Allowed reading of scan descriptions from Raw Files (#736)

Co-authored-by: trishorts <mshort@chem.wisc.edu>
smith-chem-wisc · Nov 27, 2023 · 6c77ca0 · 6c77ca0
1 parent d147f54
commit 6c77ca0
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Showing 5 changed files with 28 additions and 2 deletions.
diff --git a/mzLib/MassSpectrometry/MsDataScan.cs b/mzLib/MassSpectrometry/MsDataScan.cs
@@ -20,6 +20,7 @@
 using System;
 using System.Collections;
 using System.Collections.Generic;
+using System.ComponentModel;
 using System.Linq;
 
 namespace MassSpectrometry
@@ -28,7 +29,7 @@ public class MsDataScan
     {
         public MsDataScan(MzSpectrum massSpectrum, int oneBasedScanNumber, int msnOrder, bool isCentroid, Polarity polarity, double retentionTime, MzRange scanWindowRange, string scanFilter, MZAnalyzerType mzAnalyzer,
             double totalIonCurrent, double? injectionTime, double[,] noiseData, string nativeId, double? selectedIonMz = null, int? selectedIonChargeStateGuess = null, double? selectedIonIntensity = null, double? isolationMZ = null,
-            double? isolationWidth = null, DissociationType? dissociationType = null, int? oneBasedPrecursorScanNumber = null, double? selectedIonMonoisotopicGuessMz = null, string hcdEnergy = null)
+            double? isolationWidth = null, DissociationType? dissociationType = null, int? oneBasedPrecursorScanNumber = null, double? selectedIonMonoisotopicGuessMz = null, string hcdEnergy = null, string scanDescription = null)
         {
             OneBasedScanNumber = oneBasedScanNumber;
             MsnOrder = msnOrder;
@@ -52,6 +53,7 @@ public MsDataScan(MzSpectrum massSpectrum, int oneBasedScanNumber, int msnOrder,
             SelectedIonChargeStateGuess = selectedIonChargeStateGuess;
             SelectedIonMonoisotopicGuessMz = selectedIonMonoisotopicGuessMz;
             HcdEnergy = hcdEnergy;
+            ScanDescription = scanDescription;
         }
 
         /// <summary>
@@ -84,6 +86,7 @@ public MsDataScan(MzSpectrum massSpectrum, int oneBasedScanNumber, int msnOrder,
         public double? SelectedIonMonoisotopicGuessIntensity { get; private set; } // May be refined
         public double? SelectedIonMonoisotopicGuessMz { get; private set; } // May be refined
         public string HcdEnergy { get; private set; }
+        public string ScanDescription { get; private set; }
 
         private MzRange isolationRange;
 

diff --git a/mzLib/Readers/Thermo/ThermoRawFileReader.cs b/mzLib/Readers/Thermo/ThermoRawFileReader.cs
@@ -252,6 +252,7 @@ private static MsDataScan GetOneBasedScan(IRawDataPlus rawFile, IFilteringParams
             int? precursorScanNumber = null;
             double? isolationMz = null;
             string HcdEnergy = null;
+            string scanDescript = null;
             ActivationType activationType = ActivationType.Any; // thermo enum
             DissociationType dissociationType = DissociationType.Unknown; // mzLib enum
 
@@ -306,6 +307,11 @@ private static MsDataScan GetOneBasedScan(IRawDataPlus rawFile, IFilteringParams
                 {
                     HcdEnergy = values[i];
                 }
+
+                if (labels[i].StartsWith("Scan Description", StringComparison.Ordinal))
+                {
+                    scanDescript = values[i].TrimEnd();
+                }
             }
 
             if (msOrder > 1)
@@ -397,7 +403,8 @@ private static MsDataScan GetOneBasedScan(IRawDataPlus rawFile, IFilteringParams
                 dissociationType: dissociationType,
                 oneBasedPrecursorScanNumber: precursorScanNumber,
                 selectedIonMonoisotopicGuessMz: precursorSelectedMonoisotopicIonMz,
-                hcdEnergy: HcdEnergy);
+                hcdEnergy: HcdEnergy,
+                scanDescription: scanDescript);
         }
 
         private static MzSpectrum GetSpectrum(IRawDataPlus rawFile, IFilteringParams filterParams,

diff --git a/mzLib/Test/DataFiles/ScanDescriptionTestData.raw b/mzLib/Test/DataFiles/ScanDescriptionTestData.raw
diff --git a/mzLib/Test/FileReadingTests/TestRawFileReader.cs b/mzLib/Test/FileReadingTests/TestRawFileReader.cs
@@ -1,5 +1,6 @@
 using System;
 using System.Collections.Generic;
+using System.Collections.Specialized;
 using System.Diagnostics;
 using System.IO;
 using System.Linq;
@@ -40,6 +41,18 @@ public void TestRawFileReaderFileNotFoundException()
         #endregion
 
 
+        [Test]
+        public void TestScanDescription()
+        {
+            string filePath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", "ScanDescriptionTestData.raw");
+            var scans = MsDataFileReader.GetDataFile(filePath).GetAllScansList();
+            var ms1Scans = scans.Where(x => x.MsnOrder == 1).ToList();
+            var ms2Scans = scans.Where(x => x.MsnOrder == 2).ToList();
+
+            ms1Scans.ForEach(x => Assert.That(x.ScanDescription, Is.EqualTo(null)));
+            ms2Scans.ForEach(x => Assert.That(x.ScanDescription, Is.EqualTo("Testing2")));
+        }
+
         /// <summary>
         /// Tests LoadAllStaticData for ThermoRawFileReader
         /// </summary>

diff --git a/mzLib/Test/Test.csproj b/mzLib/Test/Test.csproj
@@ -288,6 +288,9 @@
     <None Update="DataFiles\GUACUG_NegativeMode_Sliced.mzML">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>
+    <None Update="DataFiles\ScanDescriptionTestData.raw">
+      <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
+    </None>
     <None Update="FileReadingTests\ExternalFileTypes\Ms1Feature_FlashDeconvOpenMs3.0.0_ms1.feature">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>