public static void ExtractPrecursorScans(this RawDataCollection rawData, IRawDataPlus rawFile)
{
if (rawData.Performed.Contains(Operations.PrecursorScans))
{
return;
}
if (!rawData.Performed.Contains(Operations.ScanIndex))
{
rawData.ExtractScanIndex(rawFile);
}
Log.Information("Extracting scan dependents/precursor scans");
int ms2Scan = -1;
int ms3Scan = -1;
IEnumerable <int> scans = rawData.scanIndex.ScanEnumerators[MSOrderType.Ms];
ProgressIndicator progress = new ProgressIndicator(scans.Count(), "Indexing linked scan events");
foreach (int scan in scans)
{
var scanDependents = rawFile.GetScanDependents(scan, 4);
// check if the ms1 scan has dependent scans
if (scanDependents == null)
{
continue;
}
for (int i = 0; i < scanDependents.ScanDependentDetailArray.Length; i++)
{
if (rawData.scanIndex.AnalysisOrder == MSOrderType.Ms2) // it is ms2
{
ms2Scan = scanDependents.ScanDependentDetailArray[i].ScanIndex;
rawData.precursorScans.Add(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan));
}
else // it is ms3
{
ms2Scan = scanDependents.ScanDependentDetailArray[i].ScanIndex;
if (rawFile.GetScanDependents(ms2Scan, 4).ScanDependentDetailArray.Length != 0) // make sure there is ms3 data
{
ms3Scan = rawFile.GetScanDependents(ms2Scan, 4).ScanDependentDetailArray[0].ScanIndex;
rawData.precursorScans.Add(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan));
rawData.precursorScans.Add(ms3Scan, new PrecursorScanData(ms3scan: ms3Scan, ms2Scan: ms2Scan, masterScan: scan));
}
else
{
// there is no ms3 scan, so we only add the ms2 scan
rawData.precursorScans.Add(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan));
}
}
}
progress.Update();
}
progress.Done();
rawData.Performed.Add(Operations.PrecursorScans);
}
DependentsAndPrecursorScansByScanDependents(IRawDataPlus rawFile, ScanIndex index)
{
rawFile.SelectInstrument(Device.MS, 1);
Log.Information("Extracting scan dependents/precursor scans");
PrecursorScanCollection precursorScans = new PrecursorScanCollection();
ScanDependentsCollections dependents = new ScanDependentsCollections();
int ms2Scan = -1;
int ms3Scan = -1;
IEnumerable <int> scans = index.ScanEnumerators[MSOrderType.Ms];
ProgressIndicator progress = new ProgressIndicator(scans.Count(), "Indexing linked scan events");
foreach (int scan in scans)
{
var scanDependents = rawFile.GetScanDependents(scan, 4);
dependents[scan] = scanDependents;
// check if the ms1 scan has dependent scans
if (scanDependents == null)
{
continue;
}
for (int i = 0; i < scanDependents.ScanDependentDetailArray.Length; i++)
{
if (index.AnalysisOrder == MSOrderType.Ms2) // it is ms2
{
ms2Scan = scanDependents.ScanDependentDetailArray[i].ScanIndex;
precursorScans[ms2Scan] = new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan);
}
else // it is ms3
{
ms2Scan = scanDependents.ScanDependentDetailArray[i].ScanIndex;
var ms2Dependents = rawFile.GetScanDependents(ms2Scan, 4).ScanDependentDetailArray;
if (ms2Dependents.Length != 0) // make sure there is ms3 data
{
ms3Scan = ms2Dependents[0].ScanIndex;
precursorScans[ms2Scan] = new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan);
precursorScans[ms3Scan] = new PrecursorScanData(ms3scan: ms3Scan, ms2Scan: ms2Scan, masterScan: scan);
}
else
{
// there is no ms3 scan, so we only add the ms2 scan
precursorScans[ms2Scan] = new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan);
}
}
}
progress.Update();
}
progress.Done();
return(precursorScans, dependents);
}
public static ScanDependentsCollections ScanDependents(IRawDataPlus rawFile, ScanIndex index)
{
rawFile.SelectInstrument(Device.MS, 1);
ScanDependentsCollections scanDependents = new ScanDependentsCollections();
foreach (int scan in index.ScanEnumerators[MSOrderType.Ms])
{
scanDependents[scan] = rawFile.GetScanDependents(scan, 4);
}
return(scanDependents);
}
/// <summary>
/// Populate information about parent scan numbers
/// </summary>
private void ReadScanParents()
{
int firstScan = rawFile.RunHeaderEx.FirstSpectrum;
int lastScan = rawFile.RunHeaderEx.LastSpectrum;
for (int scanNumber = firstScan; scanNumber <= lastScan; scanNumber++)
{
var dependents = rawFile.GetScanDependents(scanNumber, 1);
if (dependents != null)
{
foreach (var depedent in dependents.ScanDependentDetailArray)
{
ScanParents[depedent.ScanIndex] = scanNumber;
}
}
}
}
public static void AggregateMetaData(this ScanMetaDataCollection metaData, RawDataCollection rawData, IRawDataPlus rawFile)
{
List <Operations> operations = new List <Operations>()
{
Operations.ScanIndex, Operations.MethodData,
Operations.RetentionTimes, Operations.TrailerExtras, Operations.PrecursorScans
};
if (rawData.methodData.MassAnalyzers[MSOrderType.Ms] == MassAnalyzerType.MassAnalyzerFTMS)
{
operations.Add(Operations.Ms1CentroidStreams);
}
else
{
operations.Add(Operations.Ms1SegmentedScans);
}
if (rawData.methodData.MassAnalyzers[MSOrderType.Ms2] == MassAnalyzerType.MassAnalyzerFTMS)
{
operations.Add(Operations.Ms2CentroidStreams);
}
else
{
operations.Add(Operations.Ms2SegmentedScans);
}
if (rawData.methodData.AnalysisOrder == MSOrderType.Ms3)
{
if (rawData.methodData.MassAnalyzers[MSOrderType.Ms3] == MassAnalyzerType.MassAnalyzerFTMS)
{
operations.Add(Operations.Ms3CentroidStreams);
}
else
{
operations.Add(Operations.Ms3SegmentedScans);
}
}
rawData.Check(rawFile, operations);
ProgressIndicator progress = new ProgressIndicator(rawData.scanIndex.ScanEnumerators[MSOrderType.Any].Count(),
"Formatting scan meta data");
// add a new ScanMetaData class for each scan
foreach (int scan in rawData.scanIndex.ScanEnumerators[MSOrderType.Any])
{
metaData.Add(scan, new ScanMetaData());
}
// get isolation window
double isoWindow;
if (rawData.methodData.AnalysisOrder == MSOrderType.Ms2)
{
isoWindow = rawData.methodData.IsolationWindow.MS2;
}
else
{
isoWindow = rawData.methodData.IsolationWindow.MS3.MS1Window;
}
// get topN
foreach (int scan in rawData.scanIndex.ScanEnumerators[MSOrderType.Ms])
{
// if the ms1 scan has no scan dependents then topN = 0
if (rawFile.GetScanDependents(scan, 0) == null)
{
metaData[scan].MS2ScansPerCycle = 0;
}
else
{
metaData[scan].MS2ScansPerCycle = rawFile.GetScanDependents(scan, 0).ScanDependentDetailArray.Length;
}
}
// go through scans for each ms order sequentially
foreach (MSOrderType MSOrder in new List <MSOrderType> {
MSOrderType.Ms, MSOrderType.Ms2, MSOrderType.Ms3
})
{
int[] scans = rawData.scanIndex.ScanEnumerators[MSOrder];
for (int i = 0; i < scans.Length; i++)
{
metaData[scans[i]].FillTime = rawData.trailerExtras[scans[i]].InjectionTime;
// populate duty cycle
if (i < scans.Length - 1)
{
metaData[scans[i]].DutyCycle = (rawData.retentionTimes[scans[i + 1]] - rawData.retentionTimes[scans[i]]) * 60;
}
else
{
metaData[scans[i]].DutyCycle = 0;
}
// populate scan rate
if (MSOrder == MSOrderType.Ms2 | MSOrder == MSOrderType.Ms3)
{
metaData[scans[i]].MS2ScansPerCycle = metaData[rawData.precursorScans[scans[i]].MasterScan].MS2ScansPerCycle;
}
// populate intensity distributions
if (rawData.methodData.MassAnalyzers[MSOrder] == MassAnalyzerType.MassAnalyzerFTMS)
{
metaData[scans[i]].IntensityDistribution = new Distribution(rawData.centroidStreams[scans[i]].Intensities);
metaData[scans[i]].SummedIntensity = rawData.centroidStreams[scans[i]].Intensities.Sum();
}
else
{
metaData[scans[i]].IntensityDistribution = new Distribution(rawData.segmentedScans[scans[i]].Intensities);
metaData[scans[i]].SummedIntensity = rawData.segmentedScans[scans[i]].Intensities.Sum();
}
// populate fraction of scans consuming 80% of total intensity
if (rawData.methodData.MassAnalyzers[MSOrder] == MassAnalyzerType.MassAnalyzerFTMS)
{
metaData[scans[i]].FractionConsumingTop80PercentTotalIntensity = rawData.centroidStreams[scans[i]].Intensities.FractionOfScansConsumingTotalIntensity(percent: 80);
}
else
{
metaData[scans[i]].FractionConsumingTop80PercentTotalIntensity = rawData.segmentedScans[scans[i]].Intensities.FractionOfScansConsumingTotalIntensity(percent: 80);
}
// calculate ms1 isolation interference
if (rawData.methodData.AnalysisOrder == MSOrder)
{
int preScan = rawData.precursorScans[scans[i]].MasterScan;
metaData[scans[i]].Ms1IsolationInterference = Ms1Interference.CalculateForOneScan(rawData.centroidStreams[preScan],
rawData.precursorMasses[scans[i]].MonoisotopicMZ, isoWindow, rawData.trailerExtras[scans[i]].ChargeState);
}
progress.Update();
}
}
progress.Done();
rawData.Performed.Add(Operations.MetaData);
}