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."); } 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); }
/// <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); } }