/// <summary> /// Parses a single line of the input file and returns a single LC-IMS-MS Feature. /// </summary> /// <param name="line">The line to read, as a string.</param> /// <param name="columnMapping">The column mapping for the input file.</param> /// <returns>A single LcImsMsFeature object created by using the information from the parsed line.</returns> private static LcImsMsFeature ParseLine(string line, IDictionary<string, int> columnMapping) { string[] columns = line.Split('\t'); LcImsMsFeature lcImsMsFeature = new LcImsMsFeature(); if (columnMapping.ContainsKey(FEATURE_INDEX)) lcImsMsFeature.FeatureId = int.Parse(columns[columnMapping[FEATURE_INDEX]]); if (columnMapping.ContainsKey(MONOISOTOPIC_MASS)) lcImsMsFeature.MassMonoisotopic = double.Parse(columns[columnMapping[MONOISOTOPIC_MASS]]); if (columnMapping.ContainsKey(LC_SCAN_START)) lcImsMsFeature.ScanLcStart = int.Parse(columns[columnMapping[LC_SCAN_START]]); if (columnMapping.ContainsKey(LC_SCAN_END)) lcImsMsFeature.ScanLcEnd = int.Parse(columns[columnMapping[LC_SCAN_END]]); if (columnMapping.ContainsKey(LC_SCAN_REP)) lcImsMsFeature.ScanLcRep = int.Parse(columns[columnMapping[LC_SCAN_REP]]); // Need to subtract 1 because the isos file reports the IMS Scan as 1-based and the peaks file reports it as 0-based. Need to get Slysz to fix that. if (columnMapping.ContainsKey(IMS_SCAN_REP)) lcImsMsFeature.ScanImsRep = int.Parse(columns[columnMapping[IMS_SCAN_REP]]) - 1; if (columnMapping.ContainsKey(CHARGE_STATE)) lcImsMsFeature.ChargeState = int.Parse(columns[columnMapping[CHARGE_STATE]]); if (columnMapping.ContainsKey(DRIFT_TIME)) lcImsMsFeature.DriftTime = double.Parse(columns[columnMapping[DRIFT_TIME]]); if (columnMapping.ContainsKey(ABUNDANCE)) lcImsMsFeature.Abundance = double.Parse(columns[columnMapping[ABUNDANCE]]); if (columnMapping.ContainsKey(MONOISOTOPIC_MASS) && columnMapping.ContainsKey(CHARGE_STATE)) { double mz = (lcImsMsFeature.MassMonoisotopic / lcImsMsFeature.ChargeState) + GeneralConstants.MASS_OF_PROTON; lcImsMsFeature.MzMonoisotopic = mz; } return lcImsMsFeature; }
/// <summary> /// Executes the cross-link search for LC-IMS-TOF data. /// </summary> /// <param name="settings">Settings object to control parameters for cross-linking.</param> /// <param name="proteinSequenceEnumerable">IEnumerable of protein sequences, as a .NET Bio ISequence object.</param> /// <param name="featureList">List of LC-IMS-MS Features, as LcImsMsFeature.</param> /// <param name="peakList">List of Isotopic Peaks, as IsotopicPeak.</param> /// <returns>An enumerable of CrossLinkResult objects.</returns> public static IList<CrossLinkResult> Execute( CrossLinkSettings settings, IEnumerable<ISequence> proteinSequenceEnumerable, List<LcImsMsFeature> featureList, List<IsotopicPeak> peakList) { var massToleranceBase = settings.MassTolerance; var maxMissedCleavages = settings.MaxMissedCleavages; var digestionRule = settings.TrypticType; CrossLinkUtil.StaticDeltaMass = settings.StaticDeltaMass; CrossLinkUtil.UseC13 = settings.UseC13; CrossLinkUtil.UseN15 = settings.UseN15; Console.WriteLine(); Console.WriteLine("Mass Tolerance: " + massToleranceBase + " ppm"); Console.WriteLine("Max missed cleavages: " + maxMissedCleavages); Console.WriteLine("Digestion rule: " + settings.TrypticType ); Console.WriteLine("Delta mass uses C13: " + settings.UseC13); Console.WriteLine("Delta mass uses N15: " + settings.UseN15); Console.WriteLine("Static delta mass addon: " + settings.StaticDeltaMass + " Da"); // Used for finding Isotopic Profiles in the data var msFeatureFinder = new BasicTFF(); var crossLinkList = new List<CrossLink>(); var lastProgress = DateTime.UtcNow; var proteinsProcessed = 0; // Create CrossLink objects from all of the protein sequences foreach (var proteinSequence in proteinSequenceEnumerable) { var proteinSequenceString = new string(proteinSequence.Select((a => (char)a)).ToArray()); var proteinId = proteinSequence.ID; // Get a List of Peptides from the Protein Sequence var peptideList = SequenceUtil.DigestProtein(proteinSequenceString, digestionRule, maxMissedCleavages); // Find all possible cross links from the peptide list var crossLinkEnumerable = CrossLinkUtil.GenerateTheoreticalCrossLinks(peptideList, proteinSequenceString, proteinId); crossLinkList.AddRange(crossLinkEnumerable); proteinsProcessed++; if (DateTime.UtcNow.Subtract(lastProgress).TotalSeconds >= 15) { lastProgress = DateTime.UtcNow; Console.WriteLine("Creating cross linked peptide list; " + proteinsProcessed + " proteins processed"); } } Console.WriteLine("Sorting cross-linked peptides"); // Sort the CrossLinks by mass so that the results are ordered in a friendly way IEnumerable<CrossLink> orderedCrossLinkEnumerable = crossLinkList.OrderBy(x => x.Mass); // Sort Feature by mass so we can use binary search featureList = featureList.OrderBy(x => x.MassMonoisotopic).ToList(); // Set up a Feature Comparer and Peak Comparer to use for binary search later on var featureComparer = new AnonymousComparer<LcImsMsFeature>((x, y) => x.MassMonoisotopic.CompareTo(y.MassMonoisotopic)); var peakComparer = new AnonymousComparer<IsotopicPeak>((x, y) => x.ScanLc != y.ScanLc ? x.ScanLc.CompareTo(y.ScanLc) : x.ScanIms != y.ScanIms ? x.ScanIms.CompareTo(y.ScanIms) : x.Mz.CompareTo(y.Mz)); // Sort the Isotopic Peaks by LC Scan, IMS Scan, and m/z to set them up for binary search later on peakList.Sort(peakComparer); var crossLinkResultList = new List<CrossLinkResult>(); var totalCandidatePeptides = crossLinkList.Count; Console.WriteLine("Searching isotopic data vs. " + totalCandidatePeptides.ToString("#,##0") + " candidate cross-linked peptides"); lastProgress = DateTime.UtcNow; var crosslinkCandidatesProcessed = 0; // Search the data for the existence of cross-links foreach (var crossLink in orderedCrossLinkEnumerable) { // Calculate mass tolerance to use for binary search var massTolerance = massToleranceBase * crossLink.Mass / GeneralConstants.PPM_DIVISOR; var lowFeature = new LcImsMsFeature { MassMonoisotopic = crossLink.Mass - massTolerance }; var highFeature = new LcImsMsFeature { MassMonoisotopic = crossLink.Mass + massTolerance }; var lowFeaturePosition = featureList.BinarySearch(lowFeature, featureComparer); var highFeaturePosition = featureList.BinarySearch(highFeature, featureComparer); lowFeaturePosition = lowFeaturePosition < 0 ? ~lowFeaturePosition : lowFeaturePosition; highFeaturePosition = highFeaturePosition < 0 ? ~highFeaturePosition : highFeaturePosition; // Iterate over all LC-IMS-MS Features that match the Unmodified cross-link mass for (var i = lowFeaturePosition; i < highFeaturePosition; i++) { var feature = featureList[i]; // Search for a mass shift in each of the LC Scans the unmodified cross-link mass was found for (var currentScanLc = feature.ScanLcStart; currentScanLc <= feature.ScanLcEnd; currentScanLc++) { var crossLinkResult = new CrossLinkResult(crossLink, feature, currentScanLc); var candidatePeaks = PeakUtil.FindCandidatePeaks(peakList, feature.MzMonoisotopic, currentScanLc, feature.ScanImsRep); var massShiftList = crossLink.MassShiftList; var shiftedMassList = new List<double>(); // Calculate the shifted mass values that we want to search for switch (massShiftList.Count) { case 1: { var firstNewMass = feature.MassMonoisotopic + massShiftList[0]; shiftedMassList.Add(firstNewMass); } break; case 2: { var firstNewMass = feature.MassMonoisotopic + massShiftList[0]; var secondNewMass = feature.MassMonoisotopic + massShiftList[1]; var thirdNewMass = feature.MassMonoisotopic + massShiftList[0] + massShiftList[1]; shiftedMassList.Add(firstNewMass); shiftedMassList.Add(secondNewMass); shiftedMassList.Add(thirdNewMass); } break; } // Search for shifted mass values in Isotopic Peaks foreach (var shiftedMass in shiftedMassList) { var shiftedMz = (shiftedMass / feature.ChargeState) + GeneralConstants.MASS_OF_PROTON; // Create theoretical Isotopic Peaks that will later form a theoretical Isotopic Profile var theoreticalPeakList = new List<MSPeak> { new MSPeak { XValue = shiftedMz, Height = 1 } }; for (double k = 1; k < 4; k++) { theoreticalPeakList.Add(new MSPeak { XValue = shiftedMz + (k * 1.003 / feature.ChargeState), Height = (float)(1.0 - (k / 4)) }); theoreticalPeakList.Add(new MSPeak { XValue = shiftedMz - (k * 1.003 / feature.ChargeState), Height = (float)(1.0 - (k / 4)) }); } // Sort peaks by m/z var sortPeaksQuery = from peak in theoreticalPeakList orderby peak.XValue select peak; // Create a theoretical Isotopic Profile for DeconTools to search for var isotopicProfile = new IsotopicProfile { MonoIsotopicMass = shiftedMass, MonoPeakMZ = shiftedMz, ChargeState = feature.ChargeState, Peaklist = sortPeaksQuery.ToList() }; // Search for the theoretical Isotopic Profile var foundProfile = msFeatureFinder.FindMSFeature(candidatePeaks, isotopicProfile, massToleranceBase, false); /* * It is possible that the set mono pass of the previous theoretical distribution was the right-most peak of the actual distribution * If so, we should be able to shift the theoretical distribution over to the left and find the actual distribution */ if (foundProfile == null) { foreach (var msPeak in sortPeaksQuery) { msPeak.XValue -= (1.003 / feature.ChargeState); } isotopicProfile = new IsotopicProfile { MonoIsotopicMass = shiftedMass - 1.003, MonoPeakMZ = shiftedMz - (1.003 / feature.ChargeState), ChargeState = feature.ChargeState, Peaklist = sortPeaksQuery.ToList() }; foundProfile = msFeatureFinder.FindMSFeature(candidatePeaks, isotopicProfile, massToleranceBase, false); } // Add to results, even if we did not find it. var didFindProfile = foundProfile != null; crossLinkResult.MassShiftResults.KvpList.Add(new KeyValuePair<double, bool>(shiftedMass, didFindProfile)); } crossLinkResultList.Add(crossLinkResult); } } crosslinkCandidatesProcessed++; if (DateTime.UtcNow.Subtract(lastProgress).TotalSeconds >= 10) { lastProgress = DateTime.UtcNow; var percentComplete = crosslinkCandidatesProcessed / (double)totalCandidatePeptides * 100; Console.WriteLine("Searching isotopic data; " + percentComplete.ToString("0.0") + "% complete"); } } return crossLinkResultList; }