public void Test43KProtein() { var methodName = MethodBase.GetCurrentMethod().Name; Utils.ShowStarting(methodName); // Configure amino acid set var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false); var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false); var dehydroC = new SearchModification(Modification.Dehydro, 'C', SequenceLocation.Everywhere, false); var glutathioneC = new SearchModification(Modification.Glutathione, 'C', SequenceLocation.Everywhere, false); var dethiomethylM = new SearchModification(Modification.Dethiomethyl, 'M', SequenceLocation.Everywhere, false); var deamidatedN = new SearchModification(Modification.Deamidation, 'N', SequenceLocation.Everywhere, false); var deamidatedQ = new SearchModification(Modification.Deamidation, 'Q', SequenceLocation.Everywhere, false); var pyroCarbamidomethylC = new SearchModification(Modification.PyroCarbamidomethyl, 'C', SequenceLocation.ProteinNTerm, false); var phosphoS = new SearchModification(Modification.Phosphorylation, 'S', SequenceLocation.Everywhere, false); var phosphoT = new SearchModification(Modification.Phosphorylation, 'T', SequenceLocation.Everywhere, false); var phosphoY = new SearchModification(Modification.Phosphorylation, 'Y', SequenceLocation.Everywhere, false); var nitrosylC = new SearchModification(Modification.Nitrosyl, 'C', SequenceLocation.Everywhere, false); var nethylmaleimideC = new SearchModification(Modification.Nethylmaleimide, 'C', SequenceLocation.Everywhere, false); const int numMaxModsPerProtein = 4; var searchModifications = new List <SearchModification> { dehydroC, glutathioneC, oxM, dethiomethylM, acetylN, //phosphoS, //phosphoT, //phosphoY, deamidatedN, // deamidatedQ, glutathioneC, pyroCarbamidomethylC, nitrosylC, nethylmaleimideC }; var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein); // var aaSet = new AminoAcidSet(); if (!File.Exists(TestRawFilePath)) { Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath); } var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath); const string protSequence = "AIPQSVEGQSIPSLAPMLERTTPAVVSVAVSGTHVSKQRVPDVFRYFFGPNAPQEQVQERPFRGLGSGVIIDADKGYIVTNNHVIDGADDIQVGLHDGREVKAKLIGTDSESDIALLQIEAKNLVAIKTSDSDELRVGDFAVAIGNPFGLGQTVTSGIVSALGRSGLGIEMLENFIQTDAAINSGNSGGALVNLKGELIGINTAIVAPNGGNVGIGFAIPANMVKNLIAQIAEHGEVRRGVLGIAGRDLDSQLAQGFGLDTQHGGFVNEVSAGSAAEKAGIKAGDIIVSVDGRAIKSFQELRAKVATMGAGAKVELGLIRDGDKKTVNVTLGEANQTTEKAAGAVHPMLQGASLENASKGVEITDVAQGSPAAMSGLQKGDLIVGINRTAVKDLKSLKELLKDQEGAVALKIVRGKSMLYLVLR"; const string annotation = "_." + protSequence + "._"; var seqGraph = SequenceGraph.CreateGraph(aaSet, AminoAcid.ProteinNTerm, protSequence, AminoAcid.ProteinCTerm); if (seqGraph == null) { return; } var ms1Filter = new SimpleMs1Filter(); var ms2ScorerFactory = new ProductScorerBasedOnDeconvolutedSpectra(run); foreach (var ms2ScanNum in Ms2ScanNums) { ms2ScorerFactory.GetScorer(ms2ScanNum); } for (var numNTermCleavages = 0; numNTermCleavages <= 0; numNTermCleavages++) { if (numNTermCleavages > 0) { seqGraph.CleaveNTerm(); } var numProteoforms = seqGraph.GetNumProteoformCompositions(); var modCombs = seqGraph.GetModificationCombinations(); for (var modIndex = 0; modIndex < numProteoforms; modIndex++) { seqGraph.SetSink(modIndex); var protCompositionWithH2O = seqGraph.GetSinkSequenceCompositionWithH2O(); var sequenceMass = protCompositionWithH2O.Mass; var modCombinations = modCombs[modIndex]; foreach (var ms2ScanNum in ms1Filter.GetMatchingMs2ScanNums(sequenceMass)) { var spec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum; if (spec == null) { continue; } var charge = (int) Math.Round(sequenceMass / (spec.IsolationWindow.IsolationWindowTargetMz - Constants.Proton)); var scorer = ms2ScorerFactory.GetMs2Scorer(ms2ScanNum); var score = seqGraph.GetFragmentScore(scorer); if (score <= 3) { continue; } var precursorIon = new Ion(protCompositionWithH2O, charge); var sequence = protSequence.Substring(numNTermCleavages); var pre = numNTermCleavages == 0 ? annotation[0] : annotation[numNTermCleavages + 1]; var post = annotation[annotation.Length - 1]; Console.WriteLine("{0}.{1}.{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}", pre, sequence, post, ms2ScanNum, modCombinations, precursorIon.GetMostAbundantIsotopeMz(), precursorIon.Charge, precursorIon.Composition.Mass, score); } } } }
public void Test43KProtein() { var methodName = MethodBase.GetCurrentMethod().Name; TestUtils.ShowStarting(methodName); // Configure amino acid set var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false); var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false); var dehydroC = new SearchModification(Modification.Dehydro, 'C', SequenceLocation.Everywhere, false); var glutathioneC = new SearchModification(Modification.Glutathione, 'C', SequenceLocation.Everywhere, false); var dethiomethylM = new SearchModification(Modification.Dethiomethyl, 'M', SequenceLocation.Everywhere, false); var deamidatedN = new SearchModification(Modification.Deamidation, 'N', SequenceLocation.Everywhere, false); var deamidatedQ = new SearchModification(Modification.Deamidation, 'Q', SequenceLocation.Everywhere, false); var pyroCarbamidomethylC = new SearchModification(Modification.PyroCarbamidomethyl, 'C', SequenceLocation.ProteinNTerm, false); var phosphoS = new SearchModification(Modification.Phosphorylation, 'S', SequenceLocation.Everywhere, false); var phosphoT = new SearchModification(Modification.Phosphorylation, 'T', SequenceLocation.Everywhere, false); var phosphoY = new SearchModification(Modification.Phosphorylation, 'Y', SequenceLocation.Everywhere, false); var nitrosylC = new SearchModification(Modification.Nitrosyl, 'C', SequenceLocation.Everywhere, false); var nethylmaleimideC = new SearchModification(Modification.Nethylmaleimide, 'C', SequenceLocation.Everywhere, false); const int numMaxModsPerProtein = 4; var searchModifications = new List<SearchModification> { dehydroC, glutathioneC, oxM, dethiomethylM, acetylN, //phosphoS, //phosphoT, //phosphoY, deamidatedN, // deamidatedQ, glutathioneC, pyroCarbamidomethylC, nitrosylC, nethylmaleimideC }; var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein); // var aaSet = new AminoAcidSet(); if (!File.Exists(TestRawFilePath)) { Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath); } var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath); const string protSequence = "AIPQSVEGQSIPSLAPMLERTTPAVVSVAVSGTHVSKQRVPDVFRYFFGPNAPQEQVQERPFRGLGSGVIIDADKGYIVTNNHVIDGADDIQVGLHDGREVKAKLIGTDSESDIALLQIEAKNLVAIKTSDSDELRVGDFAVAIGNPFGLGQTVTSGIVSALGRSGLGIEMLENFIQTDAAINSGNSGGALVNLKGELIGINTAIVAPNGGNVGIGFAIPANMVKNLIAQIAEHGEVRRGVLGIAGRDLDSQLAQGFGLDTQHGGFVNEVSAGSAAEKAGIKAGDIIVSVDGRAIKSFQELRAKVATMGAGAKVELGLIRDGDKKTVNVTLGEANQTTEKAAGAVHPMLQGASLENASKGVEITDVAQGSPAAMSGLQKGDLIVGINRTAVKDLKSLKELLKDQEGAVALKIVRGKSMLYLVLR"; const string annotation = "_." + protSequence + "._"; var seqGraph = SequenceGraph.CreateGraph(aaSet, AminoAcid.ProteinNTerm, protSequence, AminoAcid.ProteinCTerm); if (seqGraph == null) return; var ms1Filter = new SimpleMs1Filter(); var ms2ScorerFactory = new ProductScorerBasedOnDeconvolutedSpectra(run); foreach(var ms2ScanNum in Ms2ScanNums) ms2ScorerFactory.GetScorer(ms2ScanNum); for (var numNTermCleavages = 0; numNTermCleavages <= 0; numNTermCleavages++) { if (numNTermCleavages > 0) seqGraph.CleaveNTerm(); var numProteoforms = seqGraph.GetNumProteoformCompositions(); var modCombs = seqGraph.GetModificationCombinations(); for (var modIndex = 0; modIndex < numProteoforms; modIndex++) { seqGraph.SetSink(modIndex); var protCompositionWithH2O = seqGraph.GetSinkSequenceCompositionWithH2O(); var sequenceMass = protCompositionWithH2O.Mass; var modCombinations = modCombs[modIndex]; foreach (var ms2ScanNum in ms1Filter.GetMatchingMs2ScanNums(sequenceMass)) { var spec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum; if (spec == null) continue; var charge = (int) Math.Round(sequenceMass / (spec.IsolationWindow.IsolationWindowTargetMz - Constants.Proton)); var scorer = ms2ScorerFactory.GetMs2Scorer(ms2ScanNum); var score = seqGraph.GetFragmentScore(scorer); if (score <= 3) continue; var precursorIon = new Ion(protCompositionWithH2O, charge); var sequence = protSequence.Substring(numNTermCleavages); var pre = numNTermCleavages == 0 ? annotation[0] : annotation[numNTermCleavages + 1]; var post = annotation[annotation.Length - 1]; Console.WriteLine("{0}.{1}.{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}", pre, sequence, post, ms2ScanNum, modCombinations, precursorIon.GetMostAbundantIsotopeMz(), precursorIon.Charge, precursorIon.Composition.Mass, score); } } } }