public static void ParseDIA(IRawFileThreadManager rawFile, WorkflowParameters parameters)
{
var staticRawFile = rawFile.CreateThreadAccessor();
staticRawFile.SelectInstrument(Device.MS, 1);
staticRawFile.CheckIfBoxcar();
ScanIndex Index = Extract.ScanIndices(rawFile.CreateThreadAccessor());
TrailerExtraCollection trailerExtras = Extract.TrailerExtras(rawFile.CreateThreadAccessor(), Index);
MethodDataContainer methodData = Extract.MethodData(rawFile.CreateThreadAccessor(), Index);
PrecursorScanCollection precursorScans = Extract.PrecursorScansByMasterScanMs2Only(rawFile.CreateThreadAccessor(), trailerExtras, Index);
(CentroidStreamCollection centroidStreams, SegmentScanCollection segmentScans) =
Extract.MsData(rawFile: rawFile.CreateThreadAccessor(), index: Index);
RetentionTimeCollection retentionTimes = Extract.RetentionTimes(rawFile.CreateThreadAccessor(), Index);
ScanMetaDataCollectionDIA metaData = MetaDataProcessingDIA.AggregateMetaDataDIA(centroidStreams, segmentScans, methodData,
trailerExtras, retentionTimes, Index);
RawMetricsDataDIA metrics = null;
if (parameters.ParseParams.Metrics)
{
metrics = MetaDataProcessingDIA.GetMetricsDataDIA(metaData, methodData, staticRawFile.FileName, retentionTimes, Index);
MetricsWriter.WriteMatrix(metrics, staticRawFile.FileName, parameters.ParseParams.OutputDirectory);
}
if (parameters.ParseParams.Parse)
{
string matrixFileName = ReadWrite.GetPathToFile(parameters.ParseParams.OutputDirectory, staticRawFile.FileName, "._parse.txt");
//MatrixWriter.ParseQuantDIA()
//ParseWriter writerDIA = new ParseWriter(matrixFileName, centroidStreams, segmentScans, metaData,
// retentionTimes, trailerExtras, precursorScans, Index);
//writerDIA.WriteMatrixDIA();
}
// I'm not sure what goes into a DIA mgf file, so we aren't making one yet
//if (parameters.ParseParams.WriteMgf)
//{
// ParseWriter writerMGF = new ParseWriter(centroidStreams, segmentScans, parameters, retentionTimes, precursorMasses, precursorScans, trailerExtras, methodData, Index);
// writerMGF.WriteMGF(staticRawFile.FileName);
//}
}
public static TrailerExtraCollection TrailerExtras(IRawDataPlus rawFile, ScanIndex index)
{
rawFile.SelectInstrument(Device.MS, 1);
Log.Information("Extracting trailer extras");
TrailerExtraCollection trailerExtras = new TrailerExtraCollection();
TrailerExtraIndices trailerIndices = new TrailerExtraIndices(rawFile);
Double[] spsMasses;
var scans = index.ScanEnumerators[MSOrderType.Any];
ProgressIndicator P = new ProgressIndicator(scans.Count(), "Extracting trailer extras");
P.Start();
foreach (int scan in scans)
{
trailerExtras[scan] = ExtractOneTrailerExtra(rawFile, scan, trailerIndices);
P.Update();
}
P.Done();
return(trailerExtras);
}
public static PrecursorMassCollection PrecursorMasses(IRawDataPlus rawFile, PrecursorScanCollection precursorScans, TrailerExtraCollection trailerExtras, ScanIndex index)
{
rawFile.SelectInstrument(Device.MS, 1);
Log.Information("Extracting precursor masses");
PrecursorMassCollection precursorMasses = new PrecursorMassCollection();
var scans = index.ScanEnumerators[MSOrderType.Any];
ProgressIndicator progress = new ProgressIndicator(scans.Count(), "Extracting precursor masses");
foreach (int scan in scans)
{
if (index.allScans[scan].MSOrder == MSOrderType.Ms2)
{
double parent_mass = rawFile.GetScanEventForScanNumber(scan).GetReaction(0).PrecursorMass;
precursorMasses[scan] = new PrecursorMassData(trailerExtras[scan].MonoisotopicMZ, parent_mass);
}
if (index.allScans[scan].MSOrder == MSOrderType.Ms3)
{
int ms2scan = precursorScans[scan].MS2Scan;
double parent_mass = rawFile.GetScanEventForScanNumber(scan).GetReaction(0).PrecursorMass;
precursorMasses[scan] = new PrecursorMassData(trailerExtras[ms2scan].MonoisotopicMZ, parent_mass);
}
progress.Update();
}
progress.Done();
return(precursorMasses);
}
/// <summary>
/// Gets precursor scans directly from the trailer extra. This is intended for DIA files, and by extension only for Ms2 experiments.
/// </summary>
/// <param name="rawFile"></param>
/// <param name="index"></param>
/// <returns></returns>
public static PrecursorScanCollection PrecursorScansByMasterScanMs2Only(IRawDataPlus rawFile, TrailerExtraCollection trailerExtras, ScanIndex index)
{
rawFile.SelectInstrument(Device.MS, 1);
Log.Information("Extracting scan dependents/precursor scans");
PrecursorScanCollection precursorScans = new PrecursorScanCollection();
int ms2Scan = -1;
int ms3Scan = -1;
IEnumerable <int> scans = index.ScanEnumerators[MSOrderType.Ms];
ProgressIndicator progress = new ProgressIndicator(scans.Count(), "Indexing linked scan events");
// if it is DIA it must be MS2
scans = index.ScanEnumerators[MSOrderType.Ms2];
foreach (int scan in scans)
{
int masterScan = trailerExtras[scan].MasterScan;
precursorScans[scan] = new PrecursorScanData(ms2scan: scan, masterScan: masterScan);
}
progress.Done();
return(precursorScans);
}
public static void WriteSearchMGF(WorkflowParameters parameters, CentroidStreamCollection centroids, SegmentScanCollection segments, RetentionTimeCollection retentionTimes,
PrecursorMassCollection precursorMasses, PrecursorScanCollection precursorScans, TrailerExtraCollection trailerExtras, MethodDataContainer methodData,
ScanIndex index, string rawFileName, bool fixedScans = false)
{
var pars = parameters.QcParams.SearchParameters;
int[] scans = AdditionalMath.SelectRandomScans(scans: index.ScanEnumerators[MSOrderType.Ms2],
num: parameters.QcParams.NumberSpectra, fixedScans: parameters.QcParams.FixedScans);
string mgfFile = ReadWrite.GetPathToFile(parameters.QcParams.QcSearchDataDirectory, rawFileName, ".mgf");
MgfWriter.WriteMGF(rawFileName, centroids, segments, parameters, retentionTimes, precursorMasses, precursorScans,
trailerExtras, methodData, index, outputFile: mgfFile, scans: scans);
}
public static ScanMetaDataCollectionDDA AggregateMetaDataDDA(CentroidStreamCollection centroidStreams, SegmentScanCollection segmentScans, MethodDataContainer methodData,
PrecursorScanCollection precursorScans, TrailerExtraCollection trailerExtras, PrecursorMassCollection precursorMasses,
RetentionTimeCollection retentionTimes, ScanDependentsCollections scanDependents, ScanEventReactionCollection reactions, ScanIndex index)
{
//ProgressIndicator progress = new ProgressIndicator(index.ScanEnumerators[MSOrderType.Any].Count(),
// "Formatting scan meta data");
ScanMetaDataCollectionDDA metaData = new ScanMetaDataCollectionDDA();
int[] scans = index.ScanEnumerators[MSOrderType.Any];
double isoWindow = MetaDataCalculations.Ms1IsoWindow(methodData);
Console.WriteLine("Calculating meta data");
Console.WriteLine(" MS1 isolation interference");
metaData.Ms1IsolationInterference = MetaDataCalculations.Ms1Interference(centroidStreams, precursorMasses, trailerExtras,
precursorScans, reactions, index);
Console.WriteLine(" MS2 scan cycle density");
metaData.MS2ScansPerCycle = MetaDataCalculations.MS2ScansPerCycle(scanDependents, index);
Console.WriteLine(" Ion injection time");
metaData.FillTime = MetaDataCalculations.FillTimes(trailerExtras, index);
Console.WriteLine(" Duty cycle");
metaData.DutyCycle = MetaDataCalculations.DutyCycle(retentionTimes, index);
Console.WriteLine(" Intensity distribution");
metaData.IntensityDistribution = MetaDataCalculations.IntensityDistributions(centroidStreams, segmentScans, index);
Console.WriteLine(" Summed intensities");
metaData.SummedIntensity = MetaDataCalculations.SummedIntensities(centroidStreams, segmentScans, index);
metaData.FractionConsumingTop80PercentTotalIntensity = MetaDataCalculations.Top80Frac(centroidStreams, segmentScans, index);
//Task.WaitAll();
return(metaData);
}
public static void RefineMonoIsoMassChargeValues(WorkFlows.WorkflowParameters parameters, CentroidStreamCollection centroids, PrecursorMassCollection precursorMasses, TrailerExtraCollection trailerExtras, PrecursorPeakCollection precursorPeaks, PrecursorScanCollection precursorScans)
{
int ms2Scan, ms1Scan, refinedCharge;
double refinedMass;
ProgressIndicator P = new ProgressIndicator(precursorPeaks.Count(), "Refining precursor charge and monoisotopic mass");
P.Start();
foreach (var peak in precursorPeaks)
{
ms2Scan = peak.Value.Ms2Scan;
if (peak.Value.PeakFound)
{
ms1Scan = peak.Value.MaxScan;
}
else
{
ms1Scan = precursorScans[ms2Scan].MasterScan;
}
(refinedCharge, refinedMass) = GetMonoIsotopicMassCharge(centroids[ms1Scan], precursorMasses[ms2Scan].ParentMZ,
trailerExtras[ms2Scan].ChargeState, parameters.ConsideredChargeStates.Min, parameters.ConsideredChargeStates.Max);
precursorMasses[ms2Scan].MonoisotopicMZ = refinedMass;
trailerExtras[ms2Scan].MonoisotopicMZ = refinedMass;
trailerExtras[ms2Scan].ChargeState = refinedCharge;
P.Update();
}
P.Done();
}
