/// <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 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);
}
/// <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.");
}
var lcscanset = _chromPeakUtilities.GetLCScanSetForChromPeak(target.ChromPeak, Run, WorkflowParameters.SmartChromPeakSelectorNumMSSummed);
//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);
//Default Worst Scores
double iscore = 1;
//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 O16 profile
var observedIsoList = result.ObservedIsotopicProfile.Peaklist.Cast <Peak>().Take(4).ToList(); //first 4 peaks excludes the O18 double label peak (fifth peak)
var theorPeakList = target.TheorIsotopicProfile.Peaklist.Select(p => (Peak)p).Take(4).ToList();
result.FitScore = PeakFitter.GetFit(theorPeakList, observedIsoList, 0.05, WorkflowParameters.MSToleranceInPPM);
// fit score O18 profile
var o18Iso = ((O16O18IqResult)result).ConvertO16ProfileToO18(target.TheorIsotopicProfile, 4);
theorPeakList = o18Iso.Peaklist.Select(p => (Peak)p).ToList();
observedIsoList = result.ObservedIsotopicProfile.Peaklist.Cast <Peak>().Skip(4).ToList(); //skips the first 4 peaks and thus includes the O18 double label isotopic profile
((O16O18IqResult)result).FitScoreO18Profile = PeakFitter.GetFit(theorPeakList, observedIsoList, 0.05, WorkflowParameters.MSToleranceInPPM);
//get i_score
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;
var sigma = target.ChromPeak.Width / 2.35;
var chromScanWindowWidth = 4 * sigma;
//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.InterferenceScore = iscore;
result.IsIsotopicProfileFlagged = hasPeakTotheLeft;
result.NETError = netError;
result.MassErrorBefore = ppmError;
result.IqResultDetail.MassSpectrum = massSpectrumXYData;
result.Abundance = GetAbundance(result);
}
}
protected override void ExecuteWorkflow(IqResult result)
{
var children = result.Target.ChildTargets().ToList();
foreach (var child in children)
{
child.DoWorkflow();
var childResult = child.GetResult();
var chromPeakLevelResults = childResult.ChildResults();
var filteredChromPeakResults = chromPeakLevelResults.Where(r => r.IsotopicProfileFound).ToList();
childResult.FavoriteChild = SelectBestChromPeakIqResult(childResult, filteredChromPeakResults);
GetDataFromFavoriteChild(childResult);
}
result.FavoriteChild = SelectBestChargeStateChildResult(result);
GetDataFromFavoriteChild(result);
var favResult = result.FavoriteChild;
double?rsquaredVal, slope;
getRsquaredVal(result, out rsquaredVal, out slope);
var favChargeState = result.FavoriteChild == null ? 0 : result.FavoriteChild.Target.ChargeState;
var favMz = result.FavoriteChild == null ? 0 : result.FavoriteChild.Target.MZTheor;
if (!_headerLogged)
{
_headerLogged = true;
IqLogger.Log.Info("\t" + "TargetID" + "\t\t\t" + "M/Z" + "\t" + "Charge" + "\t" + "LCScan" + "\t" + "RSquared" + "\t" + "Slope");
}
IqLogger.Log.Info("\t" + result.Target.ID + "\t\t\t" + favMz.ToString("0.000") + "\t" + favChargeState + "\t" + result.LcScanObs + "\t" + rsquaredVal + "\t" + slope);
//now get the mass spectrum given the info from the favorite child charge state result
if (favResult != null)
{
var scanset = new ScanSetFactory().CreateScanSet(Run, favResult.LCScanSetSelected.PrimaryScanNumber,
WorkflowParameters.NumMSScansToSum);
var selectedChromPeak = favResult.ChromPeakSelected;
var sigma = selectedChromPeak.Width / 2.35;
var chromScanWindowWidth = 4 * sigma;
//Determines where to start and stop chromatogram correlation
var startScan = scanset.PrimaryScanNumber - (int)Math.Round(chromScanWindowWidth / 2, 0);
var stopScan = scanset.PrimaryScanNumber + (int)Math.Round(chromScanWindowWidth / 2, 0);
var massSpectrum = MSGenerator.GenerateMS(Run, scanset);
foreach (var iqTarget in children)
{
var childStateIqResult = (O16O18IqResult)iqTarget.GetResult();
childStateIqResult.IqResultDetail.MassSpectrum = massSpectrum.TrimData(iqTarget.MZTheor - 3, iqTarget.MZTheor + 8);
var mspeakList = _mspeakDetector.FindPeaks(childStateIqResult.IqResultDetail.MassSpectrum.Xvalues,
childStateIqResult.IqResultDetail.MassSpectrum.Yvalues);
childStateIqResult.CorrelationData = ChromatogramCorrelator.CorrelateData(Run, childStateIqResult, startScan, stopScan);
childStateIqResult.CorrelationO16O18SingleLabel = childStateIqResult.GetCorrelationO16O18SingleLabel();
childStateIqResult.CorrelationO16O18DoubleLabel = childStateIqResult.GetCorrelationO16O18DoubleLabel();
childStateIqResult.CorrelationBetweenSingleAndDoubleLabel = childStateIqResult.GetCorrelationBetweenSingleAndDoubleLabel();
childStateIqResult.RatioO16O18DoubleLabel = childStateIqResult.GetRatioO16O18DoubleLabel();
childStateIqResult.RatioO16O18SingleLabel = childStateIqResult.GetRatioO16O18SingleLabel();
childStateIqResult.RatioSingleToDoubleLabel = childStateIqResult.GetRatioSingleToDoubleLabel();
childStateIqResult.ObservedIsotopicProfile = MsfeatureFinder.IterativelyFindMSFeature(childStateIqResult.IqResultDetail.MassSpectrum,
iqTarget.TheorIsotopicProfile);
if (childStateIqResult.ObservedIsotopicProfile != null)
{
var observedIsoList = childStateIqResult.ObservedIsotopicProfile.Peaklist.Cast <Peak>().Take(4).ToList(); //first 4 peaks excludes the O18 double label peak (fifth peak)
var theorPeakList = iqTarget.TheorIsotopicProfile.Peaklist.Select(p => (Peak)p).Take(4).ToList();
childStateIqResult.FitScore = PeakFitter.GetFit(theorPeakList, observedIsoList, 0.05, WorkflowParameters.MSToleranceInPPM);
var o18Iso = childStateIqResult.ConvertO16ProfileToO18(iqTarget.TheorIsotopicProfile, 4);
theorPeakList = o18Iso.Peaklist.Select(p => (Peak)p).ToList();
observedIsoList = childStateIqResult.ObservedIsotopicProfile.Peaklist.Cast <Peak>().Skip(4).ToList(); //skips the first 4 peaks and thus includes the O18 double label isotopic profile
childStateIqResult.FitScoreO18Profile = PeakFitter.GetFit(theorPeakList, observedIsoList, 0.05, WorkflowParameters.MSToleranceInPPM);
childStateIqResult.InterferenceScore = InterferenceScorer.GetInterferenceScore(childStateIqResult.ObservedIsotopicProfile, mspeakList);
childStateIqResult.MZObs = childStateIqResult.ObservedIsotopicProfile.MonoPeakMZ;
childStateIqResult.MonoMassObs = childStateIqResult.ObservedIsotopicProfile.MonoIsotopicMass;
childStateIqResult.MZObsCalibrated = Run.GetAlignedMZ(childStateIqResult.MZObs);
childStateIqResult.MonoMassObsCalibrated = (childStateIqResult.MZObsCalibrated - DeconTools.Backend.Globals.PROTON_MASS) * childStateIqResult.Target.ChargeState;
childStateIqResult.ElutionTimeObs = ((ChromPeak)favResult.ChromPeakSelected).NETValue;
}
else
{
childStateIqResult.FitScore = -1;
childStateIqResult.InterferenceScore = -1;
}
getRsquaredVal(childStateIqResult, out rsquaredVal, out slope);
IqLogger.Log.Info("\t\t\t" + childStateIqResult.Target.ID + "\t" + childStateIqResult.Target.MZTheor.ToString("0.000") + "\t" + childStateIqResult.Target.ChargeState
+ "\t" + childStateIqResult.LcScanObs + "\t" + childStateIqResult.FitScore.ToString("0.000") + "\t" + rsquaredVal + "\t" + slope);
childStateIqResult.LCScanSetSelected = favResult.LCScanSetSelected;
childStateIqResult.LcScanObs = favResult.LcScanObs;
if (GraphsAreOutputted)
{
if (_graphGenerator == null)
{
_graphGenerator = new BasicGraphControl();
}
ExportGraphs(childStateIqResult);
}
}
}
}
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);
}
