Edited MSFragger Reader

mzLib/Readers/ExternalResults/IndividualResultRecords/MsFraggerPsm.cs

@@ -46,7 +46,7 @@ public class MsFraggerPsm : IQuantifiableRecord
         public int Charge { get; set; }
 
         [Name("Retention")]
-        public double RetentionTime { get; set; }
+        public double RetentionTimeSeconds { get; set; }
 
         [Name("Observed Mass")]
         public double ObservedMass { get; set; }
@@ -146,11 +146,13 @@ public class MsFraggerPsm : IQuantifiableRecord
         [Ignore]
         public int OneBasedScanNumber => _oneBasedScanNumber ??= int.Parse(Spectrum.Split('.')[1]);
 
+        [Ignore] public double RetentionTime => RetentionTimeSeconds / 60.0;
+
         #endregion
 
         #region IQuantifiableRecord Implementation
 
-        [Ignore] public string FileName => SpectrumFilePath;
+        [Ignore] public string FileName => FileNameWithoutExtension;
 
         [Ignore] public List<(string, string, string)> ProteinGroupInfos
         {

mzLib/Readers/InternalResults/IndividualResultRecords/SpectrumMatchFromTsv.cs

@@ -169,8 +169,8 @@ protected SpectrumMatchFromTsv(string line, char[] split, Dictionary<string, int
             NextResidue = (parsedHeader[SpectrumMatchFromTsvHeader.NextResidue] < 0) ? null : spl[parsedHeader[SpectrumMatchFromTsvHeader.NextResidue]].Trim();
             QValueNotch = (parsedHeader[SpectrumMatchFromTsvHeader.QValueNotch] < 0) ? null : (double?)double.Parse(spl[parsedHeader[SpectrumMatchFromTsvHeader.QValueNotch]].Trim(), CultureInfo.InvariantCulture);
             RetentionTime = (parsedHeader[SpectrumMatchFromTsvHeader.Ms2ScanRetentionTime] < 0) ? -1 : double.TryParse(spl[parsedHeader[SpectrumMatchFromTsvHeader.Ms2ScanRetentionTime]].Trim(), CultureInfo.InvariantCulture, out double rt) ? rt : -1;
-            PEP = double.Parse(spl[parsedHeader[SpectrumMatchFromTsvHeader.PEP]].Trim(), CultureInfo.InvariantCulture);
-            PEP_QValue = double.Parse(spl[parsedHeader[SpectrumMatchFromTsvHeader.PEP_QValue]].Trim(), CultureInfo.InvariantCulture);
+            PEP = (parsedHeader[SpectrumMatchFromTsvHeader.PEP] < 0 ) ? double.NaN : double.Parse(spl[parsedHeader[SpectrumMatchFromTsvHeader.PEP]].Trim(), CultureInfo.InvariantCulture);
+            PEP_QValue = (parsedHeader[SpectrumMatchFromTsvHeader.PEP_QValue] < 0) ? double.NaN : double.Parse(spl[parsedHeader[SpectrumMatchFromTsvHeader.PEP_QValue]].Trim(), CultureInfo.InvariantCulture);
             VariantCrossingIons = FindVariantCrossingIons();
             SpectralAngle = (parsedHeader[SpectrumMatchFromTsvHeader.SpectralAngle] < 0)
                 ? null

mzLib/Test/FileReadingTests/TestMsFraggerCombinedResults.cs

@@ -31,7 +31,7 @@ public void TestLoadResults(string path)
             MsFraggerCombinedResults ms = new MsFraggerCombinedResults(filePath);
             ms.LoadResults();
 
-            List<string> results = ms.Results.Select(psm => psm.FileName).ToList();
+            List<string> results = ms.Results.Select(psm => psm.SpectrumFilePath).ToList();
 
             NUnit.Framework.Assert.That(results.Count(s => s.Contains("A_1")).Equals(4));
             NUnit.Framework.Assert.That(results.Count(s => s.Contains("A_2")).Equals(4));

mzLib/Test/FileReadingTests/TestMsFraggerResultFiles.cs

@@ -100,7 +100,7 @@ public void TestMsFraggerPsmFirstAndLastCorrect()
             Assert.That(first.NextAminoAcid, Is.EqualTo('K'));
             Assert.That(first.PeptideLength, Is.EqualTo(7));
             Assert.That(first.Charge, Is.EqualTo(2));
-            Assert.That(first.RetentionTime, Is.EqualTo(1.9398));
+            Assert.That(first.RetentionTime, Is.EqualTo(0.03233).Within(0.0001));
             Assert.That(first.ObservedMass, Is.EqualTo(669.4164));
             Assert.That(first.CalibratedObservedMass, Is.EqualTo(669.4123));
             Assert.That(first.ObservedMz, Is.EqualTo(335.7155));
@@ -141,7 +141,7 @@ public void TestMsFraggerPsmFirstAndLastCorrect()
             Assert.That(last.NextAminoAcid, Is.EqualTo('V'));
             Assert.That(last.PeptideLength, Is.EqualTo(7));
             Assert.That(last.Charge, Is.EqualTo(2));
-            Assert.That(last.RetentionTime, Is.EqualTo(19.114));
+            Assert.That(last.RetentionTime, Is.EqualTo(0.3186).Within(0.0001));
             Assert.That(last.ObservedMass, Is.EqualTo(724.3984));
             Assert.That(last.CalibratedObservedMass, Is.EqualTo
             (724.3949));

mzLib/Test/FileReadingTests/TestPsmFromTsv.cs

@@ -10,6 +10,7 @@
 using Readers;
 using MzLibUtil;
 using FlashLFQ;
+using Easy.Common.Extensions;
 
 namespace Test.FileReadingTests
 {
@@ -133,6 +134,10 @@ public static void TestPsmFromTsvDisambiguatingConstructor()
             List<PsmFromTsv> psms = SpectrumMatchTsvReader.ReadPsmTsv(psmTsvPath, out warnings);
             PsmFromTsv psm = psms.First();
 
+            // assert that in 1st elt PEP and PEP_Q values exists and are less than one
+            Assert.That(psm.PEP, Is.LessThan(1.0));
+            Assert.That(psm.PEP_QValue, Is.LessThan(1.0));
+
             // non ambiguous construction should not be successful
             string fullSeq = psm.FullSequence;
             fullSeq = fullSeq.Substring(0, fullSeq.Length - 1);
@@ -193,6 +198,19 @@ public static void TestPsmFromTsvDisambiguatingConstructor()
             }
         }
 
+        [Test]
+        public static void TestIncompletePsmFile() 
+        {
+            string psmTsvPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"FileReadingTests\SearchResults\AllPSMs2.psmtsv");
+            List<string> warnings = new();
+            List<PsmFromTsv> psms = SpectrumMatchTsvReader.ReadPsmTsv(psmTsvPath, out warnings);
+            PsmFromTsv psm = psms.First();
+
+            Assert.That(psm.PEP, Is.NaN);
+            Assert.That(psm.PEP_QValue, Is.NaN);
+            Assert.That(psm.RetentionTime, Is.EqualTo(-1));
+        }
+
         [Test]
         public static void TestParseModification()
         {

mzLib/Test/Test.csproj

@@ -495,6 +495,9 @@
     <None Update="DoubleProtease.tsv">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>
+    <None Update="FileReadingTests\SearchResults\AllPSMs2.psmtsv">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
     <None Update="FileReadingTests\SearchResults\BottomUpExample.psmtsv">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>