public ModificationWithLocation(string id, string modificationType, ModificationMotif motif, TerminusLocalization terminusLocalization, IDictionary <string, IList <string> > linksToOtherDbs = null, List <string> keywords = null) : base(id, modificationType)
        {
            this.motif = motif;
            this.terminusLocalization = terminusLocalization;

            // Optional
            this.linksToOtherDbs = linksToOtherDbs ?? new Dictionary <string, IList <string> >();
            this.keywords        = keywords ?? new List <string>();
        }
Exemple #2
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        private static Tuple <List <PeptideSpectralMatch>, Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >, MassDiffAcceptor, bool, CompactPeptideBase, CompactPeptideBase> GetInfo(bool localizeable)
        {
            CommonParameters CommonParameters = new CommonParameters(digestionParams: new DigestionParams(maxMissedCleavages: 0, minPeptideLength: 1, maxModificationIsoforms: 2, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain, maxModsForPeptides: 1), scoreCutoff: 1);


            // Alanine = Glycine + CH2
            Protein protein1 = new Protein("MA", "protein1");
            Protein protein2 = new Protein("MG", "protein2");
            Protein protein3;
            double  monoisotopicMass = Chemistry.ChemicalFormula.ParseFormula("CH2").MonoisotopicMass;

            ModificationMotif.TryGetMotif("G", out ModificationMotif motif1);
            ModificationMotif.TryGetMotif("A", out ModificationMotif motif2);
            TerminusLocalization        modificationSites          = TerminusLocalization.Any;
            List <ModificationWithMass> allKnownFixedModifications = new List <ModificationWithMass>
            {
                new ModificationWithMass("CH2 on Glycine", null, motif1, modificationSites, monoisotopicMass)
            };
            List <ModificationWithMass> variableModifications;

            ModificationWithMass alanineMod = new ModificationWithMass("CH2 on Alanine", null, motif2, modificationSites, monoisotopicMass);

            if (localizeable)
            {
                variableModifications = new List <ModificationWithMass>();
                IDictionary <int, List <Modification> > oneBasedModifications = new Dictionary <int, List <Modification> >
                {
                    { 2, new List <Modification> {
                          alanineMod
                      } }
                };
                protein3 = new Protein("MA", "protein3", oneBasedModifications: oneBasedModifications);
            }
            else
            {
                variableModifications = new List <ModificationWithMass>();
                variableModifications = new List <ModificationWithMass> {
                    alanineMod
                };
                protein3 = new Protein("MA", "protein3");
            }

            var pepWithSetModifications1 = protein1.Digest(CommonParameters.DigestionParams, allKnownFixedModifications, variableModifications).First();

            var pepWithSetModifications2 = protein2.Digest(CommonParameters.DigestionParams, allKnownFixedModifications, variableModifications).First();

            var pepWithSetModifications3 = protein3.Digest(CommonParameters.DigestionParams, allKnownFixedModifications, variableModifications).Last();

            CompactPeptide compactPeptide1         = new CompactPeptide(pepWithSetModifications1, TerminusType.None);
            CompactPeptide compactPeptideDuplicate = new CompactPeptide(pepWithSetModifications2, TerminusType.None);

            Assert.AreEqual(compactPeptide1, compactPeptideDuplicate);
            CompactPeptide compactPeptide2 = new CompactPeptide(pepWithSetModifications3, TerminusType.None);

            string                  fullFilePath    = null;
            int                     precursorCharge = 0;
            TestDataFile            testDataFile    = new TestDataFile();
            MsDataScan              mzLibScan       = testDataFile.GetOneBasedScan(2);
            Ms2ScanWithSpecificMass scan            = new Ms2ScanWithSpecificMass(mzLibScan, 0, precursorCharge, fullFilePath);
            int                     scanIndex       = 0;
            double                  score           = 0;
            int                     notch           = 0;
            PeptideSpectralMatch    psm1            = new PeptideSpectralMatch(compactPeptide1, notch, score, scanIndex, scan, CommonParameters.DigestionParams);

            psm1.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
            PeptideSpectralMatch psm2 = new PeptideSpectralMatch(compactPeptide1, notch, score, scanIndex, scan, CommonParameters.DigestionParams);

            psm2.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
            PeptideSpectralMatch psm3 = new PeptideSpectralMatch(compactPeptide2, notch, score, scanIndex, scan, CommonParameters.DigestionParams);

            psm3.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
            var newPsms = new List <PeptideSpectralMatch>
            {
                psm1,
                psm2,
                psm3
            };

            MassDiffAcceptor massDiffAcceptors            = new SinglePpmAroundZeroSearchMode(5);
            SequencesToActualProteinPeptidesEngine stappe = new SequencesToActualProteinPeptidesEngine(newPsms, new List <Protein> {
                protein1, protein2, protein3
            },
                                                                                                       allKnownFixedModifications, variableModifications, new List <ProductType> {
                ProductType.B, ProductType.Y
            }, new List <DigestionParams> {
                CommonParameters.DigestionParams
            }, CommonParameters.ReportAllAmbiguity, CommonParameters, new List <string>());

            var haha = (SequencesToActualProteinPeptidesEngineResults)stappe.Run();
            var compactPeptideToProteinPeptideMatching = haha.CompactPeptideToProteinPeptideMatching;

            Assert.AreEqual(2, compactPeptideToProteinPeptideMatching.Count);

            psm1.MatchToProteinLinkedPeptides(compactPeptideToProteinPeptideMatching);

            bool noOneHitWonders = false;

            return(new Tuple <List <PeptideSpectralMatch>, Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >, MassDiffAcceptor, bool, CompactPeptideBase, CompactPeptideBase>
                   (
                       newPsms, compactPeptideToProteinPeptideMatching, massDiffAcceptors, noOneHitWonders, compactPeptide1, compactPeptide2
                   ));
        }
 public ModificationWithMassAndCf(string id, string modificationType, ModificationMotif motif, TerminusLocalization terminusLocalization, ChemicalFormula chemicalFormula, double?mm = null, IDictionary <string, IList <string> > linksToOtherDbs = null, List <string> keywords = null, List <double> neutralLosses = null, List <double> diagnosticIons = null)
     : base(id, modificationType, motif, terminusLocalization, mm ?? chemicalFormula.MonoisotopicMass, linksToOtherDbs, keywords, neutralLosses, diagnosticIons)
 {
     this.chemicalFormula = chemicalFormula;
 }
Exemple #4
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        public ModificationWithMass(string id, string modificationType, ModificationMotif motif, TerminusLocalization terminusLocalization, double monoisotopicMass, IDictionary <string, IList <string> > externalDatabaseReferences = null, List <string> keywords = null, List <double> neutralLosses = null, List <double> diagnosticIons = null)
            : base(id, modificationType, motif, terminusLocalization, externalDatabaseReferences, keywords)
        {
            this.monoisotopicMass = monoisotopicMass;

            // Optional
            this.neutralLosses = neutralLosses ?? new List <double> {
                0
            };
            this.diagnosticIons = diagnosticIons ?? new List <double>();

            this.neutralLosses  = this.neutralLosses.OrderBy(b => b).ToList();
            this.diagnosticIons = this.diagnosticIons.OrderBy(b => b).ToList();
        }