private ChromatogramRequestDocument GetChromatogramRequestDocument(SpectrumFilter spectrumFilter) { ChromatogramRequestDocument chromatogramRequestDocument = spectrumFilter.ToChromatogramRequestDocument(); if (null == _retentionTimePredictor) { return(chromatogramRequestDocument); } var peptidesBySequence = new Dictionary <string, PeptideDocNode>(); foreach (var peptide in _srmDocument.Molecules) { peptidesBySequence[peptide.RawTextId] = peptide; } var chromatogramGroups = new List <ChromatogramRequestDocumentChromatogramGroup>(); foreach (var chromatogramGroup in chromatogramRequestDocument.ChromatogramGroup) { PeptideDocNode peptideDocNode = null; if (!string.IsNullOrEmpty(chromatogramGroup.ModifiedSequence)) { peptidesBySequence.TryGetValue(chromatogramGroup.ModifiedSequence, out peptideDocNode); } bool isFirstPassPeptide = peptideDocNode != null && _retentionTimePredictor.IsFirstPassPeptide(peptideDocNode); if (_firstPass == isFirstPassPeptide) { chromatogramGroups.Add(chromatogramGroup); } } chromatogramRequestDocument.ChromatogramGroup = chromatogramGroups.ToArray(); return(chromatogramRequestDocument); }
public SpectrumFilter(SrmDocument document, MsDataFileUri msDataFileUri, IFilterInstrumentInfo instrumentInfo, IRetentionTimePredictor retentionTimePredictor = null, bool firstPass = false) { _fullScan = document.Settings.TransitionSettings.FullScan; _instrument = document.Settings.TransitionSettings.Instrument; _acquisitionMethod = _fullScan.AcquisitionMethod; if (instrumentInfo != null) { _isWatersFile = instrumentInfo.IsWatersFile; } IsFirstPass = firstPass; var comparer = PrecursorTextId.PrecursorTextIdComparerInstance; var dictPrecursorMzToFilter = new SortedDictionary <PrecursorTextId, SpectrumFilterPair>(comparer); if (EnabledMs || EnabledMsMs) { if (EnabledMs) { _isHighAccMsFilter = !Equals(_fullScan.PrecursorMassAnalyzer, FullScanMassAnalyzerType.qit); if (!firstPass) { var key = new PrecursorTextId(SignedMz.ZERO, null, ChromExtractor.summed); // TIC dictPrecursorMzToFilter.Add(key, new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, dictPrecursorMzToFilter.Count, _instrument.MinTime, _instrument.MaxTime, null, null, 0, _isHighAccMsFilter, _isHighAccProductFilter)); key = new PrecursorTextId(SignedMz.ZERO, null, ChromExtractor.base_peak); // BPC dictPrecursorMzToFilter.Add(key, new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, dictPrecursorMzToFilter.Count, _instrument.MinTime, _instrument.MaxTime, null, null, 0, _isHighAccMsFilter, _isHighAccProductFilter)); } } if (EnabledMsMs) { _isHighAccProductFilter = !Equals(_fullScan.ProductMassAnalyzer, FullScanMassAnalyzerType.qit); if (_fullScan.AcquisitionMethod == FullScanAcquisitionMethod.DIA && _fullScan.IsolationScheme.IsAllIons) { if (instrumentInfo != null) { _isWatersMse = _isWatersFile; _isAgilentMse = instrumentInfo.IsAgilentFile; } _mseLevel = 1; } } Func <double, double> calcWindowsQ1 = _fullScan.GetPrecursorFilterWindow; Func <double, double> calcWindowsQ3 = _fullScan.GetProductFilterWindow; _minTime = _instrument.MinTime; _maxTime = _instrument.MaxTime; bool canSchedule = CanSchedule(document, retentionTimePredictor); // TODO: Figure out a way to turn off time sharing on first SIM scan so that // times can be shared for MS1 without SIM scans _isSharedTime = !canSchedule; // If we're using bare measured drift times from spectral libraries, go get those now var libraryIonMobilityInfo = document.Settings.PeptideSettings.Prediction.UseLibraryDriftTimes ? document.Settings.GetIonMobilities(msDataFileUri) : null; foreach (var nodePep in document.Molecules) { if (firstPass && !retentionTimePredictor.IsFirstPassPeptide(nodePep)) { continue; } foreach (TransitionGroupDocNode nodeGroup in nodePep.Children) { if (nodeGroup.Children.Count == 0) { continue; } double? minTime = _minTime, maxTime = _maxTime; double? startDriftTimeMsec = null, endDriftTimeMsec = null; double windowDT; double highEnergyDriftTimeOffsetMsec = 0; DriftTimeInfo centerDriftTime = document.Settings.PeptideSettings.Prediction.GetDriftTime( nodePep, nodeGroup, libraryIonMobilityInfo, out windowDT); if (centerDriftTime.DriftTimeMsec(false).HasValue) { startDriftTimeMsec = centerDriftTime.DriftTimeMsec(false) - windowDT / 2; // Get the low energy drift time endDriftTimeMsec = startDriftTimeMsec + windowDT; highEnergyDriftTimeOffsetMsec = centerDriftTime.HighEnergyDriftTimeOffsetMsec; } if (canSchedule) { if (RetentionTimeFilterType.scheduling_windows == _fullScan.RetentionTimeFilterType) { double?centerTime = null; double windowRT = 0; if (retentionTimePredictor != null) { centerTime = retentionTimePredictor.GetPredictedRetentionTime(nodePep); } else { var prediction = document.Settings.PeptideSettings.Prediction; if (prediction.RetentionTime == null || !prediction.RetentionTime.IsAutoCalculated) { centerTime = document.Settings.PeptideSettings.Prediction.PredictRetentionTimeForChromImport( document, nodePep, nodeGroup, out windowRT); } } // Force the center time to be at least zero if (centerTime.HasValue && centerTime.Value < 0) { centerTime = 0; } if (_fullScan.RetentionTimeFilterLength != 0) { windowRT = _fullScan.RetentionTimeFilterLength * 2; } if (centerTime != null) { double startTime = centerTime.Value - windowRT / 2; double endTime = startTime + windowRT; minTime = Math.Max(minTime ?? 0, startTime); maxTime = Math.Min(maxTime ?? double.MaxValue, endTime); } } else if (RetentionTimeFilterType.ms2_ids == _fullScan.RetentionTimeFilterType) { var times = document.Settings.GetBestRetentionTimes(nodePep, msDataFileUri); if (times.Length > 0) { minTime = Math.Max(minTime ?? 0, times.Min() - _fullScan.RetentionTimeFilterLength); maxTime = Math.Min(maxTime ?? double.MaxValue, times.Max() + _fullScan.RetentionTimeFilterLength); } } } SpectrumFilterPair filter; string textId = nodePep.RawTextId; // Modified Sequence for peptides, or some other string for custom ions var mz = new SignedMz(nodeGroup.PrecursorMz, nodeGroup.PrecursorCharge < 0); var key = new PrecursorTextId(mz, textId, ChromExtractor.summed); if (!dictPrecursorMzToFilter.TryGetValue(key, out filter)) { filter = new SpectrumFilterPair(key, nodePep.Color, dictPrecursorMzToFilter.Count, minTime, maxTime, startDriftTimeMsec, endDriftTimeMsec, highEnergyDriftTimeOffsetMsec, _isHighAccMsFilter, _isHighAccProductFilter); dictPrecursorMzToFilter.Add(key, filter); } if (!EnabledMs) { filter.AddQ3FilterValues(from TransitionDocNode nodeTran in nodeGroup.Children select nodeTran.Mz, calcWindowsQ3); } else if (!EnabledMsMs) { filter.AddQ1FilterValues(GetMS1MzValues(nodeGroup), calcWindowsQ1); } else { filter.AddQ1FilterValues(GetMS1MzValues(nodeGroup), calcWindowsQ1); filter.AddQ3FilterValues(from TransitionDocNode nodeTran in nodeGroup.Children where !nodeTran.IsMs1 select nodeTran.Mz, calcWindowsQ3); } } } _filterMzValues = dictPrecursorMzToFilter.Values.ToArray(); var listChromKeyFilterIds = new List <ChromKey>(); foreach (var spectrumFilterPair in _filterMzValues) { spectrumFilterPair.AddChromKeys(listChromKeyFilterIds); } _productChromKeys = listChromKeyFilterIds.ToArray(); // Sort a copy of the filter pairs by maximum retention time so that we can detect when // filters are no longer active. _filterRTValues = new SpectrumFilterPair[_filterMzValues.Length]; Array.Copy(_filterMzValues, _filterRTValues, _filterMzValues.Length); Array.Sort(_filterRTValues, CompareByRT); } InitRTLimits(); }
public SpectrumFilter(SrmDocument document, MsDataFileUri msDataFileUri, IFilterInstrumentInfo instrumentInfo, IRetentionTimePredictor retentionTimePredictor = null, bool firstPass = false) { _fullScan = document.Settings.TransitionSettings.FullScan; _instrument = document.Settings.TransitionSettings.Instrument; _acquisitionMethod = _fullScan.AcquisitionMethod; if (instrumentInfo != null) _isWatersFile = instrumentInfo.IsWatersFile; IsFirstPass = firstPass; var comparer = PrecursorTextId.PrecursorTextIdComparerInstance; var dictPrecursorMzToFilter = new SortedDictionary<PrecursorTextId, SpectrumFilterPair>(comparer); if (EnabledMs || EnabledMsMs) { if (EnabledMs) { _isHighAccMsFilter = !Equals(_fullScan.PrecursorMassAnalyzer, FullScanMassAnalyzerType.qit); if (!firstPass) { var key = new PrecursorTextId(0, null, ChromExtractor.summed); // TIC dictPrecursorMzToFilter.Add(key, new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, dictPrecursorMzToFilter.Count, _instrument.MinTime, _instrument.MaxTime, null, null, 0, _isHighAccMsFilter, _isHighAccProductFilter)); key = new PrecursorTextId(0, null, ChromExtractor.base_peak); // BPC dictPrecursorMzToFilter.Add(key, new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, dictPrecursorMzToFilter.Count, _instrument.MinTime, _instrument.MaxTime, null, null, 0, _isHighAccMsFilter, _isHighAccProductFilter)); } } if (EnabledMsMs) { _isHighAccProductFilter = !Equals(_fullScan.ProductMassAnalyzer, FullScanMassAnalyzerType.qit); if (_fullScan.AcquisitionMethod == FullScanAcquisitionMethod.DIA && _fullScan.IsolationScheme.IsAllIons) { if (instrumentInfo != null) { _isWatersMse = _isWatersFile; _isAgilentMse = instrumentInfo.IsAgilentFile; } _mseLevel = 1; } } Func<double, double> calcWindowsQ1 = _fullScan.GetPrecursorFilterWindow; Func<double, double> calcWindowsQ3 = _fullScan.GetProductFilterWindow; _minTime = _instrument.MinTime; _maxTime = _instrument.MaxTime; bool canSchedule = CanSchedule(document, retentionTimePredictor); // TODO: Figure out a way to turn off time sharing on first SIM scan so that // times can be shared for MS1 without SIM scans _isSharedTime = !canSchedule; // If we're using bare measured drift times from spectral libraries, go get those now var libraryIonMobilityInfo = document.Settings.PeptideSettings.Prediction.UseLibraryDriftTimes ? document.Settings.GetIonMobilities(msDataFileUri) : null; foreach (var nodePep in document.Molecules) { if (firstPass && !retentionTimePredictor.IsFirstPassPeptide(nodePep)) continue; foreach (TransitionGroupDocNode nodeGroup in nodePep.Children) { if (nodeGroup.Children.Count == 0) continue; double? minTime = _minTime, maxTime = _maxTime; double? startDriftTimeMsec = null, endDriftTimeMsec = null; double windowDT; double highEnergyDriftTimeOffsetMsec = 0; DriftTimeInfo centerDriftTime = document.Settings.PeptideSettings.Prediction.GetDriftTime( nodePep, nodeGroup, libraryIonMobilityInfo, out windowDT); if (centerDriftTime.DriftTimeMsec(false).HasValue) { startDriftTimeMsec = centerDriftTime.DriftTimeMsec(false) - windowDT / 2; // Get the low energy drift time endDriftTimeMsec = startDriftTimeMsec + windowDT; highEnergyDriftTimeOffsetMsec = centerDriftTime.HighEnergyDriftTimeOffsetMsec; } if (canSchedule) { if (RetentionTimeFilterType.scheduling_windows == _fullScan.RetentionTimeFilterType) { double? centerTime = null; double windowRT = 0; if (retentionTimePredictor != null) { centerTime = retentionTimePredictor.GetPredictedRetentionTime(nodePep); } else { var prediction = document.Settings.PeptideSettings.Prediction; if (prediction.RetentionTime == null || !prediction.RetentionTime.IsAutoCalculated) { centerTime = document.Settings.PeptideSettings.Prediction.PredictRetentionTimeForChromImport( document, nodePep, nodeGroup, out windowRT); } } // Force the center time to be at least zero if (centerTime.HasValue && centerTime.Value < 0) centerTime = 0; if (_fullScan.RetentionTimeFilterLength != 0) { windowRT = _fullScan.RetentionTimeFilterLength * 2; } if (centerTime != null) { double startTime = centerTime.Value - windowRT / 2; double endTime = startTime + windowRT; minTime = Math.Max(minTime ?? 0, startTime); maxTime = Math.Min(maxTime ?? double.MaxValue, endTime); } } else if (RetentionTimeFilterType.ms2_ids == _fullScan.RetentionTimeFilterType) { var times = document.Settings.GetBestRetentionTimes(nodePep, msDataFileUri); if (times.Length > 0) { minTime = Math.Max(minTime ?? 0, times.Min() - _fullScan.RetentionTimeFilterLength); maxTime = Math.Min(maxTime ?? double.MaxValue, times.Max() + _fullScan.RetentionTimeFilterLength); } } } SpectrumFilterPair filter; string textId = nodePep.RawTextId; // Modified Sequence for peptides, or some other string for custom ions double mz = nodeGroup.PrecursorMz; var key = new PrecursorTextId(mz, textId, ChromExtractor.summed); if (!dictPrecursorMzToFilter.TryGetValue(key, out filter)) { filter = new SpectrumFilterPair(key, nodePep.Color, dictPrecursorMzToFilter.Count, minTime, maxTime, startDriftTimeMsec, endDriftTimeMsec, highEnergyDriftTimeOffsetMsec, _isHighAccMsFilter, _isHighAccProductFilter); dictPrecursorMzToFilter.Add(key, filter); } if (!EnabledMs) { filter.AddQ3FilterValues(from TransitionDocNode nodeTran in nodeGroup.Children select nodeTran.Mz, calcWindowsQ3); } else if (!EnabledMsMs) { filter.AddQ1FilterValues(GetMS1MzValues(nodeGroup), calcWindowsQ1); } else { filter.AddQ1FilterValues(GetMS1MzValues(nodeGroup), calcWindowsQ1); filter.AddQ3FilterValues(from TransitionDocNode nodeTran in nodeGroup.Children where !nodeTran.IsMs1 select nodeTran.Mz, calcWindowsQ3); } } } _filterMzValues = dictPrecursorMzToFilter.Values.ToArray(); var listChromKeyFilterIds = new List<ChromKey>(); foreach (var spectrumFilterPair in _filterMzValues) { spectrumFilterPair.AddChromKeys(listChromKeyFilterIds); } _productChromKeys = listChromKeyFilterIds.ToArray(); // Sort a copy of the filter pairs by maximum retention time so that we can detect when // filters are no longer active. _filterRTValues = new SpectrumFilterPair[_filterMzValues.Length]; Array.Copy(_filterMzValues, _filterRTValues, _filterMzValues.Length); Array.Sort(_filterRTValues, CompareByRT); } InitRTLimits(); }