public double ScoreLipid(LipidTarget lipidTarget, SpectrumSearchResult spectrumSearchResult)
{
var relatedScoreModelUnits = GetRelatedScoreModelUnits(lipidTarget);
var cidResultList = spectrumSearchResult.CidSearchResultList;
var hcdResultList = spectrumSearchResult.HcdSearchResultList;
var cidMaxIntensity = spectrumSearchResult.CidSpectrum != null && spectrumSearchResult.CidSpectrum.Peaks.Any() ? spectrumSearchResult.CidSpectrum.Peaks.Max(x => x.Intensity) : 1;
var hcdMaxIntensity = spectrumSearchResult.HcdSpectrum != null && spectrumSearchResult.HcdSpectrum.Peaks.Any() ? spectrumSearchResult.HcdSpectrum.Peaks.Max(x => x.Intensity) : 1;
double lipidScore = 0;
if (cidMaxIntensity > 1)
{
// Score CID Results
lipidScore += ScoreSingleFragmentationType(cidResultList, relatedScoreModelUnits, FragmentationType.CID, cidMaxIntensity);
}
if (hcdMaxIntensity > 1)
{
// Score CID Results
lipidScore += ScoreSingleFragmentationType(hcdResultList, relatedScoreModelUnits, FragmentationType.HCD, hcdMaxIntensity);
}
return(lipidScore);
}
private List <ScoreModelUnit> GetRelatedScoreModelUnits(LipidTarget lipidTarget)
{
var lipidClass = lipidTarget.LipidClass;
var lipidType = lipidTarget.LipidType;
var fragmentationMode = lipidTarget.FragmentationMode;
return(ScoreModelUnitList.Where(x => x.LipidClass == lipidClass && x.LipidType == lipidType && x.FragmentationMode == fragmentationMode).ToList());
}
public List <SpectrumSearchResult> RunInformedWorkflow(LipidTarget target, double hcdMassError, double cidMassError)
{
return(RunInformedWorkflow(target, LcMsRun, hcdMassError, cidMassError));
}
public static List <SpectrumSearchResult> RunInformedWorkflow(
LipidTarget target,
LcMsRun lcmsRun,
double hcdMassError,
double cidMassError,
ScoreModel scoreModel = null)
{
IEnumerable <MsMsSearchUnit> msMsSearchUnits = target.GetMsMsSearchUnits();
// I have to subtract an H for the target Ion since InformedProteomics will assume protenated
var targetIon = new Ion(target.Composition - Composition.Hydrogen, 1);
var targetMz = target.MzRounded;
var hcdTolerance = new Tolerance(hcdMassError, ToleranceUnit.Ppm);
var cidTolerance = new Tolerance(cidMassError, ToleranceUnit.Ppm);
var activationMethodCombination = GlobalWorkflow.FigureOutActivationMethodCombination(lcmsRun);
// Find out which MS/MS scans have a precursor m/z that matches the target
//List<int> matchingMsMsScanNumbers = lcmsRun.GetFragmentationSpectraScanNums(targetIon).ToList();
var matchingMsMsScanNumbers = lcmsRun.GetFragmentationSpectraScanNums(targetMz).ToList();
var spectrumSearchResultList = new List <SpectrumSearchResult>();
for (var i = 0; i + 1 < matchingMsMsScanNumbers.Count; i += 2)
{
var firstScanNumber = matchingMsMsScanNumbers[i];
var secondScanNumber = matchingMsMsScanNumbers[i + 1];
// Scan numbers should be consecutive.
/*
* if (secondScanNumber - firstScanNumber != 1)
* {
* i--;
* continue;
* }
* */
ProductSpectrum firstMsMsSpectrum = null;
ProductSpectrum secondMsMsSpectrum = null;
if (activationMethodCombination == ActivationMethodCombination.CidThenHcd ||
activationMethodCombination == ActivationMethodCombination.HcdThenCid)
{
// Lookup the MS/MS Spectrum
firstMsMsSpectrum = lcmsRun.GetSpectrum(firstScanNumber) as ProductSpectrum;
if (firstMsMsSpectrum == null)
{
continue;
}
// Lookup the MS/MS Spectrum
secondMsMsSpectrum = lcmsRun.GetSpectrum(secondScanNumber) as ProductSpectrum;
if (secondMsMsSpectrum == null)
{
continue;
}
}
else if (activationMethodCombination == ActivationMethodCombination.CidOnly ||
activationMethodCombination == ActivationMethodCombination.HcdOnly)
{
firstMsMsSpectrum = lcmsRun.GetSpectrum(firstScanNumber) as ProductSpectrum;
}
if (firstMsMsSpectrum == null)
{
continue;
}
// Filter MS/MS Spectrum based on mass error
var msMsPrecursorMz = firstMsMsSpectrum.IsolationWindow.IsolationWindowTargetMz;
//if (Math.Abs(msMsPrecursorMz - targetMz) > 0.4) continue;
var ppmError = LipidUtil.PpmError(targetMz, msMsPrecursorMz);
if (Math.Abs(ppmError) > hcdMassError)
{
continue;
}
// Assign each MS/MS spectrum to HCD or CID
ProductSpectrum hcdSpectrum;
ProductSpectrum cidSpectrum;
if (firstMsMsSpectrum.ActivationMethod == ActivationMethod.HCD)
{
hcdSpectrum = firstMsMsSpectrum;
cidSpectrum = secondMsMsSpectrum;
}
else
{
hcdSpectrum = secondMsMsSpectrum;
cidSpectrum = firstMsMsSpectrum;
}
// Get all matching peaks
var hcdSearchResultList = hcdSpectrum != null ? (from msMsSearchUnit in msMsSearchUnits let peak = hcdSpectrum.FindPeak(msMsSearchUnit.Mz, hcdTolerance) select new MsMsSearchResult(msMsSearchUnit, peak)).ToList() : new List <MsMsSearchResult>();
var cidSearchResultList = cidSpectrum != null ? (from msMsSearchUnit in msMsSearchUnits let peak = cidSpectrum.FindPeak(msMsSearchUnit.Mz, cidTolerance) select new MsMsSearchResult(msMsSearchUnit, peak)).ToList() : new List <MsMsSearchResult>();
// Find the MS1 data
//Xic xic = lcmsRun.GetPrecursorExtractedIonChromatogram(targetMz, hcdTolerance, firstScanNumber);
var precursorScanNumber = 0;
if (lcmsRun.MinMsLevel == 1) //Make sure there are precursor scans in file
{
precursorScanNumber = lcmsRun.GetPrecursorScanNum(matchingMsMsScanNumbers[i]);
}
var precursorSpectrum = lcmsRun.GetSpectrum(precursorScanNumber);
var xic = lcmsRun.GetFullPrecursorIonExtractedIonChromatogram(targetMz, hcdTolerance);
// Bogus data
if (precursorSpectrum != null && (xic.GetApexScanNum() < 0 || xic.GetSumIntensities() <= 0))
{
continue;
}
SpectrumSearchResult spectrumSearchResult;
if (precursorSpectrum != null)
{
spectrumSearchResult = new SpectrumSearchResult(hcdSpectrum, cidSpectrum, precursorSpectrum, hcdSearchResultList, cidSearchResultList, xic, lcmsRun, scoreModel, target)
{
PrecursorTolerance = new Tolerance(hcdMassError, ToleranceUnit.Ppm)
};
}
else //If there are no precursor scans in this file
{
spectrumSearchResult = new SpectrumSearchResult(hcdSpectrum, cidSpectrum, hcdSearchResultList, cidSearchResultList, lcmsRun, scoreModel, target)
{
PrecursorTolerance = new Tolerance(hcdMassError, ToleranceUnit.Ppm),
};
}
spectrumSearchResultList.Add(spectrumSearchResult);
}
return(spectrumSearchResultList);
}
public void OnLipidTargetChange(LipidTarget lipidTarget)
{
CurrentLipidTarget = lipidTarget;
OnPropertyChanged("CurrentLipidTarget");
}
