public static void ExtractPrecursorMasses(this RawDataCollection rawData, IRawDataPlus rawFile)
{
if (rawData.Performed.Contains(Operations.PrecursorMasses))
{
return;
}
CheckIfDone.Check(rawData, rawFile, new List <Operations> {
Operations.ScanIndex, Operations.TrailerExtras, Operations.PrecursorScans
});
Log.Information("Extracting precursor masses");
rawData.precursorMasses = new Dictionary <int, PrecursorMassData>();
IEnumerable <int> scans = rawData.scanIndex.ScanEnumerators[MSOrderType.Any];
ProgressIndicator progress = new ProgressIndicator(scans.Count(), "Extracting precursor masses");
foreach (int scan in scans)
{
try
{
ExtractPrecursorMasses(rawData, rawFile, scan);
}
catch (Exception e)
{
Log.Error(e, "Failed during extraction of precursor mass for scan {Scan}", scan);
throw e;
}
progress.Update();
}
progress.Done();
rawData.Performed.Add(Operations.PrecursorMasses);
}
public static void CalcPeakRetTimesAndInts(this RawDataCollection rawData, IRawDataPlus rawFile)
{
CheckIfDone.Check(rawData, rawFile, new List <Operations> {
Operations.ScanIndex, Operations.PrecursorMasses, Operations.PrecursorScans, Operations.Ms1CentroidStreams, Operations.RetentionTimes
});
if (rawData.Performed.Contains(Operations.PeakRetAndInt))
{
return;
}
int[] scans = rawData.scanIndex.ScanEnumerators[MSOrderType.Ms2];
PrecursorPeakDataCollection peaks = new PrecursorPeakDataCollection();
ProgressIndicator P = new ProgressIndicator(total: scans.Length, message: "Analyzing precursor peaks");
foreach (int scan in scans)
{
peaks.Add(scan, OnePeak(rawData: rawData, monoIsoMass: rawData.precursorMasses[scan].MonoisotopicMZ, parentScan: rawData.precursorScans[scan].MasterScan, ddScan: scan));
P.Update();
}
P.Done();
rawData.peakData = peaks;
rawData.Performed.Add(Operations.PeakRetAndInt);
rawData.Performed.RemoveWhere(x => x == Operations.PeakArea);
}
public static void WriteMatrix(RawDataCollection rawData, ScanMetaDataCollection metaData, IRawDataPlus rawFile, QuantDataCollection quantData = null, string outputDirectory = null)
{
string fileName = ReadWrite.GetPathToFile(outputDirectory, rawData.rawFileName, "_Matrix.txt");
CheckIfDone.Check(rawData, rawFile, new List <Operations> {
Operations.ScanIndex, Operations.MethodData, Operations.PrecursorScans,
Operations.RetentionTimes, Operations.PrecursorMasses, Operations.TrailerExtras, Operations.MetaData
});
using (StreamWriter f = new StreamWriter(fileName)) //Open a new file
{
List <int> scans;
if (!rawData.isBoxCar)
{
scans = rawData.scanIndex.ScanEnumerators[rawData.scanIndex.AnalysisOrder].ToList();
}
else
{
scans = rawData.precursorScans.Keys.ToList();
scans.Sort();
}
ProgressIndicator progress = new ProgressIndicator(scans.Count(), "Writing matrix to disk");
f.Write("MS3ScanNumber\tMS2ScanNumber\tMS1ScanNumber\tQuantScanRetTime\tParentScanRetTime\tDutyCycle" +
"\tMS2ScansPerCycle\tParentIonMass\tMonoisotopicMass\tPrecursorCharge\tMS1IsolationInterference");
if (!rawData.isBoxCar)
{
f.Write("\tParentPeakFound");
}
if (rawData.Performed.Contains(Operations.PeakArea) & !rawData.isBoxCar)
{
f.Write("\tParentPeakArea");
}
if (!rawData.isBoxCar)
{
f.Write("\tPeakFirstScan\tPeakMaxScan\tPeakLastScan\tBaseLinePeakWidth(s)\tPeakParentScanIntensity\tPeakMaxIntensity");
}
f.Write("\tMS1IonInjectionTime\tMS2IonInjectionTime" +
"\tMS3IonInjectionTime\tHCDEnergy\tMS1MedianIntensity\tMS2MedianIntensity\t");
if (quantData != null)
{
string reagents = quantData.LabelingReagents;
foreach (string label in new LabelingReagents().Reagents[reagents].Labels)
{
f.Write(label + "Intensity\t");
}
foreach (string label in new LabelingReagents().Reagents[reagents].Labels)
{
f.Write(label + "Mass\t");
}
foreach (string label in new LabelingReagents().Reagents[reagents].Labels)
{
f.Write(label + "Noise\t");
}
foreach (string label in new LabelingReagents().Reagents[reagents].Labels)
{
f.Write(label + "Resolution\t");
}
foreach (string label in new LabelingReagents().Reagents[reagents].Labels)
{
f.Write(label + "Baseline\t");
}
}
f.Write("\n");
foreach (int scan in scans)
{
int ms3scan, ms2scan, masterScan;
if (rawData.scanIndex.AnalysisOrder == MSOrderType.Ms3)
{
ms3scan = rawData.precursorScans[scan].MS3Scan;
ms2scan = rawData.precursorScans[scan].MS2Scan;
masterScan = rawData.precursorScans[scan].MasterScan;
}
else
{
ms3scan = -1;
ms2scan = rawData.precursorScans[scan].MS2Scan;
masterScan = rawData.precursorScans[scan].MasterScan;
}
f.Write(ms3scan.ToString() + "\t" + ms2scan.ToString() + "\t" + masterScan.ToString() + "\t");
f.Write(rawData.retentionTimes[scan].ToString() + "\t" + rawData.retentionTimes[masterScan].ToString() + "\t");
f.Write(metaData[masterScan].DutyCycle.ToString() + "\t" + metaData[masterScan].MS2ScansPerCycle.ToString() + "\t");
f.Write(rawData.precursorMasses[ms2scan].ParentMZ.ToString() + "\t");
f.Write(rawData.precursorMasses[ms2scan].MonoisotopicMZ.ToString() + "\t");
f.Write(rawData.trailerExtras[ms2scan].ChargeState.ToString() + "\t");
f.Write(rawData.metaData[scan].Ms1IsolationInterference.ToString() + "\t");
if (!rawData.isBoxCar)
{
f.Write(rawData.peakData[ms2scan].PeakFound.ToString() + "\t");
}
if (rawData.Performed.Contains(Operations.PeakArea) & !rawData.isBoxCar)
{
f.Write(rawData.peakData[ms2scan].Area.ToString() + "\t");
}
if (!rawData.isBoxCar)
{
f.Write(rawData.peakData[ms2scan].FirstScan.ToString() + "\t");
f.Write(rawData.peakData[ms2scan].MaxScan.ToString() + "\t");
f.Write(rawData.peakData[ms2scan].LastScan.ToString() + "\t");
f.Write((rawData.peakData[ms2scan].BaselineWidth * 60).ToString() + "\t");
f.Write(rawData.peakData[ms2scan].ParentIntensity.ToString() + "\t");
f.Write(rawData.peakData[ms2scan].MaximumIntensity.ToString() + "\t");
}
f.Write(rawData.trailerExtras[masterScan].InjectionTime.ToString() + "\t");
if (rawData.scanIndex.AnalysisOrder == MSOrderType.Ms3)
{
f.Write(rawData.trailerExtras[ms2scan].InjectionTime.ToString() + "\t");
f.Write(rawData.trailerExtras[ms3scan].InjectionTime.ToString() + "\t");
}
else
{
f.Write(rawData.trailerExtras[ms2scan].InjectionTime.ToString() + "\t");
f.Write("-1\t");
}
f.Write(rawData.trailerExtras[scan].HCDEnergy + "\t");
f.Write(metaData[masterScan].IntensityDistribution.P50 + "\t");
f.Write(metaData[ms2scan].IntensityDistribution.P50 + "\t");
if (quantData != null)
{
foreach (string label in quantData[scan].Keys)
{
f.Write(quantData[scan][label].Intensity + "\t");
}
foreach (string label in quantData[scan].Keys)
{
f.Write(quantData[scan][label].Mass + "\t");
}
foreach (string label in quantData[scan].Keys)
{
f.Write(quantData[scan][label].Noise + "\t");
}
foreach (string label in quantData[scan].Keys)
{
f.Write(quantData[scan][label].Resolution + "\t");
}
foreach (string label in quantData[scan].Keys)
{
f.Write(quantData[scan][label].Baseline + "\t");
}
}
f.Write("\n");
progress.Update();
}
progress.Done();
}
}
public static void WriteChromatogram(this RawDataCollection rawData, IRawDataPlus rawFile, MSOrderType order, bool TIC, bool BP, string outputDirectory)
{
List <Operations> operations = new List <Operations>()
{
Operations.RetentionTimes
};
//MSOrderType order = (MSOrderType)msOrder;
MassAnalyzerType analyzer = rawData.methodData.MassAnalyzers[order];
if (analyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
if (order == MSOrderType.Ms)
{
operations.Add(Operations.Ms1CentroidStreams);
}
if (order == MSOrderType.Ms2)
{
operations.Add(Operations.Ms2CentroidStreams);
}
if (order == MSOrderType.Ms3)
{
operations.Add(Operations.Ms3CentroidStreams);
}
}
else
{
if (order == MSOrderType.Ms)
{
operations.Add(Operations.Ms1SegmentedScans);
}
if (order == MSOrderType.Ms2)
{
operations.Add(Operations.Ms2SegmentedScans);
}
if (order == MSOrderType.Ms3)
{
operations.Add(Operations.Ms3SegmentedScans);
}
}
CheckIfDone.Check(rawData, rawFile, operations);
int[] scans = rawData.scanIndex.ScanEnumerators[order];
if (TIC)
{
ProgressIndicator progress = new ProgressIndicator(scans.Length, String.Format("Writing {0} TIC chromatogram", order));
progress.Start();
string fileName = ReadWrite.GetPathToFile(outputDirectory, rawData.rawFileName, "_" + order + "_TIC_chromatogram.txt");
using (StreamWriter f = new StreamWriter(fileName))
{
f.WriteLine("RetentionTime\tIntensity");
if (analyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
foreach (int scan in scans)
{
if (rawData.centroidStreams[scan].Intensities.Length > 0)
{
f.WriteLine("{0}\t{1}", rawData.retentionTimes[scan], rawData.centroidStreams[scan].Intensities.Sum());
}
else
{
f.WriteLine("{0}\t{1}", rawData.retentionTimes[scan], 0);
}
progress.Update();
}
}
else
{
foreach (int scan in scans)
{
if (rawData.segmentedScans[scan].Intensities.Length > 0)
{
f.WriteLine("{0}\t{1}", rawData.retentionTimes[scan], rawData.segmentedScans[scan].Intensities.Sum());
}
else
{
f.WriteLine("{0}\t{1}", rawData.retentionTimes[scan], 0);
}
progress.Update();
}
}
}
progress.Done();
}
if (BP)
{
ProgressIndicator progress = new ProgressIndicator(scans.Length, String.Format("Writing {0} base peak chromatogram", order));
progress.Start();
string fileName = ReadWrite.GetPathToFile(outputDirectory, rawData.rawFileName, "_" + order + "_BP_chromatogram.txt");
using (StreamWriter f = new StreamWriter(fileName))
{
f.WriteLine("RetentionTime\tIntensity");
if (analyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
foreach (int scan in scans)
{
if (rawData.centroidStreams[scan].Intensities.Length > 0)
{
f.WriteLine("{0}\t{1}", rawData.retentionTimes[scan], rawData.centroidStreams[scan].Intensities.Max());
}
else
{
f.WriteLine("{0}\t{1}", rawData.retentionTimes[scan], 0);
}
progress.Update();
}
}
else
{
foreach (int scan in scans)
{
if (rawData.segmentedScans[scan].Intensities.Length > 0)
{
f.WriteLine("{0}\t{1}", rawData.retentionTimes[scan], rawData.segmentedScans[scan].Intensities.Max());
}
else
{
f.WriteLine("{0}\t{1}", rawData.retentionTimes[scan], 0);
}
progress.Update();
}
}
}
progress.Done();
}
}
public static void WriteMGF(RawDataCollection rawData, IRawDataPlus rawFile, string outputDirectory, double cutoff = 0, int[] scans = null, double intensityCutoff = 0.01)
{
double intCutoff = 0;
string fileName = ReadWrite.GetPathToFile(outputDirectory, rawData.rawFileName, ".mgf");
MassAnalyzerType ms2MassAnalyzer = rawData.methodData.MassAnalyzers[MSOrderType.Ms2];
List <Operations> operations = new List <Operations> {
Operations.ScanIndex, Operations.MethodData, Operations.TrailerExtras, Operations.RetentionTimes
};
if (ms2MassAnalyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
operations.Add(Operations.Ms2CentroidStreams);
}
else
{
operations.Add(Operations.Ms2SegmentedScans);
}
CheckIfDone.Check(rawData, rawFile, operations);
const int BufferSize = 65536; // 64 Kilobytes
using (StreamWriter f = new StreamWriter(fileName, false, Encoding.UTF8, BufferSize)) //Open a new file, the MGF file
{
// if the scans argument is null, use all scans
if (scans == null)
{
scans = rawData.scanIndex.ScanEnumerators[MSOrderType.Ms2];
}
ProgressIndicator progress = new ProgressIndicator(scans.Count(), String.Format("Writing MGF file"));
foreach (int i in scans)
{
f.WriteLine("\nBEGIN IONS");
f.WriteLine("RAWFILE={0}", rawData.rawFileName);
f.WriteLine("TITLE=Spectrum_{0}", i);
f.WriteLine("SCAN={0}", i);
f.WriteLine("RTINSECONDS={0}", rawData.retentionTimes[i]);
f.WriteLine("PEPMASS={0}", rawData.trailerExtras[i].MonoisotopicMZ);
f.WriteLine("CHARGE={0}", rawData.trailerExtras[i].ChargeState);
if (ms2MassAnalyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
CentroidStreamData centroid = rawData.centroidStreams[i];
if (centroid.Intensities.Length > 0)
{
intCutoff = centroid.Intensities.Max() * intensityCutoff;
}
else
{
intCutoff = 0;
}
for (int j = 0; j < centroid.Masses.Length; j++)
{
//f.WriteLine(Math.Round(centroid.Masses[j], 4).ToString() + " " + Math.Round(centroid.Intensities[j], 4).ToString());
if (centroid.Masses[j] > cutoff & centroid.Intensities[j] > intCutoff)
{
f.WriteLine("{0} {1}", Math.Round(centroid.Masses[j], 5), Math.Round(centroid.Intensities[j], 4));
}
}
}
else
{
SegmentedScanData segments = rawData.segmentedScans[i];
if (segments.Intensities.Length > 0)
{
intCutoff = segments.Intensities.Max() * intensityCutoff;
}
else
{
intCutoff = 0;
}
for (int j = 0; j < segments.Positions.Length; j++)
{
if (segments.Positions[j] > cutoff & segments.Intensities[j] > intCutoff)
{
f.WriteLine("{0} {1}", Math.Round(segments.Positions[j], 5), Math.Round(segments.Intensities[j], 4));
}
}
}
f.WriteLine("END IONS");
progress.Update();
}
progress.Done();
}
Utilities.ConsoleUtils.ClearLastLine();
}
