public void TestConstruction()
{
NeutralLossCandidates candidates = new NeutralLossCandidates("R.FAS*K.F");
Assert.IsTrue(candidates.CanLossWater);
Assert.IsTrue(candidates.CanLossAmmonia);
Assert.IsFalse(candidates.BLossWater[0]);
Assert.IsFalse(candidates.BLossWater[1]);
Assert.IsTrue(candidates.BLossWater[2]);
Assert.IsTrue(candidates.BLossWater[3]);
Assert.IsFalse(candidates.YLossWater[0]);
Assert.IsTrue(candidates.YLossWater[1]);
Assert.IsTrue(candidates.YLossWater[2]);
Assert.IsTrue(candidates.YLossWater[3]);
Assert.IsFalse(candidates.BLossAmmonia[0]);
Assert.IsFalse(candidates.BLossAmmonia[1]);
Assert.IsFalse(candidates.BLossAmmonia[2]);
Assert.IsTrue(candidates.BLossAmmonia[3]);
Assert.IsTrue(candidates.YLossAmmonia[0]);
Assert.IsTrue(candidates.YLossAmmonia[1]);
Assert.IsTrue(candidates.YLossAmmonia[2]);
Assert.IsTrue(candidates.YLossAmmonia[3]);
}
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);
}
public List <MatchedPeak> GetPhosphoNeutralLossPeaks(IIdentifiedPeptideResult sr, NeutralLossCandidates candidates)
{
List <MatchedPeak> result = new List <MatchedPeak>();
Dictionary <int, string> bModifiedPosition = GetPhosphoModificationPositionMapB(sr.Peptide);
Dictionary <int, string> yModifiedPosition = GetPhosphoModificationPositionMapY(sr.Peptide);
result.AddRange(GetPhosphoNeutralLossPeaks(sr.GetIonSeries()[IonType.B], IonType.B_NEUTRAL_LOSS_PHOSPHO, 1, bModifiedPosition, candidates.BLossWater, candidates.BLossAmmonia));
result.AddRange(GetPhosphoNeutralLossPeaks(sr.GetIonSeries()[IonType.Y], IonType.B_NEUTRAL_LOSS_PHOSPHO, 1, yModifiedPosition, candidates.YLossWater, candidates.YLossAmmonia));
if (sr.ExperimentalPeakList.PrecursorCharge > 1)
{
result.AddRange(GetPhosphoNeutralLossPeaks(sr.GetIonSeries()[IonType.B2], IonType.B_NEUTRAL_LOSS_PHOSPHO, 2, bModifiedPosition, candidates.BLossWater, candidates.BLossAmmonia));
result.AddRange(GetPhosphoNeutralLossPeaks(sr.GetIonSeries()[IonType.Y2], IonType.B_NEUTRAL_LOSS_PHOSPHO, 2, yModifiedPosition, candidates.YLossWater, candidates.YLossAmmonia));
}
return(result);
}