public static void XlTestXlPosCal() { var prot = new Protein("MNNNKQQQQ", null); Protease protease = new Protease("New Custom Protease", new List <Tuple <string, TerminusType> > { new Tuple <string, TerminusType>("K", TerminusType.C) }, new List <Tuple <string, TerminusType> >(), CleavageSpecificity.Full, null, null, null); ProteaseDictionary.Dictionary.Add(protease.Name, protease); DigestionParams digestionParams = new DigestionParams(protease: protease.Name, minPeptideLength: 1, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain); List <ModificationWithMass> variableModifications = new List <ModificationWithMass>(); var ye = prot.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList(); var pep = ye[0]; Assert.AreEqual(pep.BaseSequence, "MNNNK"); CrosslinkerTypeClass crosslinker = new CrosslinkerTypeClass(); crosslinker.SelectCrosslinker(CrosslinkerType.DSS); Assert.AreEqual(crosslinker.CrosslinkerModSites, "K"); Assert.AreEqual(Residue.GetResidue(crosslinker.CrosslinkerModSites).MonoisotopicMass, 128.09496301518999, 1e-9); var n = pep.CompactPeptide(TerminusType.None).NTerminalMasses; var c = pep.CompactPeptide(TerminusType.None).CTerminalMasses; Assert.AreEqual(n.Count(), 4); Assert.AreEqual(c.Count(), 4); Assert.AreEqual(c[0], 128.09496301518999, 1e-6); var x = PsmCross.XlPosCal(pep.CompactPeptide(TerminusType.None), crosslinker.CrosslinkerModSites).ToArray(); Assert.AreEqual(x[0], 4); var pep2 = ye[2]; Assert.AreEqual("MNNNKQQQQ", pep2.BaseSequence); var n2 = pep2.CompactPeptide(TerminusType.None).NTerminalMasses; var c2 = pep2.CompactPeptide(TerminusType.None).CTerminalMasses; Assert.AreEqual(n2.Count(), 8); Assert.AreEqual(c2.Count(), 8); Assert.AreEqual(n2[4] - n2[3], 128.09496301518999, 1e-6); var x2 = PsmCross.XlPosCal(pep2.CompactPeptide(TerminusType.None), crosslinker.CrosslinkerModSites).ToArray(); Assert.AreEqual(x2[0], 4); //Test crosslinker with multiple types of mod var protSTC = new Protein("GASTACK", null); var peps = protSTC.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList(); var pepSTC = peps[0]; Assert.AreEqual(pepSTC.BaseSequence, "GASTACK"); CrosslinkerTypeClass crosslinker2 = new CrosslinkerTypeClass("ST", "C", "crosslinkerSTC", false, -18.01056, 0, 0, 0, 0, 0, 0); string crosslinkerModSitesAll = new string((crosslinker2.CrosslinkerModSites + crosslinker2.CrosslinkerModSites2).ToCharArray().Distinct().ToArray()); Assert.AreEqual(crosslinkerModSitesAll, "STC"); }
public static void XlTestXlPosCal() { var prot = new Protein("MNNNKQQQQ", null); var protease = new Protease("Custom Protease", new List <string> { "K" }, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null); DigestionParams digestionParams = new DigestionParams { InitiatorMethionineBehavior = InitiatorMethionineBehavior.Retain, MaxMissedCleavages = 2, Protease = protease, MinPeptideLength = 1 }; List <ModificationWithMass> variableModifications = new List <ModificationWithMass>(); var ye = prot.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList(); var pep = ye[0]; Assert.AreEqual(pep.BaseSequence, "MNNNK"); CrosslinkerTypeClass crosslinker = new CrosslinkerTypeClass(); crosslinker.SelectCrosslinker(CrosslinkerType.DSS); Assert.AreEqual(crosslinker.CrosslinkerModSite, 'K'); Assert.AreEqual(Residue.GetResidue(crosslinker.CrosslinkerModSite).MonoisotopicMass, 128.09496301518999, 1e-9); var n = pep.CompactPeptide(TerminusType.None).NTerminalMasses; var c = pep.CompactPeptide(TerminusType.None).CTerminalMasses; Assert.AreEqual(n.Count(), 4); Assert.AreEqual(c.Count(), 4); Assert.AreEqual(c[0], 128.09496301518999, 1e-6); var x = PsmCross.XlPosCal(pep.CompactPeptide(TerminusType.None), crosslinker).ToArray(); Assert.AreEqual(x[0], 4); var pep2 = ye[2]; Assert.AreEqual("MNNNKQQQQ", pep2.BaseSequence); var n2 = pep2.CompactPeptide(TerminusType.None).NTerminalMasses; var c2 = pep2.CompactPeptide(TerminusType.None).CTerminalMasses; Assert.AreEqual(n2.Count(), 8); Assert.AreEqual(c2.Count(), 8); Assert.AreEqual(n2[4] - n2[3], 128.09496301518999, 1e-6); var x2 = PsmCross.XlPosCal(pep2.CompactPeptide(TerminusType.None), crosslinker).ToArray(); Assert.AreEqual(x2[0], 4); }
public static void XlTest_BSA_DSSO() { //Generate parameters var commonParameters = new CommonParameters(doPrecursorDeconvolution: false, cIons: true, zDotIons: true, scoreCutoff: 2, digestionParams: new DigestionParams(minPeptideLength: 5)); var xlSearchParameters = new XlSearchParameters { XlCharge_2_3_PrimeFragment = true }; //Create databases contain two protein. var proteinList = new List <Protein> { new Protein("EKVLTSSAR", "Fake01"), new Protein("LSQKFPK", "Fake02") }; ModificationMotif.TryGetMotif("M", out ModificationMotif motif1); ModificationWithMass mod1 = new ModificationWithMass("Oxidation of M", "Common Variable", motif1, TerminusLocalization.Any, 15.99491461957); ModificationMotif.TryGetMotif("C", out ModificationMotif motif2); ModificationWithMass mod2 = new ModificationWithMass("Carbamidomethyl of C", "Common Fixed", motif2, TerminusLocalization.Any, 57.02146372068994); var variableModifications = new List <ModificationWithMass>() { mod1 }; var fixedModifications = new List <ModificationWithMass>() { mod2 }; var localizeableModifications = new List <ModificationWithMass>(); var lp = new List <ProductType> { ProductType.BnoB1ions, ProductType.Y, ProductType.C, ProductType.Zdot }; Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>(); foreach (var mod in fixedModifications) { modsDictionary.Add(mod, 0); } int i = 1; foreach (var mod in variableModifications) { modsDictionary.Add(mod, (ushort)i); i++; } foreach (var mod in localizeableModifications) { modsDictionary.Add(mod, (ushort)i); i++; } //Generate digested peptide lists. List <PeptideWithSetModifications> digestedList = new List <PeptideWithSetModifications>(); foreach (var item in proteinList) { var digested = item.Digest(commonParameters.DigestionParams, fixedModifications, variableModifications).ToList(); digestedList.AddRange(digested); } foreach (var fdfd in digestedList) { fdfd.CompactPeptide(TerminusType.None); } //Run index engine var indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, lp, 1, DecoyType.Reverse, new List <DigestionParams> { commonParameters.DigestionParams }, commonParameters, 30000, new List <string>()); var indexResults = (IndexingResults)indexEngine.Run(); var fragmentIndexCount = indexResults.FragmentIndex.Count(p => p != null); var fragmentIndexAll = indexResults.FragmentIndex.Select((s, j) => new { j, s }).Where(p => p.s != null).Select(t => t.j).ToList(); Assert.IsTrue(fragmentIndexAll.Count() > 0); //Get MS2 scans. var myMsDataFile = new XLTestDataFile(); var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, commonParameters.DoPrecursorDeconvolution, commonParameters.UseProvidedPrecursorInfo, commonParameters.DeconvolutionIntensityRatio, commonParameters.DeconvolutionMaxAssumedChargeState, commonParameters.DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray(); //Generate crosslinker, which is DSSO here. CrosslinkerTypeClass crosslinker = new CrosslinkerTypeClass(); crosslinker.SelectCrosslinker(xlSearchParameters.CrosslinkerType); //TwoPassCrosslinkSearchEngine.Run(). List <PsmCross> newPsms = new List <PsmCross>(); new TwoPassCrosslinkSearchEngine(newPsms, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, lp, 0, commonParameters, false, xlSearchParameters.XlPrecusorMsTl, crosslinker, xlSearchParameters.CrosslinkSearchTop, xlSearchParameters.CrosslinkSearchTopNum, xlSearchParameters.XlQuench_H2O, xlSearchParameters.XlQuench_NH2, xlSearchParameters.XlQuench_Tris, xlSearchParameters.XlCharge_2_3, xlSearchParameters.XlCharge_2_3_PrimeFragment, new List <string> { }).Run(); var compactPeptideToProteinPeptideMatch = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >(); new CrosslinkAnalysisEngine(newPsms, compactPeptideToProteinPeptideMatch, proteinList, variableModifications, fixedModifications, lp, null, crosslinker, TerminusType.None, commonParameters, new List <string> { }).Run(); foreach (var item in newPsms) { item.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false); } //Test newPsms Assert.AreEqual(newPsms.Count(), 3); //Test Output var task = new XLSearchTask(); task.WriteAllToTsv(newPsms, TestContext.CurrentContext.TestDirectory, "allPsms", new List <string> { }); task.WritePepXML_xl(newPsms, proteinList, null, variableModifications, fixedModifications, null, TestContext.CurrentContext.TestDirectory, "pep.XML", new List <string> { }); task.WriteSingleToTsv(newPsms.Where(p => p.CrossType == PsmCrossType.Singe).ToList(), TestContext.CurrentContext.TestDirectory, "singlePsms", new List <string> { }); //Test PsmCross.XlCalculateTotalProductMasses. var psmCrossAlpha = new PsmCross(digestedList[1].CompactPeptide(TerminusType.None), 0, 0, i, listOfSortedms2Scans[0], commonParameters.DigestionParams); var psmCrossBeta = new PsmCross(digestedList[2].CompactPeptide(TerminusType.None), 0, 0, i, listOfSortedms2Scans[0], commonParameters.DigestionParams); var linkPos = PsmCross.XlPosCal(psmCrossAlpha.compactPeptide, crosslinker.CrosslinkerModSites); var productMassesAlphaList = PsmCross.XlCalculateTotalProductMasses(psmCrossAlpha, psmCrossBeta.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.TotalMass, crosslinker, lp, true, false, linkPos); Assert.AreEqual(productMassesAlphaList[0].ProductMz.Length, 99); }
protected override MyTaskResults RunSpecific(string OutputFolder, List <DbForTask> dbFilenameList, List <string> currentRawFileList, string taskId, FileSpecificParameters[] fileSettingsList) { MyTaskResults = new MyTaskResults(this); List <PsmCross> allPsms = new List <PsmCross>(); var compactPeptideToProteinPeptideMatch = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >(); Status("Loading modifications...", taskId); List <ModificationWithMass> variableModifications = GlobalVariables.AllModsKnown.OfType <ModificationWithMass>().Where(b => CommonParameters.ListOfModsVariable.Contains((b.modificationType, b.id))).ToList(); List <ModificationWithMass> fixedModifications = GlobalVariables.AllModsKnown.OfType <ModificationWithMass>().Where(b => CommonParameters.ListOfModsFixed.Contains((b.modificationType, b.id))).ToList(); List <string> localizeableModificationTypes = GlobalVariables.AllModTypesKnown.ToList(); // load proteins List <Protein> proteinList = LoadProteins(taskId, dbFilenameList, true, XlSearchParameters.DecoyType, localizeableModificationTypes, CommonParameters); List <ProductType> ionTypes = new List <ProductType>(); if (CommonParameters.BIons) { ionTypes.Add(ProductType.BnoB1ions); } if (CommonParameters.YIons) { ionTypes.Add(ProductType.Y); } if (CommonParameters.ZdotIons) { ionTypes.Add(ProductType.Zdot); } if (CommonParameters.CIons) { ionTypes.Add(ProductType.C); } TerminusType terminusType = ProductTypeMethods.IdentifyTerminusType(ionTypes); var crosslinker = new CrosslinkerTypeClass(); crosslinker.SelectCrosslinker(XlSearchParameters.CrosslinkerType); if (XlSearchParameters.CrosslinkerType == CrosslinkerType.UserDefined) { crosslinker = GenerateUserDefinedCrosslinker(XlSearchParameters); } MyFileManager myFileManager = new MyFileManager(XlSearchParameters.DisposeOfFileWhenDone); var fileSpecificCommonParams = fileSettingsList.Select(b => SetAllFileSpecificCommonParams(CommonParameters, b)); HashSet <DigestionParams> ListOfDigestionParams = new HashSet <DigestionParams>(fileSpecificCommonParams.Select(p => p.DigestionParams)); int completedFiles = 0; object indexLock = new object(); object psmLock = new object(); Status("Searching files...", taskId); ProseCreatedWhileRunning.Append("The following crosslink discovery were used: "); ProseCreatedWhileRunning.Append("crosslinker name = " + crosslinker.CrosslinkerName + "; "); ProseCreatedWhileRunning.Append("crosslinker type = " + crosslinker.Cleavable + "; "); ProseCreatedWhileRunning.Append("crosslinker mass = " + crosslinker.TotalMass + "; "); ProseCreatedWhileRunning.Append("crosslinker modification site(s) = " + crosslinker.CrosslinkerModSites + "; "); ProseCreatedWhileRunning.Append("protease = " + CommonParameters.DigestionParams.Protease + "; "); ProseCreatedWhileRunning.Append("maximum missed cleavages = " + CommonParameters.DigestionParams.MaxMissedCleavages + "; "); ProseCreatedWhileRunning.Append("minimum peptide length = " + CommonParameters.DigestionParams.MinPeptideLength + "; "); ProseCreatedWhileRunning.Append(CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ? "maximum peptide length = unspecified; " : "maximum peptide length = " + CommonParameters.DigestionParams.MaxPeptideLength + "; "); ProseCreatedWhileRunning.Append("initiator methionine behavior = " + CommonParameters.DigestionParams.InitiatorMethionineBehavior + "; "); ProseCreatedWhileRunning.Append("max modification isoforms = " + CommonParameters.DigestionParams.MaxModificationIsoforms + "; "); ProseCreatedWhileRunning.Append("fixed modifications = " + string.Join(", ", fixedModifications.Select(m => m.id)) + "; "); ProseCreatedWhileRunning.Append("variable modifications = " + string.Join(", ", variableModifications.Select(m => m.id)) + "; "); ProseCreatedWhileRunning.Append("parent mass tolerance(s) = " + XlSearchParameters.XlPrecusorMsTl + "; "); ProseCreatedWhileRunning.Append("product mass tolerance = " + CommonParameters.ProductMassTolerance + "; "); ProseCreatedWhileRunning.Append("The combined search database contained " + proteinList.Count + " total entries including " + proteinList.Where(p => p.IsContaminant).Count() + " contaminant sequences. "); for (int spectraFileIndex = 0; spectraFileIndex < currentRawFileList.Count; spectraFileIndex++) { if (GlobalVariables.StopLoops) { break; } var origDataFile = currentRawFileList[spectraFileIndex]; CommonParameters combinedParams = SetAllFileSpecificCommonParams(CommonParameters, fileSettingsList[spectraFileIndex]); List <PsmCross> newPsms = new List <PsmCross>(); var thisId = new List <string> { taskId, "Individual Spectra Files", origDataFile }; NewCollection(Path.GetFileName(origDataFile), thisId); Status("Loading spectra file...", thisId); MsDataFile myMsDataFile = myFileManager.LoadFile(origDataFile, combinedParams.TopNpeaks, combinedParams.MinRatio, combinedParams.TrimMs1Peaks, combinedParams.TrimMsMsPeaks, combinedParams); Status("Getting ms2 scans...", thisId); Ms2ScanWithSpecificMass[] arrayOfMs2ScansSortedByMass = GetMs2Scans(myMsDataFile, origDataFile, combinedParams.DoPrecursorDeconvolution, combinedParams.UseProvidedPrecursorInfo, combinedParams.DeconvolutionIntensityRatio, combinedParams.DeconvolutionMaxAssumedChargeState, combinedParams.DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray(); for (int currentPartition = 0; currentPartition < CommonParameters.TotalPartitions; currentPartition++) { List <CompactPeptide> peptideIndex = null; List <Protein> proteinListSubset = proteinList.GetRange(currentPartition * proteinList.Count() / combinedParams.TotalPartitions, ((currentPartition + 1) * proteinList.Count() / combinedParams.TotalPartitions) - (currentPartition * proteinList.Count() / combinedParams.TotalPartitions)); Status("Getting fragment dictionary...", new List <string> { taskId }); var indexEngine = new IndexingEngine(proteinListSubset, variableModifications, fixedModifications, ionTypes, currentPartition, UsefulProteomicsDatabases.DecoyType.Reverse, ListOfDigestionParams, combinedParams, 30000.0, new List <string> { taskId }); List <int>[] fragmentIndex = null; lock (indexLock) GenerateIndexes(indexEngine, dbFilenameList, ref peptideIndex, ref fragmentIndex, taskId); Status("Searching files...", taskId); new TwoPassCrosslinkSearchEngine(newPsms, arrayOfMs2ScansSortedByMass, peptideIndex, fragmentIndex, ionTypes, currentPartition, combinedParams, false, XlSearchParameters.XlPrecusorMsTl, crosslinker, XlSearchParameters.CrosslinkSearchTop, XlSearchParameters.CrosslinkSearchTopNum, XlSearchParameters.XlQuench_H2O, XlSearchParameters.XlQuench_NH2, XlSearchParameters.XlQuench_Tris, XlSearchParameters.XlCharge_2_3, XlSearchParameters.XlCharge_2_3_PrimeFragment, thisId).Run(); ReportProgress(new ProgressEventArgs(100, "Done with search " + (currentPartition + 1) + "/" + CommonParameters.TotalPartitions + "!", thisId)); } lock (psmLock) { allPsms.AddRange(newPsms.Where(p => p != null)); } completedFiles++; ReportProgress(new ProgressEventArgs(completedFiles / currentRawFileList.Count, "Searching...", new List <string> { taskId, "Individual Spectra Files" })); } ReportProgress(new ProgressEventArgs(100, "Done with all searches!", new List <string> { taskId, "Individual Spectra Files" })); Status("Crosslink analysis engine", taskId); MetaMorpheusEngineResults allcrosslinkanalysisResults; allcrosslinkanalysisResults = new CrosslinkAnalysisEngine(allPsms, compactPeptideToProteinPeptideMatch, proteinList, variableModifications, fixedModifications, ionTypes, OutputFolder, crosslinker, terminusType, CommonParameters, new List <string> { taskId }).Run(); allPsms = allPsms.ToList(); if (XlSearchParameters.XlOutAll) { try { WriteAllToTsv(allPsms, OutputFolder, "allPsms", new List <string> { taskId }); } catch (Exception) { throw; } } var allPsmsXL = allPsms.Where(p => p.CrossType == PsmCrossType.Cross).Where(p => p.XLBestScore >= CommonParameters.ScoreCutoff && p.BetaPsmCross.XLBestScore >= CommonParameters.ScoreCutoff).ToList(); foreach (var item in allPsmsXL) { if (item.OneBasedStartResidueInProtein.HasValue) { item.XlProteinPos = item.OneBasedStartResidueInProtein.Value + item.XlPos - 1; } if (item.BetaPsmCross.OneBasedStartResidueInProtein.HasValue) { item.BetaPsmCross.XlProteinPos = item.BetaPsmCross.OneBasedStartResidueInProtein.Value + item.BetaPsmCross.XlPos - 1; } } //Write Inter Psms FDR var interPsmsXL = allPsmsXL.Where(p => !p.CompactPeptides.First().Value.Item2.Select(b => b.Protein.Accession).First().Contains(p.BetaPsmCross.CompactPeptides.First().Value.Item2.Select(b => b.Protein.Accession).First()) && !p.BetaPsmCross.CompactPeptides.First().Value.Item2.Select(b => b.Protein.Accession).First().Contains(p.CompactPeptides.First().Value.Item2.Select(b => b.Protein.Accession).First())).OrderByDescending(p => p.XLQvalueTotalScore).ToList(); foreach (var item in interPsmsXL) { item.CrossType = PsmCrossType.Inter; } var interPsmsXLFDR = CrosslinkDoFalseDiscoveryRateAnalysis(interPsmsXL).ToList(); //var interPsmsXLFDR = CrosslinkFDRAnalysis(interPsmsXL).ToList(); if (XlSearchParameters.XlOutCrosslink) { WriteCrosslinkToTsv(interPsmsXLFDR, OutputFolder, "xl_inter_fdr", new List <string> { taskId }); } if (XlSearchParameters.XlOutPercolator) { try { var interPsmsXLPercolator = interPsmsXL.Where(p => p.XLBestScore >= 2 && p.BetaPsmCross.XLBestScore >= 2).OrderBy(p => p.ScanNumber).ToList(); WriteCrosslinkToTxtForPercolator(interPsmsXLPercolator, OutputFolder, "xl_inter_perc", crosslinker, new List <string> { taskId }); } catch (Exception) { throw; } } //Write Intra Psms FDR var intraPsmsXL = allPsmsXL.Where(p => p.CompactPeptides.First().Value.Item2.Select(b => b.Protein.Accession).First() == p.BetaPsmCross.CompactPeptides.First().Value.Item2.Select(b => b.Protein.Accession).First() || p.CompactPeptides.First().Value.Item2.Select(b => b.Protein.Accession).First().Contains(p.BetaPsmCross.CompactPeptides.First().Value.Item2.Select(b => b.Protein.Accession).First()) || p.BetaPsmCross.CompactPeptides.First().Value.Item2.Select(b => b.Protein.Accession).First().Contains(p.CompactPeptides.First().Value.Item2.Select(b => b.Protein.Accession).First())).OrderByDescending(p => p.XLQvalueTotalScore).ToList(); foreach (var item in intraPsmsXL) { item.CrossType = PsmCrossType.Intra; } var intraPsmsXLFDR = CrosslinkDoFalseDiscoveryRateAnalysis(intraPsmsXL).ToList(); //var intraPsmsXLFDR = CrosslinkFDRAnalysis(intraPsmsXL).ToList(); if (XlSearchParameters.XlOutCrosslink) { WriteCrosslinkToTsv(intraPsmsXLFDR, OutputFolder, "xl_intra_fdr", new List <string> { taskId }); } if (XlSearchParameters.XlOutPercolator) { try { var intraPsmsXLPercolator = intraPsmsXL.Where(p => p.XLBestScore >= 2 && p.BetaPsmCross.XLBestScore >= 2).OrderBy(p => p.ScanNumber).ToList(); WriteCrosslinkToTxtForPercolator(intraPsmsXLPercolator, OutputFolder, "xl_intra_perc", crosslinker, new List <string> { taskId }); } catch (Exception) { throw; } } var singlePsms = allPsms.Where(p => p.CrossType == PsmCrossType.Singe && p.FullSequence != null && !p.FullSequence.Contains("Crosslink")).OrderByDescending(p => p.Score).ToList(); var singlePsmsFDR = SingleFDRAnalysis(singlePsms).ToList(); if (XlSearchParameters.XlOutAll) { WriteSingleToTsv(singlePsmsFDR, OutputFolder, "single_fdr", new List <string> { taskId }); } var loopPsms = allPsms.Where(p => p.CrossType == PsmCrossType.Loop).OrderByDescending(p => p.XLTotalScore).ToList(); var loopPsmsFDR = SingleFDRAnalysis(loopPsms).ToList(); if (XlSearchParameters.XlOutAll) { WriteSingleToTsv(loopPsmsFDR, OutputFolder, "loop_fdr", new List <string> { taskId }); } var deadendPsms = allPsms.Where(p => p.CrossType == PsmCrossType.DeadEnd || p.CrossType == PsmCrossType.DeadEndH2O || p.CrossType == PsmCrossType.DeadEndNH2 || p.CrossType == PsmCrossType.DeadEndTris).OrderByDescending(p => p.XLTotalScore).ToList(); deadendPsms.AddRange(allPsms.Where(p => p.CrossType == PsmCrossType.Singe && p.FullSequence != null && p.FullSequence.Contains("Crosslink")).ToList()); var deadendPsmsFDR = SingleFDRAnalysis(deadendPsms).ToList(); if (XlSearchParameters.XlOutAll) { WriteSingleToTsv(deadendPsmsFDR, OutputFolder, "deadend_fdr", new List <string> { taskId }); } if (XlSearchParameters.XlOutPepXML) { List <PsmCross> allPsmsFDR = new List <PsmCross>(); allPsmsFDR.AddRange(intraPsmsXLFDR.Where(p => p.IsDecoy != true && p.BetaPsmCross.IsDecoy != true && p.FdrInfo.QValue <= 0.05).ToList()); allPsmsFDR.AddRange(interPsmsXLFDR.Where(p => p.IsDecoy != true && p.BetaPsmCross.IsDecoy != true && p.FdrInfo.QValue <= 0.05).ToList()); allPsmsFDR.AddRange(singlePsmsFDR.Where(p => p.IsDecoy != true && p.FdrInfo.QValue <= 0.05).ToList()); allPsmsFDR.AddRange(loopPsmsFDR.Where(p => p.IsDecoy != true && p.FdrInfo.QValue <= 0.05).ToList()); allPsmsFDR.AddRange(deadendPsmsFDR.Where(p => p.IsDecoy != true && p.FdrInfo.QValue <= 0.05).ToList()); allPsmsFDR = allPsmsFDR.OrderBy(p => p.ScanNumber).ToList(); foreach (var fullFilePath in currentRawFileList) { string fileNameNoExtension = Path.GetFileNameWithoutExtension(fullFilePath); WritePepXML_xl(allPsmsFDR.Where(p => p.FullFilePath == fullFilePath).ToList(), proteinList, dbFilenameList[0].FilePath, variableModifications, fixedModifications, localizeableModificationTypes, OutputFolder, fileNameNoExtension, new List <string> { taskId }); } } if (XlSearchParameters.XlOutAll) { List <PsmCross> allPsmsXLFDR = new List <PsmCross>(); allPsmsXLFDR.AddRange(intraPsmsXLFDR.Where(p => p.IsDecoy != true && p.BetaPsmCross.IsDecoy != true && p.FdrInfo.QValue <= 0.05).ToList()); allPsmsXLFDR.AddRange(interPsmsXLFDR.Where(p => p.IsDecoy != true && p.BetaPsmCross.IsDecoy != true && p.FdrInfo.QValue <= 0.05).ToList()); try { allPsmsXLFDR = allPsmsXLFDR.OrderByDescending(p => p.XLQvalueTotalScore).ToList(); var allPsmsXLFDRGroup = FindCrosslinks(allPsmsXLFDR); WriteCrosslinkToTsv(allPsmsXLFDRGroup, OutputFolder, "allPsmsXLFDRGroup", new List <string> { taskId }); } catch (Exception) { throw; } } return(MyTaskResults); }
public static void XlTestLocalization() { var CommonParameters = new CommonParameters(); var proteinList = new List <Protein> { new Protein("CASIQKFGERLCVLHEKTPVSEK", null) }; ModificationMotif.TryGetMotif("M", out ModificationMotif motif1); ModificationWithMass mod1 = new ModificationWithMass("Oxidation of M", "Common Variable", motif1, TerminusLocalization.Any, 15.99491461957); ModificationMotif.TryGetMotif("C", out ModificationMotif motif2); ModificationWithMass mod2 = new ModificationWithMass("Carbamidomethyl of C", "Common Fixed", motif2, TerminusLocalization.Any, 57.02146372068994); var variableModifications = new List <ModificationWithMass>() { mod1 }; var fixedModifications = new List <ModificationWithMass>() { mod2 }; var localizeableModifications = new List <ModificationWithMass>(); var lp = new List <ProductType> { ProductType.BnoB1ions, ProductType.Y }; Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>(); foreach (var mod in fixedModifications) { modsDictionary.Add(mod, 0); } int i = 1; foreach (var mod in variableModifications) { modsDictionary.Add(mod, (ushort)i); i++; } foreach (var mod in localizeableModifications) { modsDictionary.Add(mod, (ushort)i); i++; } var engine = new IndexingEngine(proteinList, variableModifications, fixedModifications, lp, 1, DecoyType.Reverse, new List <IDigestionParams> { CommonParameters.DigestionParams }, CommonParameters, 30000, new List <string>()); var results = (IndexingResults)engine.Run(); var digestedList = proteinList[0].Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList(); foreach (var fdfd in digestedList) { fdfd.CompactPeptide(TerminusType.None); //Assert.Contains(fdfd.CompactPeptide(TerminusType.None), results.PeptideIndex); } var productMasses = digestedList[3].CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> { ProductType.B, ProductType.Y }); CrosslinkerTypeClass crosslinker = new CrosslinkerTypeClass(); crosslinker.SelectCrosslinker(CrosslinkerType.DSS); var x = PsmCross.XlPosCal(digestedList[3].CompactPeptide(TerminusType.None), crosslinker).ToArray(); Assert.AreEqual(x[0], 5); var myMsDataFile = new XLTestDataFile(); var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, CommonParameters.DoPrecursorDeconvolution, CommonParameters.UseProvidedPrecursorInfo, CommonParameters.DeconvolutionIntensityRatio, CommonParameters.DeconvolutionMaxAssumedChargeState, CommonParameters.DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray(); var psmCrossAlpha = new PsmCross(digestedList[3].CompactPeptide(TerminusType.None), 0, 0, i, listOfSortedms2Scans[0]); var psmCrossBeta = new PsmCross(digestedList[5].CompactPeptide(TerminusType.None), 0, 0, i, listOfSortedms2Scans[0]); var modMassAlpha1 = psmCrossBeta.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.TotalMass; //Another method to calculate modification mass of cross-linked peptides //var modMassAlpha2 = listOfSortedms2Scans[0].PrecursorMass - psmCrossAlpha.compactPeptide.MonoisotopicMassIncludingFixedMods; var linkPos = PsmCross.XlPosCal(psmCrossAlpha.compactPeptide, crosslinker); var productMassesAlphaList = PsmCross.XlCalculateTotalProductMasses(psmCrossAlpha, modMassAlpha1, crosslinker, lp, true, false, linkPos); Assert.AreEqual(productMassesAlphaList[0].ProductMz.Length, 35); Assert.AreEqual(productMassesAlphaList[0].ProductMz[26], 2312.21985342336); }