public static RawMetricsDataDDA GetMetricsDataDDA(ScanMetaDataCollectionDDA metaData, MethodDataContainer methodData,
string rawFileName, RetentionTimeCollection retentionTimes, ScanIndex index, PrecursorPeakCollection peakData,
PrecursorScanCollection precursorScans, QuantDataCollection quantData = null)
{
RawMetricsDataDDA metricsData = new RawMetricsDataDDA();
metricsData.DateAcquired = methodData.CreationDate;
metricsData.Instrument = methodData.Instrument;
Console.WriteLine("Calculating metrics");
metricsData.RawFileName = rawFileName;
metricsData.Instrument = methodData.Instrument;
metricsData.MS1Analyzer = methodData.MassAnalyzers[MSOrderType.Ms];
metricsData.MS2Analyzer = methodData.MassAnalyzers[MSOrderType.Ms2];
metricsData.TotalAnalysisTime = retentionTimes[index.ScanEnumerators[MSOrderType.Any].Last()] -
retentionTimes[index.ScanEnumerators[MSOrderType.Any].First()];
metricsData.NumberOfEsiFlags = MetricsCalculations.NumberOfEsiFlags(metaData, index);
metricsData.TotalScans = index.TotalScans;
metricsData.MS1Scans = index.ScanEnumerators[MSOrderType.Ms].Length;
metricsData.MS2Scans = index.ScanEnumerators[MSOrderType.Ms2].Length;
if (methodData.AnalysisOrder == MSOrderType.Ms3)
{
metricsData.MS3Analyzer = methodData.MassAnalyzers[MSOrderType.Ms3];
metricsData.MS3Scans = index.ScanEnumerators[MSOrderType.Ms3].Length;
}
else
{
metricsData.MS3Analyzer = MassAnalyzerType.Any;
metricsData.MS3Scans = 0;
}
var pickedMs1 = new HashSet <int>((from x in index.ScanEnumerators[methodData.AnalysisOrder]
select precursorScans[x].MasterScan)).ToList();
metricsData.MSOrder = methodData.AnalysisOrder;
metricsData.MedianSummedMS1Intensity = MetricsCalculations.GetMedianSummedMSIntensity(metaData.SummedIntensity, index, MSOrderType.Ms);
metricsData.MedianSummedMS2Intensity = MetricsCalculations.GetMedianSummedMSIntensity(metaData.SummedIntensity, index, MSOrderType.Ms2);
metricsData.MedianPrecursorIntensity = (from x in peakData.Keys select peakData[x].ParentIntensity).ToArray().Percentile(50);
metricsData.MedianMS1FillTime = MetricsCalculations.GetMedianMSFillTime(metaData.FillTime, index, MSOrderType.Ms);
metricsData.MedianMS2FillTime = MetricsCalculations.GetMedianMSFillTime(metaData.FillTime, index, MSOrderType.Ms2);
if (methodData.AnalysisOrder == MSOrderType.Ms3)
{
metricsData.MedianMS3FillTime = MetricsCalculations.GetMedianMSFillTime(metaData.FillTime, index, MSOrderType.Ms3);
}
metricsData.MeanTopN = MetricsCalculations.GetMeanMs2ScansPerCycle(metaData.MS2ScansPerCycle);
metricsData.MeanDutyCycle = MetricsCalculations.GetMedianDutyCycle(metaData.DutyCycle, index);
metricsData.MedianMs2FractionConsumingTop80PercentTotalIntensity =
MetricsCalculations.GetMedianMs2FractionConsumingTop80PercentTotalIntensity(
metaData.FractionConsumingTop80PercentTotalIntensity, index);
metricsData.MS1ScanRate = metricsData.MS1Scans / metricsData.TotalAnalysisTime;
metricsData.MS2ScanRate = metricsData.MS2Scans / metricsData.TotalAnalysisTime;
if (methodData.AnalysisOrder == MSOrderType.Ms3)
{
metricsData.MS3ScanRate = metricsData.MS3Scans / metricsData.TotalAnalysisTime;
}
metricsData.MedianBaselinePeakWidth = peakData.PeakShapeMedians.Width.P10;
metricsData.MedianHalfHeightPeakWidth = peakData.PeakShapeMedians.Width.P50;
// we can't access the instrument method in Linux, so we will assume the gradient length is the length of the MS acquisition
metricsData.Gradient = retentionTimes[index.allScans.Keys.Max()];
metricsData.PeakCapacity = metricsData.Gradient / metricsData.MedianHalfHeightPeakWidth;
metricsData.MedianAsymmetryFactor = peakData.PeakShapeMedians.Asymmetry.P10;
// add isolation interference
metricsData.MedianMs1IsolationInterference = (from scan in index.ScanEnumerators[methodData.AnalysisOrder]
select metaData.Ms1IsolationInterference[scan]).ToArray().Percentile(50);
(double timeBefore, double timeAfter, double fracAbove) = MetricsCalculations.ChromIntensityMetrics(metaData, retentionTimes, index);
metricsData.TimeBeforeFirstScanToExceedPoint1MaxIntensity = timeBefore;
metricsData.TimeAfterLastScanToExceedPoint1MaxIntensity = timeAfter;
metricsData.FractionOfRunAbovePoint1MaxIntensity = fracAbove;
metricsData.Ms1FillTimeDistribution = new Distribution((from x in index.ScanEnumerators[MSOrderType.Ms] select metaData.FillTime[x]).ToArray());
metricsData.Ms2FillTimeDistribution = new Distribution((from x in index.ScanEnumerators[MSOrderType.Ms2] select metaData.FillTime[x]).ToArray());
if (methodData.AnalysisOrder == MSOrderType.Ms3)
{
metricsData.Ms3FillTimeDistribution = new Distribution((from x in index.ScanEnumerators[MSOrderType.Ms3] select metaData.FillTime[x]).ToArray());
}
metricsData.PeakShape.Asymmetry.P10 = peakData.PeakShapeMedians.Asymmetry.P10;
metricsData.PeakShape.Asymmetry.P50 = peakData.PeakShapeMedians.Asymmetry.P50;
metricsData.PeakShape.Width.P10 = peakData.PeakShapeMedians.Width.P10;
metricsData.PeakShape.Width.P50 = peakData.PeakShapeMedians.Width.P50;
// now add the quant meta data, if quant was performed
double medianReporterIntensity = 0;
QuantMetaData quantMetaData = new QuantMetaData();
SerializableDictionary <string, double> medianReporterIntensityByChannel = new SerializableDictionary <string, double>();
if (quantData != null)
{
string reagent = quantData.LabelingReagents;
string[] allTags = new LabelingReagents().Reagents[reagent].Labels;
List <double> allChannels = new List <double>();
Dictionary <string, List <double> > byChannel = new Dictionary <string, List <double> >();
foreach (string tag in allTags)
{
byChannel.Add(tag, new List <double>());
}
foreach (int scan in index.ScanEnumerators[methodData.AnalysisOrder])
{
foreach (string tag in allTags)
{
byChannel[tag].Add(quantData[scan][tag].Intensity);
allChannels.Add(quantData[scan][tag].Intensity);
}
}
medianReporterIntensity = allChannels.ToArray().Percentile(50);
foreach (string tag in allTags)
{
medianReporterIntensityByChannel[tag] = byChannel[tag].ToArray().Percentile(50);
}
quantMetaData.medianReporterIntensity = medianReporterIntensity;
quantMetaData.medianReporterIntensityByChannel = medianReporterIntensityByChannel;
quantMetaData.quantTags = allTags;
metricsData.QuantMeta = quantMetaData;
metricsData.IncludesQuant = true;
}
return(metricsData);
}
public static void ParseDDA(IRawFileThreadManager rawFileThreadManager, WorkflowParameters parameters)
{
MethodDataContainer methodData;
CentroidStreamCollection centroidStreams;
SegmentScanCollection segmentScans;
TrailerExtraCollection trailerExtras;
PrecursorMassCollection precursorMasses;
RetentionTimeCollection retentionTimes;
ScanEventReactionCollection reactions;
ScanMetaDataCollectionDDA metaData = null;
PrecursorPeakCollection peakData = null;
RawMetricsDataDDA rawMetrics = null;
QuantDataCollection quantData = null;
var staticRawFile = rawFileThreadManager.CreateThreadAccessor();
staticRawFile.SelectInstrument(Device.MS, 1);
//staticRawFile.CheckIfBoxcar();
(ScanIndex Index, PrecursorScanCollection precursorScans, ScanDependentsCollections scanDependents) =
Extract.ScanIndicesPrecursorsDependents(rawFileThreadManager);
using (var rawFile = rawFileThreadManager.CreateThreadAccessor())
{
reactions = Extract.ScanEvents(rawFile, Index);
methodData = Extract.MethodData(rawFile, Index);
(centroidStreams, segmentScans) = Extract.MsData(rawFile: rawFile, index: Index);
trailerExtras = Extract.TrailerExtras(rawFile, Index);
precursorMasses = Extract.PrecursorMasses(rawFile, precursorScans, trailerExtras, Index);
retentionTimes = Extract.RetentionTimes(rawFile, Index);
}
if (parameters.ParseParams.Parse | parameters.ParseParams.Quant | parameters.ParseParams.Metrics | parameters.RefineMassCharge)
{
peakData = AnalyzePeaks.AnalyzeAllPeaks(centroidStreams, retentionTimes, precursorMasses, precursorScans, Index);
if (parameters.RefineMassCharge)
{
MonoIsoPredictor.RefineMonoIsoMassChargeValues(centroidStreams, precursorMasses, trailerExtras, peakData, precursorScans);
}
metaData = MetaDataProcessingDDA.AggregateMetaDataDDA(centroidStreams, segmentScans, methodData, precursorScans,
trailerExtras, precursorMasses, retentionTimes, scanDependents, reactions, Index);
}
if (parameters.ParseParams.Quant)
{
quantData = Quantification.Quantify(centroidStreams, segmentScans, parameters, methodData, Index);
}
if (parameters.ParseParams.Metrics)
{
rawMetrics = MetaDataProcessingDDA.GetMetricsDataDDA(metaData, methodData, staticRawFile.FileName, retentionTimes, Index, peakData, precursorScans, quantData);
MetricsWriter.WriteMatrix(rawMetrics, null, staticRawFile.FileName, parameters.ParseParams.OutputDirectory);
}
if (parameters.ParseParams.Parse | parameters.ParseParams.Quant)
{
string matrixFileName = ReadWrite.GetPathToFile(parameters.ParseParams.OutputDirectory, staticRawFile.FileName, "_Matrix.txt");
/*
* ParseWriter writerDDA = new ParseWriter(matrixFileName, centroidStreams, segmentScans, metaData, retentionTimes,
* precursorMasses, precursorScans, peakData, trailerExtras, Index, quantData);
* writerDDA.WriteMatrixDDA(methodData.AnalysisOrder);
*/
MatrixWriter.ParseQuantDDA(matrixFileName, centroidStreams, segmentScans, metaData, retentionTimes,
precursorMasses, precursorScans, peakData, trailerExtras, Index, quantData);
}
if (parameters.ParseParams.WriteMgf)
{
//ParseWriter writerMGF = new ParseWriter(centroidStreams, segmentScans, parameters, retentionTimes, precursorMasses, precursorScans, trailerExtras, methodData, Index);
//writerMGF.WriteMGF(staticRawFile.FileName);
MgfWriter.WriteMGF(staticRawFile.FileName, centroidStreams, segmentScans, parameters, retentionTimes, precursorMasses, precursorScans, trailerExtras, methodData, Index);
}
if (parameters.ParseParams.Chromatogram != null)
{
ChromatogramWriter.WriteChromatogram(centroidStreams, segmentScans, retentionTimes, methodData, Index, parameters, staticRawFile.FileName);
}
}
public static void UniversalDDA(IRawFileThreadManager rawFileThreadManager, WorkflowParameters parameters, QcDataCollection qcDataCollection)
{
MethodDataContainer methodData;
CentroidStreamCollection centroidStreams;
SegmentScanCollection segmentScans;
TrailerExtraCollection trailerExtras;
PrecursorMassCollection precursorMasses;
RetentionTimeCollection retentionTimes;
ScanEventReactionCollection reactions;
ScanMetaDataCollectionDDA metaData = null;
PrecursorPeakCollection peakData = null;
int nScans;
var staticRawFile = rawFileThreadManager.CreateThreadAccessor();
staticRawFile.SelectInstrument(Device.MS, 1);
var err = staticRawFile.FileError;
if (err.HasError)
{
Console.WriteLine("ERROR: {0} reports error code: {1}. The associated message is: {2}",
Path.GetFileName(staticRawFile.FileName), err.ErrorCode, err.ErrorMessage);
Console.WriteLine("Skipping this file");
Log.Error("{FILE} reports error code: {ERRORCODE}. The associated message is: {ERRORMESSAGE}",
Path.GetFileName(staticRawFile.FileName), err.ErrorCode, err.ErrorMessage);
return;
}
//staticRawFile.CheckIfBoxcar();
(ScanIndex Index, PrecursorScanCollection precursorScans, ScanDependentsCollections scanDependents) =
Extract.ScanIndicesPrecursorsDependents(rawFileThreadManager, MaxProcesses: parameters.MaxProcesses);
nScans = Index.ScanEnumerators[MSOrderType.Ms2].Length;
using (var rawFile = rawFileThreadManager.CreateThreadAccessor())
{
reactions = Extract.ScanEvents(rawFile, Index);
methodData = Extract.MethodData(rawFile, Index);
(centroidStreams, segmentScans) = Extract.MsData(rawFile: rawFile, index: Index);
trailerExtras = Extract.TrailerExtras(rawFile, Index);
precursorMasses = Extract.PrecursorMasses(rawFile, precursorScans, trailerExtras, Index);
retentionTimes = Extract.RetentionTimes(rawFile, Index);
}
if (parameters.ParseParams.Parse | parameters.ParseParams.Quant | parameters.ParseParams.Metrics | parameters.RefineMassCharge | parameters.QcParams.QcDirectory != null)
{
peakData = AnalyzePeaks.AnalyzeAllPeaks(centroidStreams, retentionTimes, precursorMasses, precursorScans, Index, parameters.MaxProcesses);
if (parameters.RefineMassCharge)
{
MonoIsoPredictor.RefineMonoIsoMassChargeValues(parameters, centroidStreams, precursorMasses, trailerExtras, peakData, precursorScans);
}
metaData = MetaDataProcessingDDA.AggregateMetaDataDDA(centroidStreams, segmentScans, methodData, precursorScans,
trailerExtras, precursorMasses, retentionTimes, scanDependents, reactions, Index, parameters.MaxProcesses);
}
QuantDataCollection quantData = null;
if (parameters.ParseParams.Quant)
{
quantData = Quantification.Quantify(centroidStreams, segmentScans, parameters, methodData, Index);
}
RawMetricsDataDDA rawMetrics = null;
if (parameters.ParseParams.Metrics | parameters.QcParams.QcDirectory != null)
{
rawMetrics = MetaDataProcessingDDA.GetMetricsDataDDA(metaData, methodData, staticRawFile.FileName, retentionTimes, Index, peakData, precursorScans, quantData);
}
if (parameters.ParseParams.Metrics)
{
MetricsWriter.WriteMatrix(rawMetrics, null, staticRawFile.FileName, parameters.ParseParams.OutputDirectory);
}
if (parameters.ParseParams.Parse | parameters.ParseParams.Quant)
{
string matrixFileName = ReadWrite.GetPathToFile(parameters.ParseParams.OutputDirectory, staticRawFile.FileName, "_Matrix.txt");
/*
* ParseWriter writerDDA = new ParseWriter(matrixFileName, centroidStreams, segmentScans, metaData, retentionTimes,
* precursorMasses, precursorScans, peakData, trailerExtras, Index, quantData);
* writerDDA.WriteMatrixDDA(methodData.AnalysisOrder);
*/
MatrixWriter.ParseQuantDDA(matrixFileName, centroidStreams, segmentScans, metaData, retentionTimes,
precursorMasses, precursorScans, peakData, trailerExtras, Index, quantData);
}
if (parameters.ParseParams.WriteMgf)
{
//ParseWriter writerMGF = new ParseWriter(centroidStreams, segmentScans, parameters, retentionTimes, precursorMasses, precursorScans, trailerExtras, methodData, Index);
//writerMGF.WriteMGF(staticRawFile.FileName);
MgfWriter.WriteMGF(staticRawFile.FileName, centroidStreams, segmentScans, parameters, retentionTimes, precursorMasses, precursorScans, trailerExtras, methodData, Index);
}
if (parameters.ParseParams.Chromatogram != null)
{
ChromatogramWriter.WriteChromatogram(centroidStreams, segmentScans, retentionTimes, methodData, Index, parameters, staticRawFile.FileName);
}
if (parameters.QcParams.QcDirectory != null)
{
qcDataCollection = QC.QcWorkflow.LoadOrCreateQcCollection(parameters);
SearchMetricsContainer searchMetrics = new SearchMetricsContainer(staticRawFile.FileName, staticRawFile.CreationDate, methodData);
// check if the raw file already exists in the QC data with a different name
if (QcWorkflow.CheckIfFilePresentInQcCollection(staticRawFile.FileName, qcDataCollection))
{
Log.Information("A file with the same creation date and time as {File} already exists in the QC data", staticRawFile.FileName);
Console.WriteLine("A file with the same creation date and time as {File} already exists in the QC data. Skipping to next file.",
staticRawFile.FileName);
}
else
{
if (parameters.QcParams.PerformSearch)
{
Search.WriteSearchMGF(parameters, centroidStreams, segmentScans, retentionTimes, precursorMasses, precursorScans, trailerExtras, methodData,
Index, staticRawFile.FileName, parameters.QcParams.FixedScans);
Search.RunSearch(parameters, methodData, staticRawFile.FileName);
searchMetrics = SearchQC.ParseSearchResults(searchMetrics, parameters, staticRawFile.FileName, nScans);
}
QcDataContainer qcData = new QcDataContainer();
qcData.DDA = rawMetrics;
qcData.SearchMetrics = searchMetrics;
QC.QcWorkflow.UpdateQcCollection(qcDataCollection, qcData, methodData, staticRawFile.FileName);
}
}
}
public static void QcDDA(IRawFileThreadManager rawFileThreadManager, WorkflowParameters parameters)
{
MethodDataContainer methodData;
CentroidStreamCollection centroidStreams;
SegmentScanCollection segmentScans;
TrailerExtraCollection trailerExtras;
PrecursorMassCollection precursorMasses;
RetentionTimeCollection retentionTimes;
ScanEventReactionCollection reactions;
var staticRawFile = rawFileThreadManager.CreateThreadAccessor();
staticRawFile.SelectInstrument(Device.MS, 1);
staticRawFile.CheckIfBoxcar();
(ScanIndex Index, PrecursorScanCollection precursorScans, ScanDependentsCollections scanDependents) =
Extract.ScanIndicesPrecursorsDependents(rawFileThreadManager);
using (var rawFile = rawFileThreadManager.CreateThreadAccessor())
{
methodData = Extract.MethodData(rawFile, Index);
reactions = Extract.ScanEvents(rawFile, Index);
(centroidStreams, segmentScans) = Extract.MsData(rawFile: rawFile, index: Index);
trailerExtras = Extract.TrailerExtras(rawFile, Index);
precursorMasses = Extract.PrecursorMasses(rawFile, precursorScans, trailerExtras, Index);
retentionTimes = Extract.RetentionTimes(rawFile, Index);
}
PrecursorPeakCollection peakData = AnalyzePeaks.AnalyzeAllPeaks(centroidStreams, retentionTimes, precursorMasses, precursorScans, Index);
if (parameters.RefineMassCharge)
{
MonoIsoPredictor.RefineMonoIsoMassChargeValues(centroidStreams, precursorMasses, trailerExtras, peakData, precursorScans);
}
ScanMetaDataCollectionDDA metaData = MetaDataProcessingDDA.AggregateMetaDataDDA(centroidStreams, segmentScans, methodData, precursorScans,
trailerExtras, precursorMasses, retentionTimes, scanDependents, reactions, Index);
RawMetricsDataDDA rawMetrics = MetaDataProcessingDDA.GetMetricsDataDDA(metaData, methodData, staticRawFile.FileName, retentionTimes, Index, peakData, precursorScans);
QcDataCollection qcDataCollection = QC.QcWorkflow.LoadOrCreateQcCollection(parameters);
SearchMetricsContainer searchMetrics = new SearchMetricsContainer(staticRawFile.FileName, staticRawFile.CreationDate, methodData);
if (parameters.QcParams.PerformSearch)
{
Search.WriteSearchMGF(parameters, centroidStreams, segmentScans, retentionTimes, precursorMasses, precursorScans, trailerExtras, methodData,
Index, staticRawFile.FileName, parameters.QcParams.FixedScans);
Search.RunSearch(parameters, methodData, staticRawFile.FileName);
searchMetrics = SearchQC.ParseSearchResults(searchMetrics, parameters, staticRawFile.FileName);
}
QcDataContainer qcData = new QcDataContainer();
qcData.DDA = rawMetrics;
qcData.SearchMetrics = searchMetrics;
QC.QcWorkflow.UpdateQcCollection(qcDataCollection, qcData, methodData, staticRawFile.FileName);
staticRawFile.Dispose();
}
