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

        public void WriteSampleProtease(Protease protease)
        {
            if (CurrentStage != Stage.RunSummary)
                throw new ArgumentException("You must be in the Run Summary stage to write proteases");

            _writer.WriteStartElement("sample_enzyme");
            _writer.WriteAttributeString("name", protease.Name);
            _writer.WriteStartElement("specificity");
            _writer.WriteAttributeString("sense", Enum.GetName(typeof (Terminus), protease.Terminal));
            //_writer.WriteAttributeString("pattern", protease.CleavagePattern); // not part of the schema
            _writer.WriteAttributeString("cut", protease.Cut);
            _writer.WriteAttributeString("no_cut", protease.NoCut);
            _writer.WriteEndElement(); // specificity
            _writer.WriteEndElement(); // sample_enzyme
        }

        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();
            }
        }