Exemple #1
0
            public PhosphoRSConfig()
            {
                fragmentMassTolerance = 0.5;
                scoreNLToo            = "true";
                phosphorylationSymbol = 1;
                maxIsoformCount       = 2000;
                maxPTMCount           = 20;
                maxPackageSize        = 3000;

                scoredAA = new phosphoRS.AminoAcidModification(phosphorylationSymbol.ToString()[0], "Phosphorylation", "Pho", "H3PO4", 79.966331, 97.976896, phosphoRS.AminoAcidSequence.ParseAASequence("STY"));
                pwizMod  = new proteome.Modification("H1P1O3");
            }
        private phosphoRS.PeptideSpectrumMatch getPhosphoRS_PSM(PhosphoRSConfig config, PhosphoPeptideAttestationRow variant)
        {
            // Get the phosphorylated peptide and add all modifications to the base sequence.
            proteome.Peptide phosphoPeptide = new proteome.Peptide(variant.UnphosphorylatedSequence, proteome.ModificationParsing.ModificationParsing_Auto, proteome.ModificationDelimiter.ModificationDelimiter_Brackets);
            proteome.ModificationMap variantPeptideMods = phosphoPeptide.modifications();
            variant.OriginalPhosphoSites.Keys.ToList().ForEach(location => { variantPeptideMods[location].Add(config.pwizMod); });

            // This modification ID is used to tell phosphoRS how to modify the sequence.
            int modificationID = config.phosphorylationSymbol + 1;

            // Build a string representation of all modificaitons in a peptide for phospoRS
            // "0.00011000000000.0" : 1 is the ID of the modification. All phosphos in a data
            // set need to have one ID. This ID is used by the PhosphoRS to figure out which
            // mods need to be scored.
            var ptmRepresentation = new StringBuilder();

            // Store all modifications in phosphoRS modification objects
            var modifications = new List<phosphoRS.AminoAcidModification>();

            // Get the n-terminal modifications.
            if (variantPeptideMods.ContainsKey(proteome.ModificationMap.NTerminus()))
            {
                phosphoRS.AminoAcidModification otherMod = new phosphoRS.AminoAcidModification('2', "unknown", "unk", "none", variantPeptideMods[proteome.ModificationMap.NTerminus()].monoisotopicDeltaMass(), 0.0, null);
                modifications.Add(otherMod);
                ptmRepresentation.Append(modificationID.ToString() + ".");
                //++modificationID;
            }
            else
            {
                ptmRepresentation.Append("0.");
            }

            // Process all other modifications.
            for (int aaIndex = 0; aaIndex < phosphoPeptide.sequence.Length; ++aaIndex)
            {
                // If phosphorylation, use the existing scoredAA variable.
                if (variantPeptideMods.ContainsKey(aaIndex))
                {
                    if (variant.OriginalPhosphoSites.Keys.Contains(aaIndex))
                    {
                        modifications.Add(config.scoredAA);
                        ptmRepresentation.Append(config.phosphorylationSymbol.ToString()[0]);
                    }
                    else
                    {
                        // Otherwise, make an "unknown" modification with a separate modification ID.
                        var otherMod = new phosphoRS.AminoAcidModification(modificationID.ToString()[0], "unknown", "unk", "none", variantPeptideMods[aaIndex].monoisotopicDeltaMass(), 0.0, phosphoRS.AminoAcidSequence.ParseAASequence("" + phosphoPeptide.sequence[aaIndex]));
                        modifications.Add(otherMod);
                        ptmRepresentation.Append(modificationID.ToString());
                        //++modificationID;
                    }
                }
                else
                {
                    ptmRepresentation.Append("0");
                }
            }
            // Process any c-terminal modifications.
            if (variantPeptideMods.ContainsKey(proteome.ModificationMap.CTerminus()))
            {
                var otherMod = new phosphoRS.AminoAcidModification(modificationID.ToString()[0], "unknown", "unk", "none", variantPeptideMods[proteome.ModificationMap.CTerminus()].monoisotopicDeltaMass(), 0.0, null);
                modifications.Add(otherMod);
                ptmRepresentation.Append("." + modificationID.ToString());
            }
            else
            {
                ptmRepresentation.Append(".0");
            }

            // Get the phosphoRS peptide sequence.
            // Assign spectrum ID, amino acid sequence, list of all modifications, a so-called 'modification position string' (here every digit represents an amino acid within the peptide sequence
            // '0' indicates not modified, values != '0' indicate the unique identifier of the amino acid's modification the first digit represents the n-terminus the last digit represents the c-terminus)
            var AAS = phosphoRS.AminoAcidSequence.Create((int)variant.SpectrumId, phosphoPeptide.sequence, modifications, ptmRepresentation.ToString());
            // Make a phosphoRS peptide-spectrum match.
            return new phosphoRS.PeptideSpectrumMatch((int)variant.PSMId, variant.SpectrumType, variant.Charge, variant.PrecursorMZ, variant.Peaks, AAS);
        }
            public PhosphoRSConfig()
            {
                fragmentMassTolerance = 0.5;
                scoreNLToo = "true";
                phosphorylationSymbol = 1;
                maxIsoformCount = 2000;
                maxPTMCount = 20;
                maxPackageSize = 3000;

                scoredAA = new phosphoRS.AminoAcidModification(phosphorylationSymbol.ToString()[0], "Phosphorylation", "Pho", "H3PO4", 79.966331, 97.976896, phosphoRS.AminoAcidSequence.ParseAASequence("STY"));
                pwizMod = new proteome.Modification("H1P1O3");
            }
Exemple #4
0
        private phosphoRS.PeptideSpectrumMatch getPhosphoRS_PSM(PhosphoRSConfig config, PhosphoPeptideAttestationRow variant)
        {
            // Get the phosphorylated peptide and add all modifications to the base sequence.
            proteome.Peptide         phosphoPeptide     = new proteome.Peptide(variant.UnphosphorylatedSequence, proteome.ModificationParsing.ModificationParsing_Auto, proteome.ModificationDelimiter.ModificationDelimiter_Brackets);
            proteome.ModificationMap variantPeptideMods = phosphoPeptide.modifications();
            variant.OriginalPhosphoSites.Keys.ToList().ForEach(location => { variantPeptideMods[location].Add(config.pwizMod); });

            // This modification ID is used to tell phosphoRS how to modify the sequence.
            int modificationID = config.phosphorylationSymbol + 1;

            // Build a string representation of all modificaitons in a peptide for phospoRS
            // "0.00011000000000.0" : 1 is the ID of the modification. All phosphos in a data
            // set need to have one ID. This ID is used by the PhosphoRS to figure out which
            // mods need to be scored.
            var ptmRepresentation = new StringBuilder();

            // Store all modifications in phosphoRS modification objects
            var modifications = new List <phosphoRS.AminoAcidModification>();

            // Get the n-terminal modifications.
            if (variantPeptideMods.ContainsKey(proteome.ModificationMap.NTerminus()))
            {
                phosphoRS.AminoAcidModification otherMod = new phosphoRS.AminoAcidModification('2', "unknown", "unk", "none", variantPeptideMods[proteome.ModificationMap.NTerminus()].monoisotopicDeltaMass(), 0.0, null);
                modifications.Add(otherMod);
                ptmRepresentation.Append(modificationID.ToString() + ".");
                //++modificationID;
            }
            else
            {
                ptmRepresentation.Append("0.");
            }

            // Process all other modifications.
            for (int aaIndex = 0; aaIndex < phosphoPeptide.sequence.Length; ++aaIndex)
            {
                // If phosphorylation, use the existing scoredAA variable.
                if (variantPeptideMods.ContainsKey(aaIndex))
                {
                    if (variant.OriginalPhosphoSites.Keys.Contains(aaIndex))
                    {
                        modifications.Add(config.scoredAA);
                        ptmRepresentation.Append(config.phosphorylationSymbol.ToString()[0]);
                    }
                    else
                    {
                        // Otherwise, make an "unknown" modification with a separate modification ID.
                        var otherMod = new phosphoRS.AminoAcidModification(modificationID.ToString()[0], "unknown", "unk", "none", variantPeptideMods[aaIndex].monoisotopicDeltaMass(), 0.0, phosphoRS.AminoAcidSequence.ParseAASequence("" + phosphoPeptide.sequence[aaIndex]));
                        modifications.Add(otherMod);
                        ptmRepresentation.Append(modificationID.ToString());
                        //++modificationID;
                    }
                }
                else
                {
                    ptmRepresentation.Append("0");
                }
            }
            // Process any c-terminal modifications.
            if (variantPeptideMods.ContainsKey(proteome.ModificationMap.CTerminus()))
            {
                var otherMod = new phosphoRS.AminoAcidModification(modificationID.ToString()[0], "unknown", "unk", "none", variantPeptideMods[proteome.ModificationMap.CTerminus()].monoisotopicDeltaMass(), 0.0, null);
                modifications.Add(otherMod);
                ptmRepresentation.Append("." + modificationID.ToString());
            }
            else
            {
                ptmRepresentation.Append(".0");
            }

            // Get the phosphoRS peptide sequence.
            // Assign spectrum ID, amino acid sequence, list of all modifications, a so-called 'modification position string' (here every digit represents an amino acid within the peptide sequence
            // '0' indicates not modified, values != '0' indicate the unique identifier of the amino acid's modification the first digit represents the n-terminus the last digit represents the c-terminus)
            var AAS = phosphoRS.AminoAcidSequence.Create((int)variant.SpectrumId, phosphoPeptide.sequence, modifications, ptmRepresentation.ToString());

            // Make a phosphoRS peptide-spectrum match.
            return(new phosphoRS.PeptideSpectrumMatch((int)variant.PSMId, variant.SpectrumType, variant.Charge, variant.PrecursorMZ, variant.Peaks, AAS));
        }