smith-chem-wisc · nbollis · May 21, 2024 · May 21, 2024 · May 30, 2024 · Jun 10, 2024
diff --git a/MetaMorpheus/CMD/CMD.csproj b/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="1.0.552" />
+    <PackageReference Include="mzLib" Version="5.2.8" />
     <PackageReference Include="Nett" Version="0.15.0" />
   </ItemGroup>
 

diff --git a/MetaMorpheus/CMD/CommandLineSettings.cs b/MetaMorpheus/CMD/CommandLineSettings.cs
@@ -21,7 +21,7 @@ public class CommandLineSettings
         [Option('d', HelpText = "Protein sequence databases (.fasta, .xml, .fasta.gz, .xml.gz file formats); space-delimited")]
         public IEnumerable<string> _databases { get; set; }
 
-        [Option('s', HelpText = "Spectra to analyze (.raw, .mzML, .mgf file formats) or folder(s) containing spectra; space-delimited")]
+        [Option('s', HelpText = "Spectra to analyze (.raw, .mzML, .mgf, ms2.msalign file formats) or folder(s) containing spectra; space-delimited")]
         public IEnumerable<string> _spectra { get; set; }
 
         [Option('o', HelpText = "[Optional] Output folder")]

diff --git a/MetaMorpheus/EngineLayer/EngineLayer.csproj b/MetaMorpheus/EngineLayer/EngineLayer.csproj
@@ -21,7 +21,7 @@
     <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="1.0.552" />
+    <PackageReference Include="mzLib" Version="5.2.8" />
     <PackageReference Include="NETStandard.Library" Version="2.0.3" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="Newtonsoft.Json" Version="13.0.3" />

diff --git a/MetaMorpheus/EngineLayer/GlobalVariables.cs b/MetaMorpheus/EngineLayer/GlobalVariables.cs
@@ -64,7 +64,7 @@ public static void SetUpGlobalVariables()
         {
             Loaders.LoadElements();
             AcceptedDatabaseFormats = new List<string> { ".fasta", ".fa", ".xml", ".msp" };
-            AcceptedSpectraFormats = new List<string> { ".raw", ".mzml", ".mgf" };
+            AcceptedSpectraFormats = new List<string> { ".raw", ".mzml", ".mgf", ".msalign" };
             AnalyteType = "Peptide";
             _InvalidAminoAcids = new char[] { 'X', 'B', 'J', 'Z', ':', '|', ';', '[', ']', '{', '}', '(', ')', '+', '-' };
             ExperimentalDesignFileName = "ExperimentalDesign.tsv";

diff --git a/MetaMorpheus/EngineLayer/Ms2ScanWithSpecificMass.cs b/MetaMorpheus/EngineLayer/Ms2ScanWithSpecificMass.cs
@@ -8,6 +8,8 @@ namespace EngineLayer
 {
     public class Ms2ScanWithSpecificMass
     {
+        // Most of the processing here is done on the deconvoluted masses. SO we can make the do all of the processing in mzlib with a derived class
+        // We just need to make sure all of the neutral mass outputs are correct. This should translate to charged fragment ions. 
         public Ms2ScanWithSpecificMass(MsDataScan mzLibScan, double precursorMonoisotopicPeakMz, int precursorCharge, string fullFilePath, CommonParameters commonParam, 
             IsotopicEnvelope[] neutralExperimentalFragments = null, double? precursorIntensity = null, int? envelopePeakCount = null, double? precursorFractionalIntensity = null)
         {
@@ -23,6 +25,7 @@ public Ms2ScanWithSpecificMass(MsDataScan mzLibScan, double precursorMonoisotopi
 
             TheScan = mzLibScan;
 
+
             if (commonParam.DissociationType != DissociationType.LowCID)
             {
                 ExperimentalFragments = neutralExperimentalFragments ?? GetNeutralExperimentalFragments(mzLibScan, commonParam);
@@ -65,22 +68,22 @@ public static IsotopicEnvelope[] GetNeutralExperimentalFragments(MsDataScan scan
             var neutralExperimentalFragmentMasses =
                 Deconvoluter.Deconvolute(scan, commonParam.ProductDeconvolutionParameters, scan.MassSpectrum.Range).ToList();
 
-            if (commonParam.AssumeOrphanPeaksAreZ1Fragments)
+            if (!commonParam.AssumeOrphanPeaksAreZ1Fragments || scan.MassSpectrum is NeutralMassSpectrum)
+                return neutralExperimentalFragmentMasses.OrderBy(p => p.MonoisotopicMass).ToArray();
+
+            HashSet<double> alreadyClaimedMzs = new HashSet<double>(neutralExperimentalFragmentMasses
+                .SelectMany(p => p.Peaks.Select(v => ClassExtensions.RoundedDouble(v.mz).Value)));
+
+            for (int i = 0; i < scan.MassSpectrum.XArray.Length; i++)
             {
-                HashSet<double> alreadyClaimedMzs = new HashSet<double>(neutralExperimentalFragmentMasses
-                    .SelectMany(p => p.Peaks.Select(v => ClassExtensions.RoundedDouble(v.mz).Value)));
+                double mz = scan.MassSpectrum.XArray[i];
+                double intensity = scan.MassSpectrum.YArray[i];
 
-                for (int i = 0; i < scan.MassSpectrum.XArray.Length; i++)
+                if (!alreadyClaimedMzs.Contains(ClassExtensions.RoundedDouble(mz).Value))
                 {
-                    double mz = scan.MassSpectrum.XArray[i];
-                    double intensity = scan.MassSpectrum.YArray[i];
-
-                    if (!alreadyClaimedMzs.Contains(ClassExtensions.RoundedDouble(mz).Value))
-                    {
-                        neutralExperimentalFragmentMasses.Add(new IsotopicEnvelope(
-                            new List<(double mz, double intensity)> { (mz, intensity) },
-                            mz.ToMass(1), 1, intensity, 0, 0));
-                    }
+                    neutralExperimentalFragmentMasses.Add(new IsotopicEnvelope(
+                        new List<(double mz, double intensity)> { (mz, intensity) },
+                        mz.ToMass(1), 1, intensity, 0));
                 }
             }
 

diff --git a/MetaMorpheus/GUI/GUI.csproj b/MetaMorpheus/GUI/GUI.csproj
@@ -55,7 +55,7 @@
     <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="1.0.552" />
+    <PackageReference Include="mzLib" Version="5.2.8" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="Newtonsoft.Json" Version="13.0.3" />
     <PackageReference Include="OxyPlot.Core" Version="2.0.0" />

diff --git a/MetaMorpheus/GUI/MainWindow.xaml b/MetaMorpheus/GUI/MainWindow.xaml
@@ -281,7 +281,7 @@
                     <!--Text content-->
                     <TextBlock Grid.Row="3" Style="{StaticResource TextBlockStyle}">
                         MetaMorpheus is a search program for MS/MS proteomics data. It takes a protein database (.xml or .fasta)
-                        as input,as well as spectra files in .mzML, .mgf, or Thermo .raw format. Optionally, a spectral library 
+                        as input,as well as spectra files in ms2.msalign, .mzML, .mgf, or Thermo .raw format. Optionally, a spectral library 
                         (.msp) can be used to improve search results.
 
                         <LineBreak />
@@ -458,7 +458,7 @@
 
                     <!--Detail text-->
                     <TextBlock Grid.Row="1" Style="{StaticResource TextBlockStyle}">
-                        Add spectra file(s) in .mzML, .mgf, or Thermo .raw format.
+                        Add spectra file(s) in ms2.msalign .mzML, .mgf, or Thermo .raw format.
                     </TextBlock>
 
                     <!--Button to add spectra files-->

diff --git a/MetaMorpheus/GUI/MainWindow.xaml.cs b/MetaMorpheus/GUI/MainWindow.xaml.cs
@@ -516,7 +516,7 @@ private void Window_Drop(object sender, DragEventArgs e)
         /// </summary>
         private void AddSpectraFile_Click(object sender, RoutedEventArgs e)
         {
-            var openPicker = StartOpenFileDialog("Spectra Files(*.raw;*.mzML;*.mgf)|*.raw;*.mzML;*.mgf");
+            var openPicker = StartOpenFileDialog("Spectra Files(*.raw;*.mzML;*.mgf;*.msalign)|*.raw;*.mzML;*.mgf;*.msalign");
 
             if (openPicker.ShowDialog() == true)
             {
@@ -710,6 +710,7 @@ private void AddGlycoSearchTask_Click(object sender, RoutedEventArgs e)
         {
             OpenNewTaskWindow(MyTask.GlycoSearch);
         }
+
         private void AddAveragingTaskButton_OnClick(object sender, RoutedEventArgs e)
         {
             OpenNewTaskWindow(MyTask.Average);
@@ -1578,6 +1579,18 @@ private void AddPreRunFile(string filePath)
                     NotificationHandler(null, new StringEventArgs(".mgf files lack MS1 spectra, which are needed for quantification and searching for coisolated peptides. All other features of MetaMorpheus will function.", null));
                     goto case ".mzml";
 
+                case ".msalign":
+                    if (filePath.Contains("_ms2."))
+                    {
+                        NotificationHandler(null, new StringEventArgs("MS2-only msalign files lack MS1 spectra, which are needed for quantification and searching for coisolated peptides. All other features of MetaMorpheus will function.", null));
+                        goto case ".mzml";
+                    }
+                    else if (filePath.Contains("_ms1."))
+                    {
+                        NotificationHandler(null, new StringEventArgs("MS1 align file type not currently supported " + theExtension, null));
+                    }
+                    break;
+
                 case ".mzml":
                     if (compressed) // not implemented yet
                     {

diff --git a/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs b/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs
@@ -34,7 +34,7 @@ public partial class MetaDraw : Window
         public PtmLegendViewModel PtmLegend;
         public ChimeraLegendViewModel ChimeraLegend;
         private ObservableCollection<ModTypeForTreeViewModel> Modifications = new ObservableCollection<ModTypeForTreeViewModel>();
-        private static List<string> AcceptedSpectraFormats = new List<string> { ".mzml", ".raw", ".mgf" };
+        private static List<string> AcceptedSpectraFormats = new List<string> { ".mzml", ".raw", ".mgf", ".msalign" };
         private static List<string> AcceptedResultsFormats = new List<string> { ".psmtsv", ".tsv" };
         private static List<string> AcceptedSpectralLibraryFormats = new List<string> { ".msp" };
         private MetaDrawSettingsViewModel SettingsView;

diff --git a/MetaMorpheus/GuiFunctions/GuiFunctions.csproj b/MetaMorpheus/GuiFunctions/GuiFunctions.csproj
@@ -16,7 +16,7 @@
   <ItemGroup>
     <PackageReference Include="itext7" Version="8.0.5" />
     <PackageReference Include="itext7.bouncy-castle-adapter" Version="8.0.5" />
-    <PackageReference Include="mzLib" Version="1.0.552" />
+    <PackageReference Include="mzLib" Version="5.2.8" />
     <PackageReference Include="OxyPlot.Wpf" Version="2.0.0" />
     <PackageReference Include="Svg" Version="3.4.7" />
   </ItemGroup>

diff --git a/MetaMorpheus/TaskLayer/MetaMorpheusTask.cs b/MetaMorpheus/TaskLayer/MetaMorpheusTask.cs
@@ -21,6 +21,7 @@
 using SpectralAveraging;
 using UsefulProteomicsDatabases;
 using Easy.Common.Extensions;
+using Readers;
 
 namespace TaskLayer
 {
@@ -129,6 +130,66 @@ public static List<Ms2ScanWithSpecificMass>[] _GetMs2Scans(MsDataFile myMSDataFi
                 return scansWithPrecursors;
             }
 
+            // short circuit for already deconvoluted files
+            if (myMSDataFile is MsAlign align)
+            {
+                // if only ms2align, no precursor scans
+                if (align.All(scan => scan.MsnOrder == 2))
+                {
+                    for (int i = 0; i < ms2Scans.Length; i++)
+                    {
+
+                        scansWithPrecursors[i] = new List<Ms2ScanWithSpecificMass>()
+                        {
+                            new Ms2ScanWithSpecificMass(ms2Scans[i], ms2Scans[i].SelectedIonMonoisotopicGuessMz!.Value,
+                                ms2Scans[i].SelectedIonChargeStateGuess!.Value, fullFilePath, commonParameters, null,
+                                ms2Scans[i].SelectedIonIntensity ?? 1)
+                        };
+                    }
+                    return scansWithPrecursors;
+                }
+
+                // If precursor scans are present
+                var groups = align.GroupBy(p => p.OneBasedPrecursorScanNumber)
+                    .ToDictionary(p => p.Key, p => p.ToArray());
+                scansWithPrecursors = new List<Ms2ScanWithSpecificMass>[groups.Count];
+
+                for (var index = 0; index < groups.Count; index++)
+                {
+                    var precursorScanNumber = groups.ElementAt(index).Key;
+                    var fragmentationScans = groups.ElementAt(index).Value;
+                    var localScansWithPrecursors = new List<Ms2ScanWithSpecificMass>(fragmentationScans.Length);
+
+                    // no precursor scan
+                    if (precursorScanNumber is null)
+                    {
+                        for (int i = 0; i < fragmentationScans.Length; i++)
+                        {
+                            localScansWithPrecursors[i] = new Ms2ScanWithSpecificMass(ms2Scans[i],
+                                ms2Scans[i].SelectedIonMonoisotopicGuessMz!.Value,
+                                ms2Scans[i].SelectedIonChargeStateGuess!.Value, fullFilePath, commonParameters, null,
+                                ms2Scans[i].SelectedIonIntensity ?? 1);
+                        }
+                    }
+                    else
+                    {
+                        // TODO: use the ms1.align to determine if chimeric spectra occurred
+                        double sumOfIntensity = fragmentationScans.Sum(p => p.SelectedIonIntensity ?? 1);
+                        for (int i = 0; i < fragmentationScans.Length; i++)
+                        {
+                            localScansWithPrecursors[i] = new Ms2ScanWithSpecificMass(ms2Scans[i],
+                                ms2Scans[i].SelectedIonMonoisotopicGuessMz!.Value,
+                                ms2Scans[i].SelectedIonChargeStateGuess!.Value, fullFilePath, commonParameters, null,
+                                ms2Scans[i].SelectedIonIntensity!.Value / sumOfIntensity);
+                        }
+                    }
+
+                    scansWithPrecursors[index] = localScansWithPrecursors;
+                }
+
+                return scansWithPrecursors;
+            }
+
             Parallel.ForEach(Partitioner.Create(0, ms2Scans.Length), new ParallelOptions { MaxDegreeOfParallelism = commonParameters.MaxThreadsToUsePerFile },
                 (partitionRange, loopState) =>
                 {
@@ -145,6 +206,9 @@ public static List<Ms2ScanWithSpecificMass>[] _GetMs2Scans(MsDataFile myMSDataFi
                         {
                             MsDataScan precursorSpectrum = myMSDataFile.GetOneBasedScan(ms2scan.OneBasedPrecursorScanNumber.Value);
 
+                            if (precursorSpectrum is null)
+                                goto PrecursorFromScanHeader;
+
                             try
                             {
                                 ms2scan.RefineSelectedMzAndIntensity(precursorSpectrum.MassSpectrum);
@@ -191,6 +255,7 @@ public static List<Ms2ScanWithSpecificMass>[] _GetMs2Scans(MsDataFile myMSDataFi
                         }
 
                         //if use precursor info from scan header and scan header has charge state
+                        PrecursorFromScanHeader:
                         if (commonParameters.UseProvidedPrecursorInfo && ms2scan.SelectedIonChargeStateGuess.HasValue) 
                         {
                             int precursorCharge = ms2scan.SelectedIonChargeStateGuess.Value;

diff --git a/MetaMorpheus/TaskLayer/SearchTask/SearchTask.cs b/MetaMorpheus/TaskLayer/SearchTask/SearchTask.cs
@@ -97,7 +97,7 @@ protected override MyTaskResults RunSpecific(string OutputFolder, List<DbForTask
             if (SearchParameters.DoLabelFreeQuantification)
             {
                 // disable quantification if a .mgf is being used
-                if (currentRawFileList.Any(x => Path.GetExtension(x).Equals(".mgf", StringComparison.OrdinalIgnoreCase)))
+                if (currentRawFileList.Any(x => x.EndsWith(".mgf", StringComparison.OrdinalIgnoreCase) || x.EndsWith("_ms2.msalign", StringComparison.OrdinalIgnoreCase)))
                 {
                     SearchParameters.DoLabelFreeQuantification = false;
                 }

diff --git a/MetaMorpheus/TaskLayer/TaskLayer.csproj b/MetaMorpheus/TaskLayer/TaskLayer.csproj
@@ -21,7 +21,7 @@
     <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="1.0.552" />
+    <PackageReference Include="mzLib" Version="5.2.8" />
     <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="Nett" Version="0.15.0" />
   </ItemGroup>

diff --git a/MetaMorpheus/Test/SearchEngineTests.cs b/MetaMorpheus/Test/SearchEngineTests.cs
@@ -123,7 +123,7 @@ public static void TestSearchEngineResultsPsmFromTsv()
         public static void TestXCorrWithNoPeaks()
         {
             MsDataScan datascan = new MsDataScan(new MzSpectrum(new double[,] { }), 0, 0, true, Polarity.Positive, 0, new MzLibUtil.MzRange(0, 2000), "", MZAnalyzerType.FTICR, 1, null, null, "");
-            Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(datascan, 0, 0, "", new CommonParameters(), new IsotopicEnvelope[] { new IsotopicEnvelope(new List<(double mz, double intensity)> { (1, 1) }, 32, 2, 23, 1, 1) });
+            Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(datascan, 0, 0, "", new CommonParameters(), new IsotopicEnvelope[] { new IsotopicEnvelope(new List<(double mz, double intensity)> { (1, 1) }, 32, 2, 23, 1) });
             scan.TheScan.MassSpectrum.XCorrPrePreprocessing(0, 1, 32);
             MetaMorpheusEngine.MatchFragmentIons(scan, new List<Product> { (new Product(ProductType.y, FragmentationTerminus.C, 0, 1, 1, 0)) }, new CommonParameters(dissociationType: DissociationType.LowCID));
         }

diff --git a/MetaMorpheus/Test/Test.csproj b/MetaMorpheus/Test/Test.csproj
@@ -24,7 +24,7 @@
     <PackageReference Include="Microsoft.ML" Version="3.0.1" />
     <PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
-    <PackageReference Include="mzLib" Version="1.0.552" />
+    <PackageReference Include="mzLib" Version="5.2.8" />
     <PackageReference Include="NUnit" Version="4.1.0" />
     <PackageReference Include="NUnit3TestAdapter" Version="4.6.0" />
     <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.10.0" />

diff --git a/MetaMorpheus/Test/TestMsAlign.cs b/MetaMorpheus/Test/TestMsAlign.cs
@@ -0,0 +1,34 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using EngineLayer;
+using NUnit.Framework;
+using Proteomics.ProteolyticDigestion;
+using TaskLayer;
+
+namespace Test
+{
+    internal class TestMsAlign
+    {
+
+        [Test]
+        public static void TESTNAME()
+        {
+            var path =
+                @"B:\Users\Nic\Chimeras\TopDown_Analysis\Jurkat\DeconResults\TopFD\02-17-20_jurkat_td_rep2_fract4_ms2.msalign";
+            var fileManager = new MyFileManager(true);
+            var dataFile = fileManager.LoadFile(path, new CommonParameters());
+
+            dataFile.LoadAllStaticData();
+
+            foreach (var scanWithMass in MetaMorpheusTask.GetMs2Scans(dataFile, path, new CommonParameters()))
+            {
+                int expectedLength = scanWithMass.TheScan.MassSpectrum.XArray.Length;
+
+                Assert.That(scanWithMass.ExperimentalFragments.Length, Is.EqualTo(expectedLength));
+            }
+        }
+    }
+}