/// <summary>
/// Calculates Metrics based on ChromPeakIqTarget
/// NET Error, Mass Error, Isotopic Fit, & Isotope Correlation
/// </summary>
protected override void ExecuteWorkflow(IqResult result)
{
result.IsExported = false;
if (MSGenerator == null)
{
MSGenerator = MSGeneratorFactory.CreateMSGenerator(Run.MSFileType);
MSGenerator.IsTICRequested = false;
}
var target = result.Target as ChromPeakIqTarget;
if (target == null)
{
throw new NullReferenceException("The ChromPeakAnalyzerIqWorkflow only works with the ChromPeakIqTarget.");
}
MSGenerator.MinMZ = target.MZTheor - 2;
MSGenerator.MaxMZ = target.MZTheor + 5;
//Sums Scan
var lcscanset = _chromPeakUtilities.GetLCScanSetForChromPeak(target.ChromPeak, Run, WorkflowParameters.NumMSScansToSum);
//Generate a mass spectrum
var massSpectrumXYData = MSGenerator.GenerateMS(Run, lcscanset);
//massSpectrumXYData = massSpectrumXYData.TrimData(result.Target.MZTheor - 5, result.Target.MZTheor + 15);
//Find isotopic profile
List <Peak> mspeakList;
result.ObservedIsotopicProfile = TargetedMSFeatureFinder.IterativelyFindMSFeature(massSpectrumXYData, target.TheorIsotopicProfile, out mspeakList);
//Get NET Error
var netError = target.ChromPeak.NETValue - target.ElutionTimeTheor;
var leftOfMonoPeakLooker = new LeftOfMonoPeakLooker();
var peakToTheLeft = leftOfMonoPeakLooker.LookforPeakToTheLeftOfMonoPeak(target.TheorIsotopicProfile.getMonoPeak(), target.ChargeState, mspeakList);
var hasPeakTotheLeft = peakToTheLeft != null;
if (result.ObservedIsotopicProfile == null)
{
result.IsotopicProfileFound = false;
result.FitScore = 1;
}
else
{
//Get fit score
var observedIsoList = result.ObservedIsotopicProfile.Peaklist.Cast <Peak>().ToList();
var minIntensityForScore = 0.05;
var fitScore = PeakFitter.GetFit(target.TheorIsotopicProfile.Peaklist.Select(p => (Peak)p).ToList(), observedIsoList, minIntensityForScore, WorkflowParameters.MSToleranceInPPM);
//get i_score
var iscore = InterferenceScorer.GetInterferenceScore(result.ObservedIsotopicProfile, mspeakList);
//get ppm error
var massErrorInDaltons = TheorMostIntensePeakMassError(target.TheorIsotopicProfile, result.ObservedIsotopicProfile, target.ChargeState);
var ppmError = (massErrorInDaltons / target.MonoMassTheor) * 1e6;
//Get Isotope Correlation
var scan = lcscanset.PrimaryScanNumber;
double chromScanWindowWidth = target.ChromPeak.Width * 2;
//Determines where to start and stop chromatogram correlation
var startScan = scan - (int)Math.Round(chromScanWindowWidth / 2, 0);
var stopScan = scan + (int)Math.Round(chromScanWindowWidth / 2, 0);
result.CorrelationData = ChromatogramCorrelator.CorrelateData(Run, result, startScan, stopScan);
result.LcScanObs = lcscanset.PrimaryScanNumber;
result.ChromPeakSelected = target.ChromPeak;
result.LCScanSetSelected = new ScanSet(lcscanset.PrimaryScanNumber);
result.IsotopicProfileFound = true;
result.FitScore = fitScore;
result.InterferenceScore = iscore;
result.IsIsotopicProfileFlagged = hasPeakTotheLeft;
result.NETError = netError;
result.MassErrorBefore = ppmError;
result.IqResultDetail.MassSpectrum = massSpectrumXYData;
result.Abundance = GetAbundance(result);
}
Display(result);
}
public IsotopicProfileComponent FindBestLabeledProfile(TargetBase target, List <Peak> massSpectrumPeakList, XYData massSpectrumXYData = null)
{
IsotopicProfile bestIso = null;
var bestFitScore = 1.0;
double bestLabelAmount = -1;
Check.Require(target != null, "Target is null. You need a valid target in order to quantify it.");
Check.Require(target.IsotopicProfile != null, "Target's theoretical isotopic profile is null. You need to create it first.");
//create theor profiles to iterate over and use in fitting
_theorLabeledProfiles.Clear();
FitScoreData.Clear();
for (var labelAmount = MinLabelAmount; labelAmount < MaxLabelAmount; labelAmount = labelAmount + StepAmountForIterator)
{
var theorIso = _isoCreator.CreateIsotopicProfileFromEmpiricalFormula(target.EmpiricalFormula,
_elementLabeled, _lightIsotope,
_heavyIsotope, labelAmount,
target.ChargeState);
var indexOfMostAbundantTheorPeak = theorIso.GetIndexOfMostIntensePeak();
var indexOfCorrespondingObservedPeak = PeakUtilities.getIndexOfClosestValue(massSpectrumPeakList,
theorIso.getMostIntensePeak().XValue, 0, massSpectrumPeakList.Count - 1, 0.1);
double fitScore;
var obsPeakListForFitter = new List <Peak>();
if (indexOfCorrespondingObservedPeak < 0) // most abundant peak isn't present in the actual theoretical profile... problem!
{
fitScore = 1;
}
else
{
//double mzOffset = massSpectrumPeakList[indexOfCorrespondingObservedPeak].XValue - theorIso.Peaklist[indexOfMostAbundantTheorPeak].XValue;
var minIntensityForFitting = 0.02;
var theorPeakListForFitter = new List <Peak>(theorIso.Peaklist).Where(p => p.Height > minIntensityForFitting).ToList();
obsPeakListForFitter = FilterPeaksBasedOnBasePeakList(theorPeakListForFitter, massSpectrumPeakList);
AddLeftZeroPads(obsPeakListForFitter, NumLeftZeroPads, theorIso.ChargeState);
AddRightZeroPads(obsPeakListForFitter, NumRightZeroPads, theorIso.ChargeState);
if (IsTheoreticalTrimmedDownToObserved)
{
theorPeakListForFitter = FilterPeaksBasedOnBasePeakList(obsPeakListForFitter, theorPeakListForFitter);
}
//foreach (var peak in obsPeakListForFitter)
//{
// Console.WriteLine(peak.XValue + "\t" + peak.Height);
//}
//foreach (var peak in theorPeakListForFitter)
//{
// Console.WriteLine(peak.XValue + "\t" + peak.Height);
//}
const int numPeaksToTheLeftForScoring = 0;
fitScore = _leastSquaresFitter.GetFit(theorPeakListForFitter, obsPeakListForFitter, 0, 30, numPeaksToTheLeftForScoring, out var ionCountUsed);
//if (double.IsNaN(fitScore) || fitScore > 1) fitScore = 1;
}
if (fitScore < bestFitScore)
{
bestFitScore = fitScore;
if (massSpectrumXYData == null)
{
bestIso = new IsotopicProfile {
Peaklist = new List <MSPeak>()
};
foreach (var peak in obsPeakListForFitter)
{
bestIso.Peaklist.Add(new MSPeak(peak.XValue, peak.Height, peak.Width, 0));
}
bestIso.ChargeState = theorIso.ChargeState;
}
else
{
bestIso = _iterativeTff.IterativelyFindMSFeature(massSpectrumXYData, theorIso);
}
if (bestIso != null)
{
bestIso.Score = fitScore;
}
bestLabelAmount = labelAmount;
}
FitScoreData.Add((decimal)labelAmount, fitScore);
_theorLabeledProfiles.Add(theorIso);
}
var isoComponent = new IsotopicProfileComponent(bestIso, 0, bestLabelAmount);
return(isoComponent);
}
public List <ChromPeakQualityData> GetChromPeakQualityData(Run run, IqTarget target, List <Peak> chromPeakList)
{
var peakQualityList = new List <ChromPeakQualityData>();
if (MSGenerator == null)
{
MSGenerator = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
MSGenerator.IsTICRequested = false;
}
//iterate over peaks within tolerance and score each peak according to MSFeature quality
#if DEBUG
var tempMinScanWithinTol = (int)run.NetAlignmentInfo.GetScanForNet(target.ElutionTimeTheor - Parameters.ChromNETTolerance);
var tempMaxScanWithinTol = (int)run.NetAlignmentInfo.GetScanForNet(target.ElutionTimeTheor + Parameters.ChromNETTolerance);
var tempCenterTol = (int)run.NetAlignmentInfo.GetScanForNet(target.ElutionTimeTheor);
Console.WriteLine("SmartPeakSelector --> NETTolerance= " + Parameters.ChromNETTolerance + "; chromMinCenterMax= " +
tempMinScanWithinTol + "\t" + tempCenterTol + "" +
"\t" + tempMaxScanWithinTol);
Console.WriteLine("MT= " + target.ID + ";z= " + target.ChargeState + "; mz= " + target.MZTheor.ToString("0.000") +
"; ------------------------- PeaksWithinTol = " + chromPeakList.Count);
#endif
//target.NumChromPeaksWithinTolerance = peaksWithinTol.Count;
foreach (ChromPeak chromPeak in chromPeakList)
{
// TODO: Currently hard-coded to sum only 1 scan
var lcscanset = _chromPeakUtilities.GetLCScanSetForChromPeak(chromPeak, run, 1);
//generate a mass spectrum
var massSpectrumXYData = MSGenerator.GenerateMS(run, lcscanset);
//find isotopic profile
var mspeakList = new List <Peak>();
var observedIso = TargetedMSFeatureFinder.IterativelyFindMSFeature(massSpectrumXYData, target.TheorIsotopicProfile, out mspeakList);
double fitScore = 1;
double iscore = 1;
//get fit score
fitScore = FitScoreCalc.CalculateFitScore(target.TheorIsotopicProfile, observedIso, massSpectrumXYData);
//get i_score
iscore = InterferenceScorer.GetInterferenceScore(target.TheorIsotopicProfile, mspeakList);
var leftOfMonoPeakLooker = new LeftOfMonoPeakLooker();
var peakToTheLeft = leftOfMonoPeakLooker.LookforPeakToTheLeftOfMonoPeak(target.TheorIsotopicProfile.getMonoPeak(), target.ChargeState,
mspeakList);
var hasPeakTotheLeft = peakToTheLeft != null;
//collect the results together
var pq = new ChromPeakQualityData(chromPeak);
if (observedIso == null)
{
pq.IsotopicProfileFound = false;
}
else
{
pq.IsotopicProfileFound = true;
pq.Abundance = observedIso.IntensityMostAbundant;
pq.FitScore = fitScore;
pq.InterferenceScore = iscore;
pq.IsotopicProfile = observedIso;
pq.IsIsotopicProfileFlagged = hasPeakTotheLeft;
pq.ScanLc = lcscanset.PrimaryScanNumber;
}
peakQualityList.Add(pq);
#if DEBUG
pq.Display();
#endif
}
return(peakQualityList);
}
protected virtual void ExecuteWorkflow(IqResult result)
{
result.Target.TheorIsotopicProfile = TheorFeatureGen.GenerateTheorProfile(result.Target.EmpiricalFormula, result.Target.ChargeState);
result.IqResultDetail.Chromatogram = ChromGen.GenerateChromatogram(Run, result.Target.TheorIsotopicProfile, result.Target.ElutionTimeTheor);
result.IqResultDetail.Chromatogram = ChromSmoother.Smooth(result.IqResultDetail.Chromatogram);
result.ChromPeakList = ChromPeakDetector.FindPeaks(result.IqResultDetail.Chromatogram);
ChromPeakDetector.CalculateElutionTimes(Run, result.ChromPeakList);
ChromPeakDetector.FilterPeaksOnNET(WorkflowParameters.ChromNETTolerance, result.Target.ElutionTimeTheor, result.ChromPeakList);
result.IqResultDetail.ChromPeakQualityData = ChromPeakAnalyzer.GetChromPeakQualityData(Run, result.Target, result.ChromPeakList);
var filterOutFlagged = result.Target.TheorIsotopicProfile.GetIndexOfMostIntensePeak() == 0;
result.ChromPeakSelected = ChromPeakSelector.SelectBestPeak(result.IqResultDetail.ChromPeakQualityData, filterOutFlagged);
result.LCScanSetSelected = ChromPeakUtilities.GetLCScanSetForChromPeak(result.ChromPeakSelected, Run,
WorkflowParameters.NumMSScansToSum);
result.LcScanObs = result.LCScanSetSelected == null ? -1 : result.LCScanSetSelected.PrimaryScanNumber;
result.IqResultDetail.MassSpectrum = MSGenerator.GenerateMS(Run, result.LCScanSetSelected);
TrimData(result.IqResultDetail.MassSpectrum, result.Target.MZTheor, MsLeftTrimAmount, MsRightTrimAmount);
List <Peak> mspeakList;
result.ObservedIsotopicProfile = MsfeatureFinder.IterativelyFindMSFeature(result.IqResultDetail.MassSpectrum, result.Target.TheorIsotopicProfile, out mspeakList);
result.FitScore = FitScoreCalc.CalculateFitScore(result.Target.TheorIsotopicProfile, result.ObservedIsotopicProfile,
result.IqResultDetail.MassSpectrum);
result.InterferenceScore = InterferenceScorer.GetInterferenceScore(result.ObservedIsotopicProfile, mspeakList);
//if (_workflowParameters.ChromatogramCorrelationIsPerformed)
//{
// ExecuteTask(_chromatogramCorrelator);
//}
result.MonoMassObs = result.ObservedIsotopicProfile == null ? 0 : result.ObservedIsotopicProfile.MonoIsotopicMass;
result.MZObs = result.ObservedIsotopicProfile == null ? 0 : result.ObservedIsotopicProfile.MonoPeakMZ;
result.MZObsCalibrated = result.ObservedIsotopicProfile == null ? 0 : Run.GetAlignedMZ(result.ObservedIsotopicProfile.MonoPeakMZ, result.LcScanObs);
result.MonoMassObsCalibrated = result.ObservedIsotopicProfile == null
? 0
: (result.MZObsCalibrated - DeconTools.Backend.Globals.PROTON_MASS) * result.Target.ChargeState;
var elutionTime = result.ChromPeakSelected == null ? 0d : ((ChromPeak)result.ChromPeakSelected).NETValue;
result.ElutionTimeObs = elutionTime;
result.Abundance = GetAbundance(result);
}
