CSMSL.IO.PepXML.PepXmlWriter.WriteSearchProtease C# (CSharp) Method

        public void WriteSearchProtease(Protease protease, int maxMissedClevages, bool semiDigested = false)
        {
            if (CurrentStage != Stage.SearchSummary)
                throw new ArgumentException("You must be in the Search Summary stage to write modifications");

            _writer.WriteStartElement("enzymatic_search_constraint");
            _writer.WriteAttributeString("enzyme", protease.Name);
            _writer.WriteAttributeString("max_num_internal_clevages", maxMissedClevages.ToString());
            _writer.WriteAttributeString("min_number_termini", (semiDigested) ? "1" : "2");
            _writer.WriteEndElement();
        }

        public static void WritePepXml()
        {
            string filePath = Path.Combine(Examples.BASE_DIRECTORY, "example.pepXML");

            Console.WriteLine("Writting to " + filePath);
            using (PepXmlWriter writer = new PepXmlWriter(filePath))
            {
                writer.WriteSampleProtease(Protease.Trypsin);

                writer.StartSearchSummary("OMSSA", true, true);

                writer.WriteProteinDatabase("Resources/yeast_uniprot_120226.fasta");

                writer.WriteSearchProtease(Protease.Trypsin, 3);

                writer.WriteModification(ModificationDictionary.GetModification("Acetyl"), ModificationSites.K | ModificationSites.NPep);
                writer.WriteModification(ModificationDictionary.GetModification("CAM"), ModificationSites.C);

                writer.WriteModification(ModificationDictionary.GetModification("Phospho"), ModificationSites.S | ModificationSites.T | ModificationSites.Y, false);

                writer.SetCurrentStage(PepXmlWriter.Stage.Spectra, true);

                writer.StartSpectrum(15, 1.234, 523.4324, 3);

                PeptideSpectralMatch psm = new PeptideSpectralMatch(PeptideSpectralMatchScoreType.OmssaEvalue);
                psm.Score = 1.5e-5;
                Protein protein = new Protein("", "Test Protein");
                psm.Peptide = new Peptide("DEREK",protein);
                psm.Charge = 3;
                writer.WritePSM(psm);

                writer.EndSpectrum();
            }
        }