public static PeptideSpectralMatch GetSilacPsm(PeptideSpectralMatch psm, SilacLabel silacLabel)
{
List <(int Notch, PeptideWithSetModifications Peptide)> updatedBestMatchingPeptides = new List <(int Notch, PeptideWithSetModifications Peptide)>();
foreach ((int Notch, PeptideWithSetModifications Peptide)notchAndPwsm in psm.BestMatchingPeptides)
{
PeptideWithSetModifications modifiedPwsm = CreateSilacPwsm(silacLabel, notchAndPwsm.Peptide);
updatedBestMatchingPeptides.Add((notchAndPwsm.Notch, modifiedPwsm));
}
return(psm.Clone(updatedBestMatchingPeptides));
}
//Needed for parsimony, where there are ambiguous psms
//Quantification ignores ambiguity
public static PeptideSpectralMatch GetSilacPsmFromAmbiguousPsm(PeptideSpectralMatch psm, List <SilacLabel> silacLabels)
{
List <(int Notch, PeptideWithSetModifications Peptide)> updatedBestMatchingPeptides = new List <(int Notch, PeptideWithSetModifications Peptide)>();
foreach ((int Notch, PeptideWithSetModifications Peptide)notchAndPwsm in psm.BestMatchingPeptides)
{
PeptideWithSetModifications pwsm = notchAndPwsm.Peptide;
SilacLabel silacLabel = GetRelevantLabelFromBaseSequence(pwsm.Protein.BaseSequence, silacLabels);
if (silacLabel == null)
{
updatedBestMatchingPeptides.Add(notchAndPwsm);
}
else
{
PeptideWithSetModifications modifiedPwsm = CreateSilacPwsm(true, silacLabel, pwsm); //create light pwsm
updatedBestMatchingPeptides.Add((notchAndPwsm.Notch, modifiedPwsm));
}
}
return(psm.Clone(updatedBestMatchingPeptides));
}
