public List <T> MatchSpecific(ISpectrum spectrum)
{
List <T> glycoPeptides = new List <T>();
if (spectrum.GetMSnOrder() > 1)
{
double mz = (spectrum as ISpectrumMSn).GetParentMZ();
int charge = (spectrum as ISpectrumMSn).GetParentCharge();
double precursorMass = calculator.CalcChargeMass(mz, charge, option);
MatchPrecursorMass(precursorMass, glycoPeptides);
MatchPrecursorMass(precursorMass - Isotope, glycoPeptides);
}
return(glycoPeptides);
}
public List <IPeptide> PeptidesFilter(ISpectrum spectrum)
{
List <IPeptide> peptides = new List <IPeptide>();
List <double> massList = new List <double>();
int parentCharge = (spectrum as ISpectrumMSn).GetParentCharge();
for (int i = 1; i <= parentCharge; i++)
{
foreach (IPeak peak in spectrum.GetPeaks())
{
massList.Add(calcualtor.CalcChargeMass(peak.GetMZ(), i, option));
}
}
if (massList.Count > 0)
{
massList.Sort();
}
foreach (IPeptide peptide in peptideDB)
{
double mass = calcualtor.CalcPeptideMass(peptide, option) + UtilMass.HexNAc;
if (MassBinarySearch.FindPPM(mass, massList, matcher.GetTolerance()))
{
peptides.Add(peptide);
}
}
return(peptides);
}
protected bool MatchPeakGlycoPeptideMass(IPeak peak, int charge, List <double> massList)
{
for (int i = 1; i <= charge; i++)
{
double mass = calculator.CalcChargeMass(peak.GetMZ(), i, option);; // peak.GetMZ() * charge;
if (MassBinarySearch.Find(mass, massList, parameter.GetTolerance()))
{
return(true);
}
}
return(false);
}
protected List <IGlycoPeptide> MatchPoints(IPeak peak, int parentCharge)
{
HashSet <IGlycoPeptide> g = new HashSet <IGlycoPeptide>();
for (int i = 1; i <= parentCharge; i++)
{
double mass = calculator.CalcChargeMass(peak.GetMZ(), i, option);
BinSearchAnnotatedPoint p = new BinSearchAnnotatedPoint(mass);
foreach (Point pt in matcher.GetSearchResult(p, parameter as BinarySearchParameter))
{
g.UnionWith((pt as BinSearchAnnotatedPoint).GetGlycoPeptide());
}
}
return(g.ToList());
}