Precursor intensity for low res scans

Author: caetera

ThermoRawFileParserTest/WriterTests.cs

@@ -1,7 +1,10 @@
 using System;
 using System.IO;
+using System.Linq;
+using System.Net.PeerToPeer.Collaboration;
 using System.Xml.Serialization;
 using IO.Mgf;
+using MzLibUtil;
 using NUnit.Framework;
 using ThermoRawFileParser;
 using ThermoRawFileParser.Writer.MzML;
@@ -66,6 +69,8 @@ public void TestMzml()
 
             Assert.AreEqual("1", testMzMl.run.chromatogramList.count);
             Assert.AreEqual(1, testMzMl.run.chromatogramList.chromatogram.Length);
+
+            Assert.AreEqual(48, testMzMl.run.chromatogramList.chromatogram[0].defaultArrayLength);
         }
 
         [Test]
@@ -98,5 +103,36 @@ public void TestIndexedMzML()
             Assert.AreEqual("chromatogram", testMzMl.indexList.index[1].name.ToString());
             Assert.AreEqual(1, testMzMl.indexList.index[1].offset.Length);
         }
+
+        [Test]
+        public void TestMzML_MS2()
+        {
+            // Get temp path for writing the test mzML
+            var tempFilePath = Path.GetTempPath();
+
+            var testRawFile = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, @"Data/small2.RAW");
+            var parseInput = new ParseInput(testRawFile, null, tempFilePath, OutputFormat.MzML);
+
+            RawFileParser.Parse(parseInput);
+
+            // Deserialize the mzML file
+            var xmlSerializer = new XmlSerializer(typeof(mzMLType));
+            var testMzMl = (mzMLType)xmlSerializer.Deserialize(new FileStream(
+                Path.Combine(tempFilePath, "small2.mzML"), FileMode.Open, FileAccess.Read, FileShare.ReadWrite));
+
+            Assert.AreEqual(95, testMzMl.run.spectrumList.spectrum.Length);
+
+            var precursor = testMzMl.run.spectrumList.spectrum[16].precursorList.precursor[0].selectedIonList.selectedIon[0];
+            var selectedMz = Double.Parse(precursor.cvParam.Where(cv => cv.accession == "MS:1000744").First().value);
+            Assert.IsTrue(selectedMz - 604.7592 < 0.001);
+
+            var selectedZ = int.Parse(precursor.cvParam.Where(cv => cv.accession == "MS:1000041").First().value);
+            Assert.AreEqual(selectedZ , 2);
+
+            var selectedI = Double.Parse(precursor.cvParam.Where(cv => cv.accession == "MS:1000042").First().value);
+            Assert.IsTrue(selectedI - 10073 < 1);
+
+            Assert.AreEqual(95, testMzMl.run.chromatogramList.chromatogram[0].defaultArrayLength);
+        }
     }
 }

Writer/SpectrumWriter.cs

@@ -178,6 +178,7 @@ public static IReaction GetReaction(IScanEvent scanEvent, int scanNumber)
             double precursorMass)
         {
             double? precursorIntensity = null;
+            double tolerance;
 
             // Get the precursor scan from the RAW file
             var scan = Scan.FromFile(rawFile, precursorScanNumber);
@@ -190,15 +191,17 @@ public static IReaction GetReaction(IScanEvent scanEvent, int scanNumber)
             {
                 masses = scan.CentroidScan.Masses;
                 intensities = scan.CentroidScan.Intensities;
+                tolerance = 0.01; //high resolution scan
             }
             else
             {
                 masses = scan.SegmentedScan.Positions;
                 intensities = scan.SegmentedScan.Intensities;
+                tolerance = 0.5; //low resolution scan
             }
 
             //find closest peak in a stream
-            var bestDelta = Tolerance;
+            var bestDelta = tolerance;
             for (var i = 0; i < masses.Length; i++)
             {
                 var delta = precursorMass - masses[i];
@@ -208,7 +211,7 @@ public static IReaction GetReaction(IScanEvent scanEvent, int scanNumber)
                     precursorIntensity = intensities[i];
                 }
 
-                if (delta < -1 * Tolerance) break;
+                if (delta < -1 * tolerance) break;
             }
 
             return precursorIntensity;