protected List <IPeptide> GetPeptidesMethod(string file, string method) { List <IPeptide> peptides = new List <IPeptide>(); string pext = Path.GetExtension(file); IPeptidesSearchRun peptideRunner; switch (pext) { case ".fasta": peptideRunner = new DoubleDigestionFastaSearchRunPeptides(); peptideRunner.SetPeptideCreator(new NGlycosylationPeptideCreator(new DoubleDigestionPeptideCreator())); IPeptideCreatorParameter peptidecreatorParameter; switch (method) { case "Reverse": peptideRunner.SetProteinCreator(new ReverseFastaProteinCreator()); break; case "Normal": break; } foreach (Proteases p in GetProteases()) { peptidecreatorParameter = new GeneralPeptideCreatorParameter(p, parameter.GetMissCleavage(), parameter.GetMiniPeptideLength()); (peptideRunner as IDoubleDigestionPeptidesSearchRun).AddPeptideParameter(peptidecreatorParameter); } peptides = peptideRunner.Run(file); break; } return(peptides); }
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 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"); }