protected override void IterateOverScans()
{
DeconMSnResults.Clear();
_scanCounter = 0;
var resultCounter = 0;
foreach (var scanSet in Run.ScanSetCollection.ScanSetList)
{
_scanCounter++;
if (BackgroundWorker != null)
{
if (BackgroundWorker.CancellationPending)
{
return;
}
}
//check ms level
var currentMSLevel = Run.GetMSLevel(scanSet.PrimaryScanNumber);
if (currentMSLevel == 1)
{
Run.ResultCollection.IsosResultBin.Clear();
Run.CurrentScanSet = scanSet;
MSGenerator.Execute(Run.ResultCollection);
_currentMS1XYValues = new XYData
{
Xvalues = Run.XYData.Xvalues,
Yvalues = Run.XYData.Yvalues
};
_currentMS1TICIntensity = Run.GetTICFromInstrumentInfo(scanSet.PrimaryScanNumber);
PeakDetector.Execute(Run.ResultCollection);
_currentMS1Peaks = new List <Peak>(Run.PeakList);
}
else if (currentMSLevel == 2)
{
if (_currentMS1Peaks == null || _currentMS1Peaks.Count == 0)
{
continue;
}
var precursorInfo = Run.GetPrecursorInfo(scanSet.PrimaryScanNumber);
Run.CurrentScanSet = scanSet;
var inaccurateParentMZ = precursorInfo.PrecursorMZ;
resultCounter++;
var deconMSnResult = new DeconMSnResult {
ParentScan = Run.GetParentScan(scanSet.PrimaryScanNumber)
};
deconMSnResult.IonInjectionTime = Run.GetIonInjectionTimeInMilliseconds(deconMSnResult.ParentScan);
deconMSnResult.ScanNum = scanSet.PrimaryScanNumber;
deconMSnResult.OriginalMZTarget = inaccurateParentMZ;
deconMSnResult.ParentScanTICIntensity = _currentMS1TICIntensity;
MSGenerator.Execute(Run.ResultCollection);
var lowerMZ = inaccurateParentMZ - 1.1;
var upperMZ = inaccurateParentMZ + 1.1;
var dataIsCentroided = Run.IsDataCentroided(scanSet.PrimaryScanNumber);
if (dataIsCentroided)
{
_ms2PeakDetectorForCentroidData.Execute(Run.ResultCollection);
}
else
{
_ms2PeakDetectorForProfileData.Execute(Run.ResultCollection);
}
var ms2Peaks = new List <Peak>(Run.PeakList);
var filteredMS1Peaks = _currentMS1Peaks.Where(p => p.XValue > lowerMZ && p.XValue < upperMZ).ToList();
IsotopicProfile selectedMS1Feature = null;
for (var attemptNum = 0; attemptNum < NumMaxAttemptsAtLowIntensitySpecies; attemptNum++)
{
var candidateMS1Features = GetCandidateMS1Features(inaccurateParentMZ, filteredMS1Peaks);
//if none were found, will regenerate MS1 spectrum and find peaks again
if (candidateMS1Features.Count == 0)
{
var numSummed = attemptNum * 2 + 3;
var ms1Scan = precursorInfo.PrecursorScan;
var ms1ScanSet = new ScanSetFactory().CreateScanSet(Run, ms1Scan, numSummed);
//get MS1 mass spectrum again. This time sum spectra
Run.CurrentScanSet = ms1ScanSet;
MSGenerator.Execute(Run.ResultCollection);
//run MS1 peak detector, with greater sensitivity
var isLastAttempt = attemptNum >= NumMaxAttemptsAtLowIntensitySpecies - 2; //need to do -2 because of the way the loop advances the counter.
if (isLastAttempt)
{
_superSensitiveMS1PeakDetector.MinX = lowerMZ;
_superSensitiveMS1PeakDetector.MaxX = upperMZ;
_superSensitiveMS1PeakDetector.Execute(Run.ResultCollection);
filteredMS1Peaks = new List <Peak>(Run.PeakList);
}
else
{
_moreSensitiveMS1PeakDetector.Execute(Run.ResultCollection);
var moreSensitiveMS1Peaks = new List <Peak>(Run.PeakList);
filteredMS1Peaks = moreSensitiveMS1Peaks.Where(p => p.XValue > lowerMZ && p.XValue < upperMZ).ToList();
}
}
else if (candidateMS1Features.Count == 1)
{
selectedMS1Feature = candidateMS1Features.First();
break; //we found something, so no need for any further attempts
}
else
{
var highQualityCandidates = candidateMS1Features.Where(p => p.Score < 0.15).ToList();
if (highQualityCandidates.Count == 0)
{
selectedMS1Feature = candidateMS1Features.OrderByDescending(p => p.IntensityMostAbundantTheor).First();
}
else if (highQualityCandidates.Count == 1)
{
selectedMS1Feature = highQualityCandidates.First();
}
else
{
selectedMS1Feature = highQualityCandidates.OrderByDescending(p => p.IntensityMostAbundantTheor).First();
}
deconMSnResult.ExtraInfo = "Warning - multiple MSFeatures found for target parent MZ";
break; //we found something, so no need for any further attempts
}
}
if (selectedMS1Feature != null)
{
deconMSnResult.ParentMZ = selectedMS1Feature.MonoPeakMZ;
deconMSnResult.ParentChargeState = selectedMS1Feature.ChargeState;
deconMSnResult.ParentIntensity = selectedMS1Feature.IntensityMostAbundantTheor;
deconMSnResult.IntensityAggregate = selectedMS1Feature.IntensityMostAbundantTheor;
deconMSnResult.IsotopicProfile = selectedMS1Feature;
}
else
{
var candidatePeaks = new List <Peak>();
foreach (var peak in filteredMS1Peaks)
{
var currentDiff = Math.Abs(peak.XValue - inaccurateParentMZ);
var toleranceInMZ = ToleranceInPPM * peak.XValue / 1e6;
if (currentDiff < toleranceInMZ)
{
candidatePeaks.Add(peak);
}
}
Peak selectedPeak = null;
if (candidatePeaks.Count == 0)
{
//cannot even find a suitable MS1 peak. So can't do anything
}
else if (candidatePeaks.Count == 1)
{
selectedPeak = candidatePeaks.First();
}
else
{
selectedPeak = candidatePeaks.OrderByDescending(p => p.Height).First();
}
if (selectedPeak != null)
{
deconMSnResult.ParentMZ = selectedPeak.XValue;
deconMSnResult.ParentChargeState = 1; //not sure what charge I should assign... Ask SangTae
deconMSnResult.ParentIntensity = selectedPeak.Height;
deconMSnResult.IsotopicProfile = null;
deconMSnResult.ExtraInfo = "Failure code 1: No MSFeature, but peak found";
}
else
{
deconMSnResult.ParentMZ = precursorInfo.PrecursorMZ; //could not find the accurate parentMZ, so just report what the instrument found.
deconMSnResult.ParentChargeState = 1; //not sure what charge I should assign... Ask SangTae
deconMSnResult.ParentIntensity = 0;
deconMSnResult.IsotopicProfile = null;
deconMSnResult.ExtraInfo = "Failure code 2: No MSFeature or peak found";
}
}
//Build export data.
var outputString = GetMGFOutputString(Run, scanSet.PrimaryScanNumber, deconMSnResult, ms2Peaks);
var includeHeader = resultCounter == 1;
var summaryString = GetSummaryString(deconMSnResult, includeHeader);
var parentProfileString = GetParentProfileString(deconMSnResult, includeHeader);
if (ExportData)
{
WriteOutMainData(outputString);
WriteOutDeconMSnSummary(summaryString);
if (IsParentProfileDataExported)
{
WriteOutParentProfileInfoString(parentProfileString);
}
}
if (deconMSnResult.ParentIntensity > 0)
{
DeconMSnResults.Add(deconMSnResult);
}
}
else
{
throw new ApplicationException(
"DeconMSn only works on MS1 and MS2 data; You are attempting MS3");
}
ReportProgress();
}
}
