public virtual void Run(int scan)
{
ISpectrum spectrum = spectrumRunner.GetSpectrum(scan);
if (spectrum.GetMSnOrder() == 1)
{
monoRunner.SetMS1Spectrum(spectrum);
}
else if ((spectrum as ISpectrumMSn).GetActivation() == TypeOfMSActivation.CID)
{
specProcessor.Process(spectrum);
List <IGlycoPeptide> glycoPeptides = null;
if (monoRunner.GetMS1Spectrum() == null)
{
glycoPeptides = precursorMatcher.Match(spectrum);
}
else
{
monoRunner.Run(spectrum as ISpectrumMSn);
glycoPeptides = precursorMatcher.Match(spectrum, monoRunner.GetMonoMass());
}
searchWorker.Search(spectrum, glycoPeptides);
resultTable[scan] = searchWorker.GetResult();
}
}
public virtual void Run(int scan)
{
ISpectrum spectrum = spectrumRunner.GetSpectrum(scan);
if (spectrum.GetMSnOrder() == 1)
{
monoRunner.SetMS1Spectrum(spectrum);
}
else if ((spectrum as ISpectrumMSn).GetActivation() == TypeOfMSActivation.ETD)
{
specProcessor.Process(spectrum);
List <IGlycoPeptide> glycoPeptides = null;
if (monoRunner.GetMS1Spectrum() == null)
{
glycoPeptides = precursorMatcher.Match(spectrum);
}
else
{
monoRunner.Run(spectrum as ISpectrumMSn);
glycoPeptides = precursorMatcher.Match(spectrum, monoRunner.GetMonoMass());
}
searchWorker.Search(spectrum, glycoPeptides);
resultTable[scan] = searchWorker.GetResult();
(discover as IGlycoPeptideScoreResultFDR).AddResult(resultTable[scan]);
//fdr
double mass = (spectrum as ISpectrumMSn).GetParentMZ() + pesudoMZ / (spectrum as ISpectrumMSn).GetParentCharge();
glycoPeptides = precursorMatcher.Match(spectrum, mass);
searchWorker.Search(spectrum, glycoPeptides);
resultFDRTable[scan] = searchWorker.GetResult();
(discover as IGlycoPeptideScoreResultFDR).AddFDRResult(resultFDRTable[scan]);
}
}
public virtual void Search(int scan)
{
ISpectrum spectrum = spectrumFactory.GetSpectrum(scan);
double monoMass = monoMassSpectrumGetter.GetMonoMass(spectrum); //assume read spectrum sequentially
if (spectrum.GetMSnOrder() < 2)
{
return;
}
// filter spectrum
if (spectrumFilter.Filter(spectrum))
{
return;
}
// precursor
spectrumProcessing.Process(spectrum);
List <IGlycoPeptide> glycoPeptides = precursorMatcher.Match(spectrum, monoMass);
// search
List <IScore> scores = new List <IScore>();
foreach (IGlycoPeptide glycoPeptide in glycoPeptides)
{
IScore score = searchEThcDRunner.Search(spectrum, glycoPeptide);
scores.Add(score);
}
// save results
if (scores.Count > 0)
{
double maxScores = scores.Max(x => x.GetScore());
results.Add(spectrum, scores.Where(x => x.GetScore() == maxScores).ToList());
}
}