvolutionTestCase(DeconvolutionParameters deconParameters, string sampleInformation, string spectrumPath, int scanNumber,
             double expectedMostAbundantObservedIsotopicMass, int expectedIonChargeState, double selectedIonMz, double precursorPpmMassTolerance)
         {
-
+            DeconvolutionParameters = deconParameters;
             SampleInformation = sampleInformation;
             ExpectedMostAbundantObservedIsotopicMass = expectedMostAbundantObservedIsotopicMass;
             ExpectedIonChargeState = expectedIonChargeState;

mzLib/Development/Development.csproj

@@ -23,13 +23,13 @@
   </ItemGroup>
 
   <ItemGroup>
-    <None Update="Deconvolution\TestData\Averaged_221110_CytoOnly.mzML">
+    <None Update="DeconvolutionDevelopment\TestData\Averaged_221110_CytoOnly.mzML">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>
-    <None Update="Deconvolution\TestData\Averaged_221110_HGHOnly.mzML">
+    <None Update="DeconvolutionDevelopment\TestData\Averaged_221110_HGHOnly.mzML">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>
-    <None Update="Deconvolution\TestData\Averaged_221110_UbiqOnly.mzML">
+    <None Update="DeconvolutionDevelopment\TestData\Averaged_221110_UbiqOnly.mzML">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>
   </ItemGroup>

mzLib/FlashLFQ/ChromatographicPeak.cs

@@ -1,9 +1,9 @@
-using MzLibUtil;
-using System;
+using System;
 using System.Collections.Generic;
 using System.Linq;
 using System.Text;
 using ClassExtensions = Chemistry.ClassExtensions;
+using FlashLFQ.PEP;
 
 namespace FlashLFQ
 {
@@ -16,20 +16,23 @@ public class ChromatographicPeak
         public int ScanCount => IsotopicEnvelopes.Count;
         public double SplitRT;
         public readonly bool IsMbrPeak;
-        public double PredictedRetentionTime { get; init; }
-
+        public double MbrScore;
+        public double PpmScore { get; set; }
+        public double IntensityScore { get; set; }
+        public double RtScore { get; set; }
+        public double ScanCountScore { get; set; }
+        public double IsotopicDistributionScore { get; set; }
         /// <summary>
-        /// A score bounded by 100 and 0, with more confident MBR-detections receiving higher scores
+        /// Stores the pearson correlation between the apex isotopic envelope and the theoretical isotopic distribution
         /// </summary>
-        public double MbrScore { get; private set; }
-
-        /// The four scores below are bounded by 0 and 1, with higher scores being better
-        public double PpmScore { get; private set; }
-        public double IntensityScore { get; private set; }
-        public double RtScore { get; private set; }
-        public double ScanCountScore { get; private set; }
-
-        public ChromatographicPeak(Identification id, bool isMbrPeak, SpectraFileInfo fileInfo)
+        public double IsotopicPearsonCorrelation => Apex?.PearsonCorrelation ?? -1;
+        public double RtPredictionError { get; set; }
+        public List<int> ChargeList { get; set; }
+        internal double MbrQValue { get; set; }
+        public ChromatographicPeakData PepPeakData { get; set; }
+        public double? MbrPep { get; set; }
+
+        public ChromatographicPeak(Identification id, bool isMbrPeak, SpectraFileInfo fileInfo, bool randomRt = false)
         {
             SplitRT = 0;
             NumChargeStatesObserved = 0;
@@ -40,12 +43,14 @@ public ChromatographicPeak(Identification id, bool isMbrPeak, SpectraFileInfo fi
             IsotopicEnvelopes = new List<IsotopicEnvelope>();
             IsMbrPeak = isMbrPeak;
             SpectraFileInfo = fileInfo;
+            RandomRt = randomRt;
         }
 
-        public ChromatographicPeak(Identification id, bool isMbrPeak, SpectraFileInfo fileInfo, double predictedRetentionTime) :
-            this(id, isMbrPeak, fileInfo)
+        public bool Equals(ChromatographicPeak peak)
         {
-            PredictedRetentionTime = predictedRetentionTime;
+            return SpectraFileInfo.Equals(peak.SpectraFileInfo) 
+                && Identifications.First().ModifiedSequence.Equals(peak.Identifications.First().ModifiedSequence)
+                && ApexRetentionTime == peak.ApexRetentionTime;
         }
 
         public IsotopicEnvelope Apex { get; private set; }
@@ -54,13 +59,18 @@ public ChromatographicPeak(Identification id, bool isMbrPeak, SpectraFileInfo fi
         public int NumIdentificationsByBaseSeq { get; private set; }
         public int NumIdentificationsByFullSeq { get; private set; }
         public double MassError { get; private set; }
+        /// <summary>
+        /// Bool that describes whether the retention time of this peak was randomized
+        /// If true, implies that this peak is a decoy peak identified by the MBR algorithm
+        /// </summary>
+        public bool RandomRt { get; }
+        public bool DecoyPeptide => Identifications.First().IsDecoy;
 
         public void CalculateIntensityForThisFeature(bool integrate)
         {
             if (IsotopicEnvelopes.Any())
             {
-                double maxIntensity = IsotopicEnvelopes.Max(p => p.Intensity);
-                Apex = IsotopicEnvelopes.First(p => p.Intensity == maxIntensity);
+                Apex = IsotopicEnvelopes.MaxBy(p => p.Intensity);
 
                 if (integrate)
                 {
@@ -123,25 +133,6 @@ public void ResolveIdentifications()
             this.NumIdentificationsByBaseSeq = Identifications.Select(v => v.BaseSequence).Distinct().Count();
             this.NumIdentificationsByFullSeq = Identifications.Select(v => v.ModifiedSequence).Distinct().Count();
         }
-
-        /// <summary>
-        /// Calculates four component scores and one overarching Mbr score for an MBR peak.
-        /// MBR Score is equal to 100 * the geometric mean of the four component scores.
-        /// </summary>
-        /// <param name="scorer"> An MbrScorer specific to the file where this peak was found </param>
-        /// <param name="donorPeak"> The donor peak used as the basis for the MBR identification. </param>
-        internal void CalculateMbrScore(MbrScorer scorer, ChromatographicPeak donorPeak)
-        {
-            if (SpectraFileInfo != scorer.AcceptorFile) throw new MzLibException("Error when performing match-between-runs: Mismatch between scorer and peak.");
-
-            IntensityScore = scorer.CalculateIntensityScore(this, donorPeak);
-            RtScore = scorer.CalculateRetentionTimeScore(this, donorPeak);
-            PpmScore = scorer.CalculatePpmErrorScore(this);
-            ScanCountScore = scorer.CalculateScanCountScore(this);
-
-            MbrScore = 100 * Math.Pow(IntensityScore * RtScore * PpmScore * ScanCountScore, 0.25);
-        }
-
         public static string TabSeparatedHeader
         {
             get
@@ -164,20 +155,18 @@ public static string TabSeparatedHeader
                 sb.Append("Peak Charge" + "\t");
                 sb.Append("Num Charge States Observed" + "\t");
                 sb.Append("Peak Detection Type" + "\t");
-                sb.Append("MBR Score" + "\t");
-                sb.Append("Ppm Score" + "\t");
-                sb.Append("Intensity Score" + "\t");
-                sb.Append("Rt Score" + "\t");
-                sb.Append("Scan Count Score" + "\t");
+                sb.Append("PIP Q-Value" + "\t");
+                sb.Append("PIP PEP" + "\t");
                 sb.Append("PSMs Mapped" + "\t");
                 sb.Append("Base Sequences Mapped" + "\t");
                 sb.Append("Full Sequences Mapped" + "\t");
                 sb.Append("Peak Split Valley RT" + "\t");
-                sb.Append("Peak Apex Mass Error (ppm)");
+                sb.Append("Peak Apex Mass Error (ppm)" + "\t");
+                sb.Append("Decoy Peptide" + "\t");
+                sb.Append("Random RT");
                 return sb.ToString();
             }
         }
-
         public override string ToString()
         {
             StringBuilder sb = new StringBuilder();
@@ -260,17 +249,16 @@ public override string ToString()
                 sb.Append("" + "MSMS" + "\t");
             }
 
-            sb.Append("" + (IsMbrPeak ? MbrScore.ToString() : "") + "\t");
-            sb.Append("" + (IsMbrPeak ? PpmScore.ToString() : "") + "\t");
-            sb.Append("" + (IsMbrPeak ? IntensityScore.ToString() : "") + "\t");
-            sb.Append("" + (IsMbrPeak ? RtScore.ToString() : "") + "\t");
-            sb.Append("" + (IsMbrPeak ? ScanCountScore.ToString() : "") + "\t");
+            sb.Append("" + (IsMbrPeak ? MbrQValue.ToString() : "") + "\t");
+            sb.Append("" + (IsMbrPeak ? MbrPep.ToString() : "") + "\t");
 
             sb.Append("" + Identifications.Count + "\t");
             sb.Append("" + NumIdentificationsByBaseSeq + "\t");
             sb.Append("" + NumIdentificationsByFullSeq + "\t");
             sb.Append("" + SplitRT + "\t");
             sb.Append("" + MassError);
+            sb.Append("\t" + DecoyPeptide);
+            sb.Append("\t" + RandomRt);
 
             return sb.ToString();
         }

mzLib/FlashLFQ/FlashLFQ.csproj

@@ -13,6 +13,8 @@
   <ItemGroup>
     <PackageReference Include="CsvHelper" Version="32.0.3" />
     <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
+    <PackageReference Include="Microsoft.ML" Version="3.0.1" />
+    <PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
     <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="SharpLearning.Optimization" Version="[0.28.0]" />
   </ItemGroup>