public static String DoJob(ProteinProphetResult ppr, ExclusionProfile exclusionProfile, int experimentNum) { String outputFile = Path.Combine(InputFileOrganizer.OutputFolderOfTheRun, "NumberOfPeptidesPerIdentifiedProtein_" + experimentNum + ".txt"); StreamWriter sw = new StreamWriter(outputFile); sw.WriteLine("Accession\tNumberOfPeptides\tSpectralCount"); List <String> confidentlyIdentifiedProts = ppr.getProteinsIdentified(); foreach (String accession in confidentlyIdentifiedProts) { Protein prot = exclusionProfile.getDatabase().getProtein(accession); HashSet <String> peptidesObserved = new HashSet <String>(); foreach (PeptideScore pepEvidence in prot.getPeptideScore()) { peptidesObserved.Add(pepEvidence.getPeptideSequence()); } sw.WriteLine("{0}\t{1}\t{2}", accession, peptidesObserved.Count, prot.getPeptideScore().Count); } sw.Close(); return(outputFile); }