public static void GetMetricsData(this MetricsData metricsData, ScanMetaDataCollection metaData, RawDataCollection rawData, IRawDataPlus rawFile, QuantDataCollection quantData = null) { List <Operations> operations = new List <Operations> { Operations.ScanIndex, Operations.RetentionTimes, Operations.MethodData, Operations.MetaData }; if (!rawData.isBoxCar) { operations.Add(Operations.PeakRetAndInt); operations.Add(Operations.PeakShape); } rawData.Check(rawFile, operations); metricsData.RawFileName = rawData.rawFileName; metricsData.Instrument = rawData.instrument; metricsData.MS1Analyzer = rawData.methodData.MassAnalyzers[MSOrderType.Ms]; metricsData.MS2Analyzer = rawData.methodData.MassAnalyzers[MSOrderType.Ms2]; metricsData.TotalAnalysisTime = rawData.retentionTimes[rawData.scanIndex.ScanEnumerators[MSOrderType.Any].Last()] - rawData.retentionTimes[rawData.scanIndex.ScanEnumerators[MSOrderType.Any].First()]; metricsData.TotalScans = rawData.scanIndex.allScans.Count(); metricsData.MS1Scans = rawData.scanIndex.ScanEnumerators[MSOrderType.Ms].Length; metricsData.MS2Scans = rawData.scanIndex.ScanEnumerators[MSOrderType.Ms2].Length; if (rawData.methodData.AnalysisOrder == MSOrderType.Ms3) { metricsData.MS3Analyzer = rawData.methodData.MassAnalyzers[MSOrderType.Ms3]; metricsData.MS3Scans = rawData.scanIndex.ScanEnumerators[MSOrderType.Ms3].Length; } else { metricsData.MS3Analyzer = MassAnalyzerType.Any; metricsData.MS3Scans = 0; } metricsData.MSOrder = rawData.methodData.AnalysisOrder; List <double> ms2intensities = new List <double>(); List <double> precursorIntensities = new List <double>(); List <double> ms1fillTimes = new List <double>(); List <double> ms2fillTimes = new List <double>(); List <double> ms3fillTimes = new List <double>(); List <double> ms2scansPerCycle = new List <double>(); List <double> dutyCycles = new List <double>(); List <double> fractionConsuming80 = new List <double>(); foreach (int scan in rawData.scanIndex.ScanEnumerators[MSOrderType.Ms]) { ms1fillTimes.Add(metaData[scan].FillTime); ms2scansPerCycle.Add(metaData[scan].MS2ScansPerCycle); dutyCycles.Add(metaData[scan].DutyCycle); } foreach (int scan in rawData.scanIndex.ScanEnumerators[MSOrderType.Ms2]) { precursorIntensities.Add(rawData.peakData[scan].ParentIntensity); ms2intensities.Add(metaData[scan].SummedIntensity); ms2fillTimes.Add(metaData[scan].FillTime); fractionConsuming80.Add(metaData[scan].FractionConsumingTop80PercentTotalIntensity); } if (rawData.methodData.AnalysisOrder == MSOrderType.Ms3) { foreach (int scan in rawData.scanIndex.ScanEnumerators[MSOrderType.Ms3]) { ms3fillTimes.Add(metaData[scan].FillTime); } } metricsData.MedianPrecursorIntensity = precursorIntensities.ToArray().Percentile(50); metricsData.MedianMs2FractionConsumingTop80PercentTotalIntensity = fractionConsuming80.ToArray().Percentile(50); metricsData.MedianSummedMS2Intensity = ms2intensities.ToArray().Percentile(50); metricsData.MedianMS1FillTime = ms1fillTimes.ToArray().Percentile(50); metricsData.MedianMS2FillTime = ms2fillTimes.ToArray().Percentile(50); if (rawData.methodData.AnalysisOrder == MSOrderType.Ms3) { metricsData.MedianMS3FillTime = ms3fillTimes.ToArray().Percentile(50); } else { metricsData.MedianMS3FillTime = -1; } metricsData.MeanTopN = ms2scansPerCycle.Average(); metricsData.MeanDutyCycle = dutyCycles.Average(); metricsData.MS1ScanRate = metricsData.MS1Scans / metricsData.TotalAnalysisTime; metricsData.MS2ScanRate = metricsData.MS2Scans / metricsData.TotalAnalysisTime; metricsData.MS3ScanRate = metricsData.MS3Scans / metricsData.TotalAnalysisTime; // only do the following if it isn't a boxcar experiment if (!rawData.isBoxCar) { metricsData.MedianBaselinePeakWidth = rawData.peakData.PeakShapeMedians.Width.P10; metricsData.MedianHalfHeightPeakWidth = rawData.peakData.PeakShapeMedians.Width.P50; // we can't access the instrument method in Linux, so we will assume the gradient length is the length of the MS acquisition metricsData.Gradient = rawData.retentionTimes[rawData.scanIndex.allScans.Keys.Max()]; metricsData.PeakCapacity = metricsData.Gradient / metricsData.MedianHalfHeightPeakWidth; metricsData.MedianAsymmetryFactor = rawData.peakData.PeakShapeMedians.Asymmetry.P10; } // add isolation interference metricsData.MedianMs1IsolationInterference = (from scan in rawData.scanIndex.ScanEnumerators[rawData.methodData.AnalysisOrder] select rawData.metaData[scan].Ms1IsolationInterference).ToArray().Percentile(50); // now add the quant meta data, if quant was performed double medianReporterIntensity = 0; QuantMetaData quantMetaData = new QuantMetaData(); SerializableDictionary <string, double> medianReporterIntensityByChannel = new SerializableDictionary <string, double>(); if (quantData != null & rawData.Performed.Contains(Operations.Quantification)) { string reagent = quantData.LabelingReagents; string[] allTags = new LabelingReagents().Reagents[reagent].Labels; List <double> allChannels = new List <double>(); Dictionary <string, List <double> > byChannel = new Dictionary <string, List <double> >(); foreach (string tag in allTags) { byChannel.Add(tag, new List <double>()); } foreach (int scan in rawData.scanIndex.ScanEnumerators[rawData.methodData.AnalysisOrder]) { foreach (string tag in allTags) { byChannel[tag].Add(quantData[scan][tag].Intensity); allChannels.Add(quantData[scan][tag].Intensity); } } medianReporterIntensity = allChannels.ToArray().Percentile(50); foreach (string tag in allTags) { medianReporterIntensityByChannel[tag] = byChannel[tag].ToArray().Percentile(50); } quantMetaData.medianReporterIntensity = medianReporterIntensity; quantMetaData.medianReporterIntensityByChannel = medianReporterIntensityByChannel; quantMetaData.quantTags = allTags; metricsData.QuantMeta = quantMetaData; metricsData.IncludesQuant = true; } }
public static void AggregateMetaData(this ScanMetaDataCollection metaData, RawDataCollection rawData, IRawDataPlus rawFile) { List <Operations> operations = new List <Operations>() { Operations.ScanIndex, Operations.MethodData, Operations.RetentionTimes, Operations.TrailerExtras, Operations.PrecursorScans }; if (rawData.methodData.MassAnalyzers[MSOrderType.Ms] == MassAnalyzerType.MassAnalyzerFTMS) { operations.Add(Operations.Ms1CentroidStreams); } else { operations.Add(Operations.Ms1SegmentedScans); } if (rawData.methodData.MassAnalyzers[MSOrderType.Ms2] == MassAnalyzerType.MassAnalyzerFTMS) { operations.Add(Operations.Ms2CentroidStreams); } else { operations.Add(Operations.Ms2SegmentedScans); } if (rawData.methodData.AnalysisOrder == MSOrderType.Ms3) { if (rawData.methodData.MassAnalyzers[MSOrderType.Ms3] == MassAnalyzerType.MassAnalyzerFTMS) { operations.Add(Operations.Ms3CentroidStreams); } else { operations.Add(Operations.Ms3SegmentedScans); } } rawData.Check(rawFile, operations); ProgressIndicator progress = new ProgressIndicator(rawData.scanIndex.ScanEnumerators[MSOrderType.Any].Count(), "Formatting scan meta data"); // add a new ScanMetaData class for each scan foreach (int scan in rawData.scanIndex.ScanEnumerators[MSOrderType.Any]) { metaData.Add(scan, new ScanMetaData()); } // get isolation window double isoWindow; if (rawData.methodData.AnalysisOrder == MSOrderType.Ms2) { isoWindow = rawData.methodData.IsolationWindow.MS2; } else { isoWindow = rawData.methodData.IsolationWindow.MS3.MS1Window; } // get topN foreach (int scan in rawData.scanIndex.ScanEnumerators[MSOrderType.Ms]) { // if the ms1 scan has no scan dependents then topN = 0 if (rawFile.GetScanDependents(scan, 0) == null) { metaData[scan].MS2ScansPerCycle = 0; } else { metaData[scan].MS2ScansPerCycle = rawFile.GetScanDependents(scan, 0).ScanDependentDetailArray.Length; } } // go through scans for each ms order sequentially foreach (MSOrderType MSOrder in new List <MSOrderType> { MSOrderType.Ms, MSOrderType.Ms2, MSOrderType.Ms3 }) { int[] scans = rawData.scanIndex.ScanEnumerators[MSOrder]; for (int i = 0; i < scans.Length; i++) { metaData[scans[i]].FillTime = rawData.trailerExtras[scans[i]].InjectionTime; // populate duty cycle if (i < scans.Length - 1) { metaData[scans[i]].DutyCycle = (rawData.retentionTimes[scans[i + 1]] - rawData.retentionTimes[scans[i]]) * 60; } else { metaData[scans[i]].DutyCycle = 0; } // populate scan rate if (MSOrder == MSOrderType.Ms2 | MSOrder == MSOrderType.Ms3) { metaData[scans[i]].MS2ScansPerCycle = metaData[rawData.precursorScans[scans[i]].MasterScan].MS2ScansPerCycle; } // populate intensity distributions if (rawData.methodData.MassAnalyzers[MSOrder] == MassAnalyzerType.MassAnalyzerFTMS) { metaData[scans[i]].IntensityDistribution = new Distribution(rawData.centroidStreams[scans[i]].Intensities); metaData[scans[i]].SummedIntensity = rawData.centroidStreams[scans[i]].Intensities.Sum(); } else { metaData[scans[i]].IntensityDistribution = new Distribution(rawData.segmentedScans[scans[i]].Intensities); metaData[scans[i]].SummedIntensity = rawData.segmentedScans[scans[i]].Intensities.Sum(); } // populate fraction of scans consuming 80% of total intensity if (rawData.methodData.MassAnalyzers[MSOrder] == MassAnalyzerType.MassAnalyzerFTMS) { metaData[scans[i]].FractionConsumingTop80PercentTotalIntensity = rawData.centroidStreams[scans[i]].Intensities.FractionOfScansConsumingTotalIntensity(percent: 80); } else { metaData[scans[i]].FractionConsumingTop80PercentTotalIntensity = rawData.segmentedScans[scans[i]].Intensities.FractionOfScansConsumingTotalIntensity(percent: 80); } // calculate ms1 isolation interference if (rawData.methodData.AnalysisOrder == MSOrder) { int preScan = rawData.precursorScans[scans[i]].MasterScan; metaData[scans[i]].Ms1IsolationInterference = Ms1Interference.CalculateForOneScan(rawData.centroidStreams[preScan], rawData.precursorMasses[scans[i]].MonoisotopicMZ, isoWindow, rawData.trailerExtras[scans[i]].ChargeState); } progress.Update(); } } progress.Done(); rawData.Performed.Add(Operations.MetaData); }