private void AddIonSeries(GraphPane peakPane, GraphPane ppmPane, PeakList <MatchedPeak> mgf, double mzTolerance, double minIntensity, IPeptideFragmentationBuilder <MatchedPeak> builder, string sequence, Color tagColor) { MatchedPeakUtils.Match(mgf, builder.Build(sequence), mzTolerance, minIntensity); var ionType = builder.SeriesType.ToString(); var matchedIons = (from m in mgf where m.Matched && m.PeakType == builder.SeriesType select m).ToList(); var ppl = new PointPairList(); foreach (var m in matchedIons) { ppl.Add(new PointPair(m.Mz, m.Intensity, m.Information)); } peakPane.AddIndividualLine("", ppl, Color.Black, tagColor); if (ppmPane != null) { var diff = new PointPairList(); foreach (var m in matchedIons) { if (isPPM) { diff.Add(new PointPair(m.Mz, PrecursorUtils.mz2ppm(m.Mz, m.Mz - m.MatchedMZ))); } else { diff.Add(new PointPair(m.Mz, m.Mz - m.MatchedMZ)); } } ppmPane.AddPoints(diff, tagColor); } }
public void Match(IIdentifiedPeptideResult sr) { List <MatchedPeak> expPeaks = sr.ExperimentalPeakList; double minIntensity = sr.ExperimentalPeakList.FindMaxIntensityPeak().Intensity *minIntensityScale; MatchedPeakUtils.Match(expPeaks, sr.GetIonSeries()[ionType], mzTolerance, minIntensity); }
public override void Match(IIdentifiedPeptideResult sr) { PeakList <MatchedPeak> peaks = sr.ExperimentalPeakList; double minBYNeutralLossIntensity = peaks.FindMaxIntensityPeak().Intensity *minBYNeutralLossIntensityScale; NeutralLossCandidates candidates = new NeutralLossCandidates(sr.Peptide); List <MatchedPeak> byNeutralLossPeaks = GetNeutralLossPeaks(sr.GetIonSeries(), sr.ExperimentalPeakList.PrecursorCharge, candidates); MatchedPeakUtils.Match(peaks, byNeutralLossPeaks, PeakMzTolerance, minBYNeutralLossIntensity); }
public override void Match(IIdentifiedPeptideResult sr) { PeakList <MatchedPeak> peaks = sr.ExperimentalPeakList; double minBYNeutralLossIntensity = peaks.FindMaxIntensityPeak().Intensity *minBYNeutralLossIntensityScale; NeutralLossCandidates candidates = new NeutralLossCandidates(sr.Peptide); List <MatchedPeak> byPhosphoNeutralLossPeaks = GetPhosphoNeutralLossPeaks(sr, candidates); //byPhosphoNeutralLossPeaks.ForEach(m => Console.WriteLine(m.DisplayName + "," + m.Mz)); MatchedPeakUtils.Match(peaks, byPhosphoNeutralLossPeaks, PeakMzTolerance, minBYNeutralLossIntensity); }
public override void Match(IIdentifiedPeptideResult sr) { NeutralLossCandidates candidates = new NeutralLossCandidates(sr.Peptide); List <INeutralLossType> nlTypes = GetNeutralLossTypes(candidates.CanLossWater, candidates.CanLossAmmonia); PeakList <MatchedPeak> expPeaks = sr.ExperimentalPeakList; List <MatchedPeak> nlPeaks = GetNeutralLossPeaks(IonType.PRECURSOR_NEUTRAL_LOSS, new MatchedPeak(expPeaks.PrecursorMZ, 0.0, expPeaks.PrecursorCharge), nlTypes, (m => true)); //nlPeaks.ForEach(m => Console.WriteLine(m.DisplayName + "," + m.Mz)); double minNeutralLossIntensity = expPeaks.FindMaxIntensityPeak().Intensity *minPrecursorNeutralLossIntensityScale; MatchedPeakUtils.Match(expPeaks, nlPeaks, PeakMzTolerance, minNeutralLossIntensity); }