Mirror

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="1.0.578" />
+    <PackageReference Include="mzLib" Version="1.0.579" />
     <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" />

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="1.0.578" />
+    <PackageReference Include="mzLib" Version="1.0.579" />
     <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/FdrAnalysis/PEPAnalysisEngine.cs

@@ -91,7 +91,7 @@
             FileSpecificParametersDictionary = fileSpecificParameters.ToDictionary(p => Path.GetFileName(p.fileName), p => p.fileSpecificParameters);
         }
 
         public PepAnalysisEngine(List<SpectralMatch> psms, string searchType, List<(string fileName, CommonParameters fileSpecificParameters)> fileSpecificParameters, string outputFolder, IRetentionTimePredictor? rtPredictor = null)
         {
             // This creates a new list of PSMs, but does not clone the Psms themselves.
             // This allows the PSMs to be modified and the order to be preserved
@@ -640,6 +640,7 @@
                 MostAbundantPrecursorPeakIntensity = mostAbundantPrecursorPeakIntensity,
                 PrecursorFractionalIntensity = fractionalIntensity,
                 InternalIonCount = internalMatchingFragmentCount,
+                PrecursorDeconvolutionScore = (float)psm.PrecursorScanDeconvolutionScore,
             };
 
             return psm.PsmData_forPEPandPercolator;

MetaMorpheus/EngineLayer/FdrAnalysis/PsmData.cs

@@ -15,9 +15,10 @@ public class PsmData
                 "standard", new[]
                 {
                     "TotalMatchingFragmentCount", "Intensity", "PrecursorChargeDiffToMode", "DeltaScore",
-                    "Notch", "ModsCount", "AbsoluteAverageFragmentMassErrorFromMedian", "MissedCleavagesCount", 
+                    "Notch", "ModsCount", "AbsoluteAverageFragmentMassErrorFromMedian", "MissedCleavagesCount",
                     "Ambiguity", "LongestFragmentIonSeries", "ComplementaryIonCount", "HydrophobicityZScore",
-                    "IsVariantPeptide", "IsDeadEnd", "IsLoop", "SpectralAngle", "HasSpectralAngle", 
+                    "IsVariantPeptide", "IsDeadEnd", "IsLoop", "SpectralAngle", "HasSpectralAngle",
+                    "PrecursorDeconvolutionScore",
                 }
             },
 
@@ -85,6 +86,7 @@ public class PsmData
             { "MostAbundantPrecursorPeakIntensity", 1 },
             { "PrecursorFractionalIntensity", 1 },
             { "InternalIonCount", 1},
+            { "PrecursorDeconvolutionScore", 1 },
             }.ToImmutableDictionary();
 
         public string ToString(string searchType)
@@ -189,5 +191,8 @@ public string ToString(string searchType)
 
         [LoadColumn(28)]
         public float InternalIonCount { get; set; }
+
+        [LoadColumn(29)]
+        public float PrecursorDeconvolutionScore { get; set; }
     }
 }

MetaMorpheus/EngineLayer/Ms2ScanWithSpecificMass.cs

@@ -10,14 +10,16 @@
     public class Ms2ScanWithSpecificMass
     {
         public Ms2ScanWithSpecificMass(MsDataScan mzLibScan, double precursorMonoisotopicPeakMz, int precursorCharge, string fullFilePath, CommonParameters commonParam,
-            IsotopicEnvelope[] neutralExperimentalFragments = null, double? precursorIntensity = null, int? envelopePeakCount = null, double? precursorFractionalIntensity = null)
+            IsotopicEnvelope[] neutralExperimentalFragments = null, double? precursorIntensity = null, int? envelopePeakCount = null, double? precursorFractionalIntensity = null,
+            double precursorDeconvolutionScore = 0)
         {
             PrecursorMonoisotopicPeakMz = precursorMonoisotopicPeakMz;
             PrecursorCharge = precursorCharge;
             PrecursorMass = PrecursorMonoisotopicPeakMz.ToMass(precursorCharge);
             PrecursorIntensity = precursorIntensity ?? 1;
             PrecursorEnvelopePeakCount = envelopePeakCount ?? 1;
             PrecursorFractionalIntensity = precursorFractionalIntensity ?? -1;
+            PrecursorDeconvolutionScore = precursorDeconvolutionScore;
             FullFilePath = fullFilePath;
             ChildScans = new List<Ms2ScanWithSpecificMass>();
             NativeId = mzLibScan.NativeId;
@@ -45,6 +47,12 @@
         public double PrecursorIntensity { get; }
         public int PrecursorEnvelopePeakCount { get; }
         public double PrecursorFractionalIntensity { get; }
+        /// <summary>
+        /// Method-agnostic envelope-quality score in [0, 1] from mzLib's DeconvolutionScorer.
+        /// 0 indicates either a maximally low-quality envelope or that no envelope was
+        /// deconvoluted for this scan (e.g. scan-header-only precursor path).
+        /// </summary>
+        public double PrecursorDeconvolutionScore { get; }
         public string FullFilePath { get; }
         public IsotopicEnvelope[] ExperimentalFragments { get; private set; }
         public List<Ms2ScanWithSpecificMass> ChildScans { get; set; } // MS2/MS3 scans that are children of this MS2 scan
@@ -59,7 +67,7 @@
         /// An array containing the intensities of the reporter ions for isobaric mass tags. 
         /// If multiplex quantification wasn't performed, this will be null
         /// </summary>
         public double[]? IsobaricMassTagReporterIonIntensities { get; private set; }
 
         public static IsotopicEnvelope[] GetNeutralExperimentalFragments(MsDataScan scan, CommonParameters commonParam)
         {

MetaMorpheus/EngineLayer/SpectralMatch.cs

@@ -34,6 +34,7 @@
             ScanPrecursorMass = scan.PrecursorMass;
             PrecursorScanEnvelopePeakCount = scan.PrecursorEnvelopePeakCount;
             PrecursorFractionalIntensity = scan.PrecursorFractionalIntensity;
+            PrecursorScanDeconvolutionScore = scan.PrecursorDeconvolutionScore;
             DigestionParams = commonParameters.DigestionParams;
             NativeId = scan.NativeId;
             RunnerUpScore = commonParameters.ScoreCutoff;
@@ -78,6 +79,12 @@
         public double PrecursorScanIntensity { get; }
         public int PrecursorScanEnvelopePeakCount { get; }
         public double PrecursorFractionalIntensity { get; }
+        /// <summary>
+        /// Method-agnostic envelope-quality score in [0, 1] from mzLib's DeconvolutionScorer for
+        /// the precursor envelope of this PSM. 0 indicates no envelope was computed or the
+        /// envelope is maximally bad; higher = better-shaped Averagine match.
+        /// </summary>
+        public double PrecursorScanDeconvolutionScore { get; }
         public double ScanPrecursorMass { get; }
         public double? ScanOneOverK0 { get; set; } // this is only used for ion mobility data, so it can be null
         public string FullFilePath { get; private set; }
@@ -161,7 +168,7 @@
         /// An array containing the intensities of the reporter ions for isobaric mass tags. 
         /// If multiplex quantification wasn't performed, this will be null
         /// </summary>
         public double[]? IsobaricMassTagReporterIonIntensities { get; private set; }
 
         public IEnumerable<SpectralMatchHypothesis> BestMatchingBioPolymersWithSetMods
         {

MetaMorpheus/EngineLayer/Util/Precursor.cs

@@ -96,11 +96,19 @@ public Precursor(IsotopicEnvelope envelope, double? intensity = null, double? fr
     /// </summary>
     public int EnvelopePeakCount { get; init; }
 
-    /// <summary> 
+    /// <summary>
     /// The fraction of the intensity in the MS1 scan isolation window that is accounted for by this precursor
     /// </summary>
     public double? FractionalIntensity { get; init; }
 
+    /// <summary>
+    /// Method-agnostic envelope-quality score in [0, 1] from mzLib's DeconvolutionScorer, computed
+    /// at deconvolution time. 0 is the sentinel for "no envelope was deconvoluted" (e.g. the
+    /// scan-header-only precursor path) and is also returned by the scorer for a maximally bad
+    /// envelope, so the model cannot distinguish those two cases — accepted limitation for now.
+    /// </summary>
+    public double DeconvolutionScore { get; init; }
+
     public bool Equals(Precursor? other, Tolerance mzTolerance)
     {
         if (other == null) return false;

MetaMorpheus/GUI/GUI.csproj

@@ -63,7 +63,7 @@
     <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="1.0.578" />
+    <PackageReference Include="mzLib" Version="1.0.579" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="Newtonsoft.Json" Version="13.0.3" />
     <PackageReference Include="OxyPlot.Core" Version="2.0.0" />

MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml

@@ -1,4 +1,4 @@
-<Window x:Class="MetaMorpheusGUI.MetaDraw"
+<Window x:Class="MetaMorpheusGUI.MetaDraw"
         x:Name="MetaDrawWindow"
         xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
         xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
@@ -704,6 +704,13 @@
                 <local:ChimeraAnalysisTabView x:Name="ChimeraAnalysisTabView" />
             </TabItem>
 
+            <!-- Mirror Plot tab -->
+            <TabItem Header="{Binding TabHeader}" IsEnabled="{Binding IsTabEnabled}" Background="DarkGray"
+                     d:DataContext="{d:DesignInstance metaDraw:MirrorPlotTabViewModel, IsDesignTimeCreatable=True}"
+                     DataContext="{Binding MirrorPlotTabViewModel, RelativeSource={RelativeSource AncestorType=Window}}">
+                <local:MirrorPlotTabView x:Name="MirrorPlotTabView" />
+            </TabItem>
+
             <!--Deconvolution Exploration tab-->
             <TabItem Header="{Binding TabHeader}" IsEnabled="{Binding IsTabEnabled}" Background="DarkGray"
                      d:DataContext="{d:DesignInstance guiFunctions:DeconExplorationTabViewModel, IsDesignTimeCreatable=True}"

MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs

@@ -44,6 +44,7 @@ public partial class MetaDraw : Window
         private static List<string> AcceptedSpectralLibraryFormats = new List<string> { ".msp" };
         private FragmentationReanalysisViewModel FragmentationReanalysisViewModel;
         public ChimeraAnalysisTabViewModel ChimeraAnalysisTabViewModel { get; set; }
+        public MirrorPlotTabViewModel MirrorPlotTabViewModel { get; set; }
         public DeconExplorationTabViewModel DeconExplorationViewModel { get; set; }
         public BioPolymerTabViewModel BioPolymerTabViewModel { get; set; }
 
@@ -61,6 +62,7 @@ public MetaDraw(string[]? filesToLoad = null)
 
             BioPolymerTabViewModel = new BioPolymerTabViewModel(MetaDrawLogic);
             ChimeraAnalysisTabViewModel = new ChimeraAnalysisTabViewModel();
+            MirrorPlotTabViewModel = new MirrorPlotTabViewModel();
             DeconExplorationViewModel = new DeconExplorationTabViewModel(MetaDrawLogic);
 
             propertyView = new DataTable();
@@ -305,25 +307,37 @@ private void dataGridScanNums_SelectedCellsChanged(object sender, SelectedCellsC
             double maxDisplayedPerRow = (int)Math.Round((UpperSequenceAnnotaiton.ActualWidth - 10) / MetaDrawSettings.AnnotatedSequenceTextSpacing, 0) + 7;
             MetaDrawSettings.SequenceAnnotationSegmentPerRow = (int)Math.Floor(maxDisplayedPerRow / (double)(MetaDrawSettings.SequenceAnnotaitonResiduesPerSegment + 1));
 
-            // draw the annotated spectrum
-            MetaDrawLogic.DisplaySequences(stationarySequenceCanvas, scrollableSequenceCanvas, sequenceAnnotationCanvas, psm);
-            MetaDrawLogic.DisplaySpectrumMatch(plotView, psm, itemsControlSampleViewModel, out var errors);
-
-            // add ptm legend if desired
-            if (MetaDrawSettings.ShowLegend)
+            List<string> errors = null;
+            try
             {
-                int descriptionLineCount = MetaDrawSettings.SpectrumDescription.Count(p => p.Value);
-                if (psm.Name.IsNotNullOrEmptyOrWhiteSpace())
+                // draw the annotated spectrum
+                MetaDrawLogic.DisplaySequences(stationarySequenceCanvas, scrollableSequenceCanvas,
+                    sequenceAnnotationCanvas, psm);
+                MetaDrawLogic.DisplaySpectrumMatch(plotView, psm, itemsControlSampleViewModel, out errors);
+
+                // add ptm legend if desired
+                if (MetaDrawSettings.ShowLegend)
                 {
-                    descriptionLineCount += (int)Math.Floor((psm.Name.Length - 20) / (double)SpectrumMatchPlot.MaxCharactersPerDescriptionLine);
+                    int descriptionLineCount = MetaDrawSettings.SpectrumDescription.Count(p => p.Value);
+                    if (psm.Name.IsNotNullOrEmptyOrWhiteSpace())
+                    {
+                        descriptionLineCount += (int)Math.Floor((psm.Name.Length - 20) /
+                                                                (double)SpectrumMatchPlot
+                                                                    .MaxCharactersPerDescriptionLine);
+                    }
+
+                    if (psm.Accession.Length > 10)
+                        descriptionLineCount++;
+                    double verticalOffset = descriptionLineCount * 1.7 * MetaDrawSettings.SpectrumDescriptionFontSize;
+
+                    PtmLegend = new PtmLegendViewModel(psm, verticalOffset);
+                    ChildScanPtmLegendControl.DataContext = PtmLegend;
+                    SequenceCoveragePtmLegendControl.DataContext = PtmLegend;
                 }
-                if (psm.Accession.Length > 10)
-                    descriptionLineCount++;
-                double verticalOffset = descriptionLineCount * 1.4 * MetaDrawSettings.SpectrumDescriptionFontSize;
-
-                PtmLegend = new PtmLegendViewModel(psm, verticalOffset);
-                ChildScanPtmLegendControl.DataContext = PtmLegend;
-                SequenceCoveragePtmLegendControl.DataContext = PtmLegend;
+            }
+            catch (Exception ex)
+            {
+                MessageBox.Show("Error drawing spectrum and sequence: " + ex.Message);
             }
 
             //draw the sequence coverage if not crosslinked
@@ -498,6 +512,7 @@ private void RefreshPlotsAfterSettingsChange(object sender, MetaDrawSettingsChan
             {
                 MetaDrawLogic.FilterPsms();
                 ChimeraAnalysisTabViewModel.ProcessChimeraData(MetaDrawLogic.FilteredListOfPsms.ToList(), MetaDrawLogic.MsDataFiles);
+                MirrorPlotTabViewModel.ProcessMirrorData(MetaDrawLogic.FilteredListOfPsms.ToList(), MetaDrawLogic.MsDataFiles);
 
                 foreach (var group in BioPolymerTabViewModel.AllGroups)
                 {
@@ -522,6 +537,11 @@ private void RefreshPlotsAfterSettingsChange(object sender, MetaDrawSettingsChan
                 ChimeraAnalysisTabViewModel.ChimeraSpectrumMatchPlot = new ChimeraSpectrumMatchPlot(ChimeraAnalysisTabView.ms2ChimeraPlot, selectedChimeraGroup);
                 ChimeraAnalysisTabViewModel.ChimeraDrawnSequence = new ChimeraDrawnSequence(ChimeraAnalysisTabView.chimeraSequenceCanvas, selectedChimeraGroup, ChimeraAnalysisTabViewModel);
             }
+
+            if (MirrorPlotTabViewModel.SelectedLeftPsm != null && MirrorPlotTabViewModel.SelectedRightPsm != null)
+            {
+                MirrorPlotTabViewModel.RefreshPlot();
+            }
         }
 
         private async void loadFilesButton_Click(object sender, RoutedEventArgs e)
@@ -554,6 +574,7 @@ private async void loadFilesButton_Click(object sender, RoutedEventArgs e)
                 loadPsms: true,
                 loadLibraries: true,
                 chimeraTabViewModel: ChimeraAnalysisTabViewModel,
+                mirrorPlotTabViewModel: MirrorPlotTabViewModel,
                 bioPolymerTabViewModel: BioPolymerTabViewModel,
                 deconExplorationTabViewModel: DeconExplorationViewModel,
                 fragmentationReanalysisViewModel: FragmentationReanalysisViewModel);