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 List <T> MatchSpecific(ISpectrum spectrum, double monoMass)
{
List <T> glycoPeptides = new List <T>();
if (spectrum.GetMSnOrder() > 1)
{
int charge = (spectrum as ISpectrumMSn).GetParentCharge();
double precursorMass = calculator.CalcChargeMass(monoMass, charge, option);
MatchPrecursorMass(precursorMass, glycoPeptides);
}
return(glycoPeptides);
}
// assume the spectrum read sequentially
public double GetMonoMass(ISpectrum spectrum)
{
if (spectrum.GetMSnOrder() == 1)
{
List <IPoint> points = new List <IPoint>();
foreach (IPeak pk in spectrum.GetPeaks())
{
points.Add(new PeakPoint(pk));
}
matcher.setData(points);
return(0);
}
ISpectrumMSn spectrumMSn = spectrum as ISpectrumMSn;
double mz = spectrumMSn.GetParentMZ();
double monoMass = mz;
// search isotopic point on full MS spectrum
int charge = spectrumMSn.GetParentCharge();
int isotopic = 0;
while (isotopic < maxIsotopic)
{
double target = mz - Proton / charge * (isotopic + 1);
if (!matcher.Found(new GeneralPoint(target)))
{
break;
}
isotopic++;
}
// get max intensity peak
if (isotopic == 0)
{
return(monoMass);
}
double isoMZ = mz - Proton / charge * isotopic;
List <IPoint> matched = matcher.Search(new GeneralPoint(isoMZ));
return(matched.OrderBy(x => Math.Abs((x as PeakPoint).MZ - isoMZ)).First().GetValue());
}
public bool Filter(ISpectrum spectrum)
{
if (spectrum.GetMSnOrder() > 1)
{
SetMatcher(spectrum);
for (int z = 1; z <= 2; z++)
{
double mz = SpectrumCalcMass.Instance.ComputeMZ(GlycanCalcMass.HexNAc, z);
if (matcher.Found(new GeneralPoint(mz)))
{
return(false);
}
}
return(true);
}
return(false);
}
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());
}
}
public override void Run()
{
IDoubleDigestionPeptidesSearchRun pepRunner = new DoubleDigestionFastaSearchRunPeptides();
pepRunner.SetPeptideCreator(new NGlycosylationPeptideCreator(new DoubleDigestionPeptideCreator()));
IPeptideCreatorParameter parameter = new GeneralPeptideCreatorParameter(Proteases.Trypsin, 2, 7);;
pepRunner.AddPeptideParameter(parameter);
//parameter = new GeneralPeptideCreatorParameter(Proteases.GluC, 2, 7);
//pepRunner.AddPeptideParameter(parameter);
List <IPeptide> peptides = pepRunner.Run(@"C:\Users\iruiz\Downloads\Human_ReviewedCanonical_20201Entries_25thJuly_2017.fasta");
IGlycanCreator glyRunner = new BruteForceNGlycanCreator();
List <IGlycan> glycans = glyRunner.Generate();
//IGlycanGenerator glyRunner = new SimpleGlycanGenerator();
//List<IGlycan> glycans = glyRunner.Generate();
ThermoRawSearchRunSpectrum specRunner = new ThermoRawSearchRunSpectrum();
//specRunner.Run(@"C:\Users\iruiz\Downloads\ZC_20171218_H95_R1.raw");
specRunner.Run(@"C:\Users\iruiz\Downloads\1.raw");
//specRunner.Run(@"C:\Users\rz20\Downloads\1.raw");
Console.Write("scan, ");
Console.Write("peptide, ");
Console.Write("glycan, ");
Console.Write("score, ");
Console.Write("mz, ");
Console.WriteLine("charge");
var watch = new System.Diagnostics.Stopwatch();
watch.Start();
IMonoMassSpectrumRun monoRunner = new BinSearchMonoMassSpectrumRun();
double pretol = 20;
IPrecursorMatcher precursorMatcher = new Y1PeptidesFilterPrecursorMatcher(
new GlycoPeptidePrecursorMatcher(peptides, glycans, pretol), peptides);
IGlycoPeptideScoreFactory searchRunner = new DPSearchSpectrumCID();
for (int i = 10621; i < 10628; i++)
//for (int i = 1; i < specRunner.GetLastScan(); i++)
{
ISpectrum spectrum = specRunner.GetSpectrum(i);
if (spectrum.GetMSnOrder() == 1)
{
monoRunner.SetMS1Spectrum(spectrum);
continue;
}
if ((spectrum as ISpectrumMSn).GetActivation() != TypeOfMSActivation.CID)
{
continue;
}
ISpectrumProcessing processor = new GeneralPeakPickingSpectrumProcessing();
processor.Process(spectrum);
monoRunner.Run(spectrum as ISpectrumMSn);
double mass = monoRunner.GetMonoMass();
List <IGlycoPeptide> glycoPeptides = precursorMatcher.Match(spectrum, mass);
searchRunner.Search(spectrum, glycoPeptides);
IGlycoPeptideScoreResultProduct result = searchRunner.GetResult();
result.MaxScore();
result.Report("test.txt");
}
watch.Stop();
Console.WriteLine($"Execution Time: {watch.ElapsedMilliseconds} ms");
Console.Read();
}
public override void Search(int scan)
{
ISpectrum spectrum = spectrumFactory.GetSpectrum(scan);
double monoMass = monoMassSpectrumGetter.GetMonoMass(spectrum); // assume read spectrum sequentially.
if (spectrum.GetMSnOrder() < 2)
{
return;
}
// ISpectrum filter
if (spectrumFilter.Filter(spectrum))
{
return;
}
// Spectrum Processing
spectrumProcessing.Process(spectrum);
// precursor
List <IGlycoPeptide> glycoPeptides = precursorMatcher.Match(spectrum, monoMass);
double charge = (spectrum as ISpectrumMSn).GetParentCharge();
List <IGlycoPeptide> decoyGlycoPeptides = precursorMatcher.Match(spectrum, monoMass + pesudoMass / charge);
// search
List <IScore> scores = new List <IScore>();
foreach (IGlycoPeptide glycoPeptide in glycoPeptides)
{
IScore score = searchEThcDRunner.Search(spectrum, glycoPeptide);
if (score.GetScore() > 0)
{
IScoreProxy scoreProxy = new FDRScoreProxy(score, true);
scores.Add(scoreProxy);
}
}
List <IScore> decoyScores = new List <IScore>();
foreach (IGlycoPeptide decoyGlycoPeptide in decoyGlycoPeptides)
{
decoyGlycoPeptide.SetPeptide(decoyGlycoPeptide.GetPeptide().Clone());
decoyGlycoPeptide.GetPeptide().SetSequence(Reverse(decoyGlycoPeptide.GetPeptide().GetSequence()));
IScore score = searchEThcDRunner.Search(spectrum, decoyGlycoPeptide);
if (score.GetScore() > 0)
{
IScoreProxy scoreProxy = new FDRScoreProxy(score, false);
decoyScores.Add(scoreProxy);
}
}
// save results
List <IScore> finalScore = new List <IScore>();
if (scores.Count > 0)
{
double maxScores = scores.Max(x => x.GetScore());
finalScore.AddRange(scores.Where(x => x.GetScore() == maxScores).ToList());
}
if (decoyScores.Count > 0)
{
double maxScores = decoyScores.Max(x => x.GetScore());
finalScore.AddRange(decoyScores.Where(x => x.GetScore() == maxScores).ToList());
}
if (finalScore.Count > 0)
{
results.Add(spectrum, finalScore);
}
}
public override void Run()
{
var watch = new System.Diagnostics.Stopwatch();
watch.Start();
IDoubleDigestionPeptidesSearchRun pepRunner = new DoubleDigestionFastaSearchRunPeptides();
pepRunner.SetPeptideCreator(new NGlycosylationPeptideCreator(new DoubleDigestionPeptideCreator()));
IPeptideCreatorParameter parameter = new GeneralPeptideCreatorParameter(Proteases.Trypsin, 2, 7);;
pepRunner.AddPeptideParameter(parameter);
parameter = new GeneralPeptideCreatorParameter(Proteases.GluC, 2, 7);
pepRunner.AddPeptideParameter(parameter);
List <IPeptide> peptides = pepRunner.Run(@"C:\Users\iruiz\Downloads\HP.fasta");
IAccumulatedMSNGlycanCreator glyRunner = new AccumulatedMSBruteForceNGlycanCreator();
List <IAccumulatedGlycanMassProxy> glycans = glyRunner.GenerateSpecific();
//IGlycanGenerator glyRunner = new SimpleGlycanGenerator();
//List<IGlycan> glycans = glyRunner.Generate();
ThermoRawSearchRunSpectrum specRunner = new ThermoRawSearchRunSpectrum();
specRunner.Run(@"C:\Users\iruiz\Downloads\ZC_20171218_H95_R1.raw");
//specRunner.Run(@"C:\Users\rz20\Downloads\1.raw");
Console.Write("scan, ");
Console.Write("peptide, ");
Console.Write("glycan, ");
Console.Write("score, ");
Console.Write("mz, ");
Console.WriteLine("charge");
for (int i = 7861; i < 7862; i++)
{
ISpectrum spectrum = specRunner.GetSpectrum(i);
if (spectrum.GetMSnOrder() == 1)
{
continue;
}
if ((spectrum as ISpectrumMSn).GetActivation() != TypeOfMSActivation.ETD)
{
continue;
}
List <IGlycan> glycanSet = new List <IGlycan>();
glycanSet.AddRange(glycans);
ISpectrumProcessing processor = new GeneralPeakPickingSpectrumProcessing();
processor.Process(spectrum);
double pretol = 20;
IAccumulatedPrecursorMatcher precursorMatcher = new AccumulatedMSNGlycoPeptidePrecursorMatcher(peptides, glycanSet, pretol);
List <IGlycoPeptide> glycoPeptides = precursorMatcher.Match(spectrum);
IGlycoPeptideScoreFactory searchRunner = new BinSearchSpectrumEThcD();
searchRunner.Search(spectrum, glycoPeptides);
IGlycoPeptideScoreResultProduct result = searchRunner.GetResult();
result.MaxScore();
result.Report("test.txt");
}
watch.Stop();
Console.WriteLine($"Execution Time: {watch.ElapsedMilliseconds} ms");
}
