public void Run() { ThermoRawSearchRunSpectrum specRunner = new ThermoRawSearchRunSpectrum(); specRunner.Run(@"C:\Users\iruiz\Downloads\ZC_20171218_H95_R1.raw"); //specRunner.Run(@"C:\Users\rz20\Downloads\ZC_20171218_H95_R1.raw"); ISpectrum spectrum = specRunner.GetSpectrum(7859); ISpectrumMSn msnSpectrum = specRunner.GetSpectrum(7861) as ISpectrumMSn; IMonoMassSpectrumRun monoRunner = new BinSearchMonoMassSpectrumRun(); monoRunner.SetMS1Spectrum(spectrum); monoRunner.Run(msnSpectrum); Console.WriteLine(monoRunner.GetIsotopic()); //ISpectrumProcessing processor = new GeneralPeakPickingSpectrumProcessing(); ////processor.Process(spectrum); //int charge = 4; //double Hydrogen = 1.0078; //int indx = PreciseMatch(1198.48413085938, Find(1198.48413085938, peaks, 10), peaks); //double ppm = UtilMass.Instance.CalcPPM(peaks[indx].GetMZ(), 1198.48413085938); //Console.WriteLine(ppm); //Console.WriteLine(peaks[indx].GetIntensity()); //double mz = peaks[indx].GetMZ(); //Console.WriteLine(peaks[FindMassPeak(mz - Hydrogen/charge, peaks, 5)].GetMZ()); //Console.WriteLine(peaks[FindMassPeak(mz - Hydrogen/charge * 2, peaks, 5)].GetMZ()); //Console.WriteLine(peaks[FindMassPeak(mz - Hydrogen/charge * 3, peaks, 5)].GetMZ()); Console.Read(); }
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(); }