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);
}