static void Main(string[] args) { Peptide peptideList = new Peptide(); List<string> peptideSeqList = new List<string>(); string file = "C:\\Users\\Dong\\Desktop\\test.pep.list"; TextReader tr = new StreamReader(file); string line; while ((line = tr.ReadLine()) != null) { string peptide; if (line.Contains(".")) { string[] strs = line.Split('.'); peptide = strs[1]; } else peptide = line; peptideSeqList.Add(peptide); } //remove duplicates of the peptides //make it a unique list peptideSeqList = removeDuplicate(peptideSeqList); //generate the peptide list //by putting the peptide foreach (var pep in peptideSeqList) { //something wrong here!!! peptideList.Add(1, ""); } //Pep2Pro pp = new Pep2Pro(); string database = "C:\\Users\\Dong\\Desktop\\yates.fasta"; ProteomeDataFile foo = new ProteomeDataFile(database); pwiz.CLI.proteome.ProteinList proteinList = foo.proteinList; List<Protein> finalProteinList = new List<Protein>(); for (int i = 0; i < proteinList.size(); i++) { Protein protein = proteinList.protein(i, true); if (!protein.id.Contains("Reverse")) { string sequence = protein.sequence; //Console.WriteLine(protein.index); foreach (var pep in peptideSeqList) { if (sequence.Contains(pep) && !finalProteinList.Contains(protein)) { finalProteinList.Add(protein); } } } } //test //results: got a protein list which corresponding all peptides //the "finalProteinList" is ready for filters. //Console.WriteLine(proteinList.size()); //Console.WriteLine(finalProteinList.Count); //filter by minDistinctPeptides //filter by filterByDistinctPeptides //filterByMinimumCoveringSet //done it! }