Two methods added and isolotaionwidth bug fixed

Author: U-NAT-SDU\vgor

Writer/MzMlSpectrumWriter.cs

@@ -1146,6 +1146,7 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
             int? charge = null;
             double? monoisotopicMz = null;
             double? ionInjectionTime = null;
+			double? isolationWidth = null;
             double? FAIMSCV = null;
             List<double> SPSMasses = new List<double>();
 
@@ -1173,6 +1174,8 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
             }
 
             /*var trailerData = _rawFile.GetTrailerExtraInformation(scanNumber);
+            double? isolationWidth = null;
+            List<double> SPSMasses = new List<double>();
             for (var i = 0; i < trailerData.Length; i++)
             {
                 if (trailerData.Labels[i] == "Charge State:")
@@ -1183,6 +1186,11 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
                     }
                 }
 
+                if (trailerData.Labels[i] == "MS" + (int)scanFilter.MSOrder + " Isolation Width:")
+                {
+                    isolationWidth = double.Parse(trailerData.Values[i], NumberStyles.Any);
+                }
+
                 if (trailerData.Labels[i] == "Monoisotopic M/Z:")
                 {
                     monoisotopicMz = double.Parse(trailerData.Values[i], NumberStyles.Any,
@@ -1267,7 +1275,7 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
 
                     // Construct and set the precursor list element of the spectrum                    
                     var precursorListType =
-                        ConstructPrecursorList(scanEvent, charge, scanFilter.MSOrder, monoisotopicMz, SPSMasses);
+                        ConstructPrecursorList(scanEvent, charge, scanFilter.MSOrder, monoisotopicMz, isolationWidth, SPSMasses);
                     spectrum.precursorList = precursorListType;
                     break;
                 case MSOrderType.Ms3:
@@ -1278,7 +1286,7 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
                         name = "MSn spectrum",
                         value = ""
                     });
-                    precursorListType = ConstructPrecursorList(scanEvent, charge, scanFilter.MSOrder, monoisotopicMz, SPSMasses);
+                    precursorListType = ConstructPrecursorList(scanEvent, charge, scanFilter.MSOrder, monoisotopicMz, isolationWidth, SPSMasses);
                     spectrum.precursorList = precursorListType;
                     break;
                 default:
@@ -1821,9 +1829,10 @@ private SpectrumType ConstructPDASpectrum(int scanNumber, int instrumentNumber)
         /// <param name="msLevel">the MS level</param>
         /// <param name="monoisotopicMz">the monoisotopic m/z value</param>
         /// <param name="isolationWidth">the isolation width</param>
+        /// <param name="SPSMasses">masses selected for SPS</param>
         /// <returns>the precursor list</returns>
         private PrecursorListType ConstructPrecursorList(IScanEventBase scanEvent, int? charge, MSOrderType msLevel,
-            double? monoisotopicMz, List<double> SPSMasses)
+            double? monoisotopicMz, double? isolationWidth, List<double> SPSMasses)
         {
             // Construct the precursor
             var precursorList = new PrecursorListType
@@ -1836,7 +1845,7 @@ private PrecursorListType ConstructPrecursorList(IScanEventBase scanEvent, int?
             int precursorScanNumber = _precursorMs1ScanNumber;
             IReaction reaction = null;
             var precursorMz = 0.0;
-            double? isolationWidth = null;
+            
             try
             {
                 switch (msLevel)
@@ -1866,7 +1875,6 @@ private PrecursorListType ConstructPrecursorList(IScanEventBase scanEvent, int?
                 }
 
                 precursorMz = reaction.PrecursorMass;
-                isolationWidth = reaction.IsolationWidth;
             }
             catch (ArgumentOutOfRangeException)
             {
@@ -1910,23 +1918,24 @@ private PrecursorListType ConstructPrecursorList(IScanEventBase scanEvent, int?
             }
 
             //Precursor intensity is disabled for now
-            //if (selectedIonMz > ZeroDelta)
-            //{
-            //    var selectedIonIntensity = CalculatePrecursorPeakIntensity(_rawFile, precursorScanNumber, selectedIonMz);
-            //    if (selectedIonIntensity != null)
-            //    {
-            //        ionCvParams.Add(new CVParamType
-            //        {
-            //            name = "peak intensity",
-            //            value = selectedIonIntensity.ToString(),
-            //            accession = "MS:1000042",
-            //            cvRef = "MS",
-            //            unitAccession = "MS:1000131",
-            //            unitCvRef = "MS",
-            //            unitName = "number of detector counts"
-            //        });
-            //    }
-            //}
+            if (selectedIonMz > ZeroDelta)
+            {
+                var selectedIonIntensity = CalculatePrecursorPeakIntensity(_rawFile, precursorScanNumber, selectedIonMz, isolationWidth, ParseInput.NoPeakPicking); //new Pwiz way
+                //var selectedIonIntensity = CalculatePrecursorPeakIntensity2(_rawFile, precursorScanNumber, selectedIonMz, isolationWidth); //old Pwiz way
+                if (selectedIonIntensity != null)
+                {
+                    ionCvParams.Add(new CVParamType
+                    {
+                        name = "peak intensity",
+                        value = selectedIonIntensity.ToString(),
+                        accession = "MS:1000042",
+                        cvRef = "MS",
+                        unitAccession = "MS:1000131",
+                        unitCvRef = "MS",
+                        unitName = "number of detector counts"
+                    });
+                }
+            }
 
             precursor.selectedIonList.selectedIon[0].cvParam = ionCvParams.ToArray();
 

Writer/SpectrumWriter.cs

@@ -5,6 +5,7 @@
 using log4net;
 using ThermoFisher.CommonCore.Data;
 using ThermoFisher.CommonCore.Data.Business;
+using ThermoFisher.CommonCore.Data.FilterEnums;
 using ThermoFisher.CommonCore.Data.Interfaces;
 
 namespace ThermoRawFileParser.Writer
@@ -176,49 +177,84 @@ public static IReaction GetReaction(IScanEvent scanEvent, int scanNumber)
         }
 
         /// <summary>
-        /// Calculate the precursor peak intensity.
+        /// Calculate the precursor peak intensity (similar to modern MSConvert).
+        /// Sum intensities of all peaks in the isolation window.
         /// </summary>
         /// <param name="rawFile">the RAW file object</param>
         /// <param name="precursorScanNumber">the precursor scan number</param>
         /// <param name="precursorMass">the precursor mass</param>
+        /// <param name="isolationWidth">the isolation width</param>
+        /// <param name="useProfile">profile/centroid switch</param>
         protected static double? CalculatePrecursorPeakIntensity(IRawDataPlus rawFile, int precursorScanNumber,
-            double precursorMass)
+            double precursorMass, double? isolationWidth, bool useProfile)
         {
-            double? precursorIntensity = null;
-            double tolerance;
-
+            double precursorIntensity = 0;
+            double halfWidth = isolationWidth is null ? 0 : (double) isolationWidth / 2; //if isolationWidth was not defined set it to 0
+            
             // Get the precursor scan from the RAW file
             var scan = Scan.FromFile(rawFile, precursorScanNumber);
 
-            //Select centroid stream if it exists, otherwise use profile one
             double[] masses;
             double[] intensities;
 
-            if (scan.HasCentroidStream)
-            {
-                masses = scan.CentroidScan.Masses;
-                intensities = scan.CentroidScan.Intensities;
-                tolerance = 0.01; //high resolution scan
-            }
-            else
+            if (useProfile)
             {
                 masses = scan.SegmentedScan.Positions;
                 intensities = scan.SegmentedScan.Intensities;
-                tolerance = 0.5; //low resolution scan
             }
-
-            //find closest peak in a stream
-            var bestDelta = tolerance;
-            for (var i = 0; i < masses.Length; i++)
+            else
             {
-                var delta = precursorMass - masses[i];
-                if (Math.Abs(delta) < bestDelta)
+                //use centroids if they exist, otherwise perform centroiding
+                if (scan.HasCentroidStream)
                 {
-                    bestDelta = delta;
-                    precursorIntensity = intensities[i];
+                    masses = scan.CentroidScan.Masses;
+                    intensities = scan.CentroidScan.Intensities;
                 }
+                else
+                {
+                    var scanEvent = rawFile.GetScanEventForScanNumber(precursorScanNumber);
+                    var centroidedScan = scanEvent.ScanData == ScanDataType.Profile //only centroid profile spectra
+                        ? Scan.ToCentroid(scan).SegmentedScan
+                        : scan.SegmentedScan;
+
+                    masses = centroidedScan.Positions;
+                    intensities = centroidedScan.Intensities;
+                }
+            }
+
+            var index = masses.FastBinarySearch(precursorMass - halfWidth); //set index to the first peak inside isolation window
+
+            while (index < masses.Length && masses[index] < precursorMass + halfWidth)
+            {
+                precursorIntensity += intensities[index];
+                index++;
+            }
+
+            return precursorIntensity;
+        }
 
-                if (delta < -1 * tolerance) break;
+        /// <summary>
+        /// Calculate the precursor peak intensity (similar to leagcy MSConvert).
+        /// Get base-peak intensity inside isolation window.
+        /// </summary>
+        /// <param name="rawFile">the RAW file object</param>
+        /// <param name="precursorScanNumber">the precursor scan number</param>
+        /// <param name="precursorMass">the precursor mass</param>
+        /// <param name="isolationWidth">the isolation width</param>
+        protected static double? CalculatePrecursorPeakIntensity2(IRawDataPlus rawFile, int precursorScanNumber, double precursorMass, double? isolationWidth)
+        {
+            double? precursorIntensity = null;
+            double halfWidth = isolationWidth is null ? 0 : (double)isolationWidth / 2; //if isolationWidth was not defined set it to 0
+
+            var chrosettings = new ChromatogramTraceSettings();
+            chrosettings.MassRanges = new Range[] { new Range(precursorMass - halfWidth, precursorMass + halfWidth) };
+            chrosettings.Trace = TraceType.BasePeak;
+
+            var chrodata = rawFile.GetChromatogramData(new ChromatogramTraceSettings[] { chrosettings }, precursorScanNumber, precursorScanNumber);
+
+            if (chrodata != null && chrodata.Length > 0)
+            {
+                precursorIntensity = chrodata.IntensitiesArray[0][0];
             }
 
             return precursorIntensity;