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);
}
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 Dictionary <int, double> Ms1Interference(CentroidStreamCollection centroidStreams, PrecursorMassCollection precursorMasses,
TrailerExtraCollection trailerExtras, PrecursorScanCollection precursorScans, ScanEventReactionCollection reactions, ScanIndex index)
{
ConcurrentDictionary <int, double> interference = new ConcurrentDictionary <int, double>();
int chunkSize = Constants.MultiThreading.ChunkSize(index.ScanEnumerators[index.AnalysisOrder].Count());
var batches = index.ScanEnumerators[index.AnalysisOrder].Chunk(chunkSize);
Parallel.ForEach(batches, Constants.MultiThreading.Options(), batch =>
{
foreach (int scan in batch)
{
int preScan = precursorScans[scan].MasterScan;
interference.AddOrUpdate(scan, Algorithms.Ms1Interference.CalculateForOneScan(centroidStreams[preScan], reactions[scan],
precursorMasses[scan].MonoisotopicMZ, trailerExtras[scan].ChargeState), (a, b) => b);
}
});
var interferenceOut = new Dictionary <int, double>();
foreach (var item in interference)
{
interferenceOut.Add(item.Key, item.Value);
}
return(interferenceOut);
}
public static PrecursorPeakCollection AnalyzeAllPeaks(CentroidStreamCollection centroids, RetentionTimeCollection retentionTimes,
PrecursorMassCollection precursorMasses, PrecursorScanCollection precursorScans, ScanIndex index, int MaxProcesses)
{
ConcurrentDictionary <int, PrecursorPeakData> peaks = new ConcurrentDictionary <int, PrecursorPeakData>();
DistributionMultiple allPeaksAsymmetry = new DistributionMultiple();
DistributionMultiple allPeaksWidths = new DistributionMultiple();
var lockTarget = new object(); // this is so we can keep track of progress in the parallel loop
int chunkSize = Constants.MultiThreading.ChunkSize(index.ScanEnumerators[MSOrderType.Ms2].Count());
var batches = index.ScanEnumerators[MSOrderType.Ms2].Chunk(chunkSize);
ProgressIndicator P = new ProgressIndicator(total: index.ScanEnumerators[MSOrderType.Ms2].Length, message: "Analyzing precursor peaks");
P.Start();
Parallel.ForEach(batches, Constants.MultiThreading.Options(MaxProcesses), batch =>
{
PrecursorPeakData peak;
foreach (int scan in batch)
{
// [2018-12-04] changing to use picked mass and not monoisomass. The monoisomass might be low in intensity and would not represent the whole elution profile
peak = OnePeak(centroids, retentionTimes, precursorMasses[scan].ParentMZ, precursorScans[scan].MasterScan, ddScan: scan, index: index);
if (peak.NScans < 5 | peak.PeakFound == false |
peak.ContainsFirstMS1Scan | peak.ContainsLastMS1Scan)
{
peak.PeakShape = null;
}
else
{
var newShape = GetPeakShape(peak);
peak.PeakShape = newShape;
allPeaksAsymmetry.Add(newShape.Asymmetry);
allPeaksWidths.Add(newShape.Width);
}
peak.Area = CalculatePeakArea(peak);
peaks.AddOrUpdate(scan, peak, (a, b) => b);
lock (lockTarget)
{
P.Update();
}
}
});
P.Done();
var peaksOut = new PrecursorPeakCollection();
foreach (var item in peaks)
{
peaksOut.Add(item.Key, item.Value);
}
if (allPeaksWidths.P50.Count() == 0)
{
peaksOut.PeakShapeMedians = new Data.Containers.PeakShape(width: new Width(), asymmetry: new Asymmetry(), peakMax: 0);
}
else
{
peaksOut.PeakShapeMedians = new Data.Containers.PeakShape(width: allPeaksWidths.GetMedians(), asymmetry: allPeaksAsymmetry.GetMedians(), peakMax: 0);
}
return(peaksOut);
}
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();
}
