private void initializeMassSpecData() { var massAnalyzer = RawData.GetScanEventForScanNumber(FirstScan).MassAnalyzer; if (massAnalyzer == MassAnalyzerType.MassAnalyzerFTMS) { spectrum = new Spectrum(RawData.GetCentroidStream(FirstScan, false)); } else { spectrum = new Spectrum(RawData.GetSegmentedScanFromScanNumber(FirstScan, null)); } }
public double[] GetSpectrumIntensities(int scanNumber) { var scanStatistics = rawFile.GetScanStatsForScanNumber(scanNumber); var centroidStream = rawFile.GetCentroidStream(scanNumber, false); if (scanStatistics.IsCentroidScan && centroidStream.Length > 0) { return(centroidStream.Intensities.ToArray()); } else { var segmentedScan = rawFile.GetSegmentedScanFromScanNumber(scanNumber, scanStatistics); return(segmentedScan.Intensities.ToArray()); } }
private static void Extract(this RawDataCollection rawData, IRawDataPlus rawFile, IEnumerable <int> scans, ProgressIndicator progress) { foreach (int scan in scans) { try { rawData.segmentedScans.Add(scan, new SegmentedScanData(rawFile.GetSegmentedScanFromScanNumber(scan, null))); } catch (Exception e) { Log.Error(e, "Failed during extraction of segment scan {Scan}", scan); throw e; } progress.Update(); } }
public static (CentroidStreamCollection centroids, SegmentScanCollection segments) MsData(IRawDataPlus rawFile, ScanIndex index) { rawFile.SelectInstrument(Device.MS, 1); CentroidStreamCollection centroids = new CentroidStreamCollection(); SegmentScanCollection segments = new SegmentScanCollection(); CentroidStream centroid; SegmentedScan segment; var scans = index.allScans; //var lockTarget = new object(); // this is so we can keep track of progress in the parallel loop ProgressIndicator P = new ProgressIndicator(scans.Count(), "Extracting scan data"); P.Start(); foreach (int scan in scans.Keys) { // first get out the mass spectrum if (index.allScans[scan].MassAnalyzer == MassAnalyzerType.MassAnalyzerFTMS) { centroid = rawFile.GetCentroidStream(scan, false); centroids[scan] = new CentroidStreamData(centroid); } else { segment = rawFile.GetSegmentedScanFromScanNumber(scan, null); segments[scan] = new SegmentedScanData(segment); } //lock (lockTarget) //{ // P.Update(); //} P.Update(); } P.Done(); return(centroids, segments); }
/// <inheritdoc /> public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastScanNumber) { ConfigureWriter(".mgf"); using (Writer) { Log.Info("Processing " + (lastScanNumber - firstScanNumber + 1) + " scans"); var lastScanProgress = 0; for (var scanNumber = firstScanNumber; scanNumber <= lastScanNumber; scanNumber++) { if (!ParseInput.Verbose) { var scanProgress = (int)((double)scanNumber / (lastScanNumber - firstScanNumber + 1) * 100); if (scanProgress % ProgressPercentageStep == 0) { if (scanProgress != lastScanProgress) { Console.Write("" + scanProgress + "% "); lastScanProgress = scanProgress; } } } // Get each scan from the RAW file var scan = Scan.FromFile(rawFile, scanNumber); // Check to see if the RAW file contains label (high-res) data and if it is present // then look for any data that is out of order var time = rawFile.RetentionTimeFromScanNumber(scanNumber); // Get the scan filter for this scan number var scanFilter = rawFile.GetFilterForScanNumber(scanNumber); // Get the scan event for this scan number var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber); IReaction reaction = null; switch (scanFilter.MSOrder) { case MSOrderType.Ms: // Keep track of scan number for precursor reference _precursorScanNumber = scanNumber; break; case MSOrderType.Ms2: try { reaction = scanEvent.GetReaction(0); } catch (ArgumentOutOfRangeException exception) { Log.Warn("No reaction found for scan " + scanNumber); } goto default; case MSOrderType.Ms3: { try { reaction = scanEvent.GetReaction(1); } catch (ArgumentOutOfRangeException) { Log.Warn("No reaction found for scan " + scanNumber); } goto default; } default: Writer.WriteLine("BEGIN IONS"); Writer.WriteLine($"TITLE={ConstructSpectrumTitle(scanNumber)}"); Writer.WriteLine($"SCANS={scanNumber}"); Writer.WriteLine( $"RTINSECONDS={(time * 60).ToString(CultureInfo.InvariantCulture)}"); // trailer extra data list var trailerData = rawFile.GetTrailerExtraInformation(scanNumber); int? charge = null; double?monoisotopicMz = null; double?isolationWidth = null; for (var i = 0; i < trailerData.Length; i++) { if (trailerData.Labels[i] == "Charge State:") { if (Convert.ToInt32(trailerData.Values[i]) > 0) { charge = Convert.ToInt32(trailerData.Values[i]); } } if (trailerData.Labels[i] == "Monoisotopic M/Z:") { monoisotopicMz = double.Parse(trailerData.Values[i], NumberStyles.Any, CultureInfo.CurrentCulture); } if (trailerData.Labels[i] == "MS" + (int)scanFilter.MSOrder + " Isolation Width:") { isolationWidth = double.Parse(trailerData.Values[i], NumberStyles.Any, CultureInfo.CurrentCulture); } } if (reaction != null) { var selectedIonMz = CalculateSelectedIonMz(reaction, monoisotopicMz, isolationWidth); Writer.WriteLine("PEPMASS=" + selectedIonMz.ToString(CultureInfo.InvariantCulture)); } // charge if (charge != null) { // Scan polarity var polarity = PositivePolarity; if (scanFilter.Polarity == PolarityType.Negative) { polarity = NegativePolarity; } Writer.WriteLine($"CHARGE={charge}{polarity}"); } // write the filter string //Writer.WriteLine($"SCANEVENT={scanEvent.ToString()}"); // Check if the scan has a centroid stream if (scan.HasCentroidStream && (scanEvent.ScanData == ScanDataType.Centroid || (scanEvent.ScanData == ScanDataType.Profile && !ParseInput.NoPeakPicking))) { var centroidStream = rawFile.GetCentroidStream(scanNumber, false); if (scan.CentroidScan.Length > 0) { for (var i = 0; i < centroidStream.Length; i++) { Writer.WriteLine( centroidStream.Masses[i].ToString("0.0000000", CultureInfo.InvariantCulture) + " " + centroidStream.Intensities[i].ToString("0.0000000000", CultureInfo.InvariantCulture)); } } } // Otherwise take the profile data else { // Get the scan statistics from the RAW file for this scan number var scanStatistics = rawFile.GetScanStatsForScanNumber(scanNumber); // Get the segmented (low res and profile) scan data var segmentedScan = rawFile.GetSegmentedScanFromScanNumber(scanNumber, scanStatistics); for (var i = 0; i < segmentedScan.Positions.Length; i++) { Writer.WriteLine( segmentedScan.Positions[i].ToString("0.0000000", CultureInfo.InvariantCulture) + " " + segmentedScan.Intensities[i].ToString("0.0000000000", CultureInfo.InvariantCulture)); } } Writer.WriteLine("END IONS"); Log.Debug("Spectrum written to file -- SCAN " + scanNumber); break; } } if (!ParseInput.Verbose) { Console.WriteLine(); } } }
/// <summary> /// Construct a spectrum element for the given scan /// </summary> /// <param name="scanNumber">the scan number</param> /// <returns>The SpectrumType object</returns> private SpectrumType ConstructSpectrum(int scanNumber) { // Get each scan from the RAW file var scan = Scan.FromFile(_rawFile, scanNumber); // Get the scan filter for this scan number var scanFilter = _rawFile.GetFilterForScanNumber(scanNumber); // Get the scan event for this scan number var scanEvent = _rawFile.GetScanEventForScanNumber(scanNumber); var spectrum = new SpectrumType { id = ConstructSpectrumTitle(scanNumber), defaultArrayLength = 0 }; // Add the ionization type if necessary if (!_ionizationTypes.ContainsKey(scanFilter.IonizationMode)) { _ionizationTypes.Add(scanFilter.IonizationMode, OntologyMapping.IonizationTypes[scanFilter.IonizationMode]); } // Add the mass analyzer if necessary if (!_massAnalyzers.ContainsKey(scanFilter.MassAnalyzer) && OntologyMapping.MassAnalyzerTypes.ContainsKey(scanFilter.MassAnalyzer)) { _massAnalyzers.Add(scanFilter.MassAnalyzer, "IC" + (_massAnalyzers.Count + 1)); } // Keep the CV params in a list and convert to array afterwards var spectrumCvParams = new List <CVParamType> { new CVParamType { name = "ms level", accession = "MS:1000511", value = ((int)scanFilter.MSOrder).ToString(CultureInfo.InvariantCulture), cvRef = "MS" } }; // Trailer extra data list var trailerData = _rawFile.GetTrailerExtraInformation(scanNumber); int? charge = null; double?monoisotopicMass = null; for (var i = 0; i < trailerData.Length; i++) { if (trailerData.Labels[i] == "Charge State:") { if (Convert.ToInt32(trailerData.Values[i]) > 0) { charge = Convert.ToInt32(trailerData.Values[i]); } } if (trailerData.Labels[i] == "Monoisotopic M/Z:") { monoisotopicMass = double.Parse(trailerData.Values[i]); } } // Construct and set the scan list element of the spectrum var scanListType = ConstructScanList(scanNumber, scan, scanFilter, scanEvent, monoisotopicMass); spectrum.scanList = scanListType; switch (scanFilter.MSOrder) { case MSOrderType.Ms: spectrumCvParams.Add(new CVParamType { accession = "MS:1000579", cvRef = "MS", name = "MS1 spectrum", value = "" }); // Keep track of scan number for precursor reference _precursorScanNumber = scanNumber; break; case MSOrderType.Ms2: spectrumCvParams.Add(new CVParamType { accession = "MS:1000580", cvRef = "MS", name = "MSn spectrum", value = "" }); // Construct and set the precursor list element of the spectrum var precursorListType = ConstructPrecursorList(scanEvent, charge); spectrum.precursorList = precursorListType; break; case MSOrderType.Ng: break; case MSOrderType.Nl: break; case MSOrderType.Par: break; case MSOrderType.Any: break; case MSOrderType.Ms3: break; case MSOrderType.Ms4: break; case MSOrderType.Ms5: break; case MSOrderType.Ms6: break; case MSOrderType.Ms7: break; case MSOrderType.Ms8: break; case MSOrderType.Ms9: break; case MSOrderType.Ms10: break; default: throw new ArgumentOutOfRangeException(); } // Scan polarity var polarityType = scanFilter.Polarity; switch (polarityType) { case PolarityType.Positive: spectrumCvParams.Add(new CVParamType { accession = "MS:1000130", cvRef = "MS", name = "positive scan", value = "" }); break; case PolarityType.Negative: spectrumCvParams.Add(new CVParamType { accession = "MS:1000129", cvRef = "MS", name = "negative scan", value = "" }); break; case PolarityType.Any: break; default: throw new ArgumentOutOfRangeException(); } // Total ion current spectrumCvParams.Add(new CVParamType { name = "total ion current", accession = "MS:1000285", value = scan.ScanStatistics.TIC.ToString(CultureInfo.InvariantCulture), cvRef = "MS" }); double?basePeakMass = null; double?basePeakIntensity = null; double?lowestObservedMz = null; double?highestObservedMz = null; double[] masses = null; double[] intensities = null; if (scan.HasCentroidStream) { var centroidStream = _rawFile.GetCentroidStream(scanNumber, false); if (scan.CentroidScan.Length > 0) { basePeakMass = centroidStream.BasePeakMass; basePeakIntensity = centroidStream.BasePeakIntensity; lowestObservedMz = centroidStream.Masses[0]; highestObservedMz = centroidStream.Masses[centroidStream.Masses.Length - 1]; masses = centroidStream.Masses; intensities = centroidStream.Intensities; // Note that although the scan data type is profile, // centroid data might be available spectrumCvParams.Add(new CVParamType { accession = "MS:1000127", cvRef = "MS", name = "centroid spectrum", value = "" }); } } else { // Get the scan statistics from the RAW file for this scan number var scanStatistics = _rawFile.GetScanStatsForScanNumber(scanNumber); basePeakMass = scanStatistics.BasePeakMass; basePeakIntensity = scanStatistics.BasePeakIntensity; // Get the segmented (low res and profile) scan data var segmentedScan = _rawFile.GetSegmentedScanFromScanNumber(scanNumber, scanStatistics); if (segmentedScan.Positions.Length > 0) { lowestObservedMz = segmentedScan.Positions[0]; highestObservedMz = segmentedScan.Positions[segmentedScan.Positions.Length - 1]; masses = segmentedScan.Positions; intensities = segmentedScan.Intensities; spectrumCvParams.Add(new CVParamType { accession = "MS:1000128", cvRef = "MS", name = "profile spectrum", value = "" }); } } // Base peak m/z if (basePeakMass != null) { spectrumCvParams.Add(new CVParamType { name = "base peak m/z", accession = "MS:1000504", value = basePeakMass.ToString(), unitCvRef = "MS", unitName = "m/z", unitAccession = "MS:1000040", cvRef = "MS" }); } // Base peak intensity if (basePeakMass != null) { spectrumCvParams.Add(new CVParamType { name = "base peak intensity", accession = "MS:1000505", value = basePeakIntensity.ToString(), unitCvRef = "MS", unitName = "number of detector counts", unitAccession = "MS:1000131", cvRef = "MS" }); } // Lowest observed mz if (lowestObservedMz != null) { spectrumCvParams.Add(new CVParamType { name = "lowest observed m/z", accession = "MS:1000528", value = lowestObservedMz.ToString(), unitCvRef = "MS", unitAccession = "MS:1000040", unitName = "m/z", cvRef = "MS" }); } // Highest observed mz if (highestObservedMz != null) { spectrumCvParams.Add(new CVParamType { name = "highest observed m/z", accession = "MS:1000527", value = highestObservedMz.ToString(), unitAccession = "MS:1000040", unitName = "m/z", unitCvRef = "MS", cvRef = "MS" }); } // Add the CV params to the spectrum spectrum.cvParam = spectrumCvParams.ToArray(); // Binary data array list var binaryData = new List <BinaryDataArrayType>(); // M/Z Data if (!masses.IsNullOrEmpty()) { // Set the spectrum default array length spectrum.defaultArrayLength = masses.Length; var massesBinaryData = new BinaryDataArrayType { binary = GetZLib64BitArray(masses) }; massesBinaryData.encodedLength = (4 * Math.Ceiling((double)massesBinaryData .binary.Length / 3)).ToString(CultureInfo.InvariantCulture); massesBinaryData.cvParam = new CVParamType[3]; massesBinaryData.cvParam[0] = new CVParamType { accession = "MS:1000514", name = "m/z array", cvRef = "MS", unitName = "m/z", value = "", unitCvRef = "MS", unitAccession = "MS:1000040" }; massesBinaryData.cvParam[1] = new CVParamType { accession = "MS:1000523", name = "64-bit float", cvRef = "MS", value = "" }; massesBinaryData.cvParam[2] = new CVParamType { accession = "MS:1000574", name = "zlib compression", cvRef = "MS", value = "" }; binaryData.Add(massesBinaryData); } // Intensity Data if (!intensities.IsNullOrEmpty()) { // Set the spectrum default array length if necessary if (spectrum.defaultArrayLength == 0) { spectrum.defaultArrayLength = masses.Length; } var intensitiesBinaryData = new BinaryDataArrayType { binary = GetZLib64BitArray(intensities) }; intensitiesBinaryData.encodedLength = (4 * Math.Ceiling((double)intensitiesBinaryData .binary.Length / 3)).ToString(CultureInfo.InvariantCulture); intensitiesBinaryData.cvParam = new CVParamType[3]; intensitiesBinaryData.cvParam[0] = new CVParamType { accession = "MS:1000515", name = "intensity array", cvRef = "MS", unitCvRef = "MS", unitAccession = "MS:1000131", unitName = "number of counts", value = "" }; intensitiesBinaryData.cvParam[1] = new CVParamType { accession = "MS:1000523", name = "64-bit float", cvRef = "MS", value = "" }; intensitiesBinaryData.cvParam[2] = new CVParamType { accession = "MS:1000574", name = "zlib compression", cvRef = "MS", value = "" }; binaryData.Add(intensitiesBinaryData); } if (!binaryData.IsNullOrEmpty()) { spectrum.binaryDataArrayList = new BinaryDataArrayListType { count = binaryData.Count.ToString(), binaryDataArray = binaryData.ToArray() }; } return(spectrum); }
/// <inheritdoc /> public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastScanNumber) { ConfigureWriter(".mgf"); using (Writer) { for (var scanNumber = firstScanNumber; scanNumber <= lastScanNumber; scanNumber++) { // Get each scan from the RAW file var scan = Scan.FromFile(rawFile, scanNumber); // Check to see if the RAW file contains label (high-res) data and if it is present // then look for any data that is out of order var time = rawFile.RetentionTimeFromScanNumber(scanNumber); // Get the scan filter for this scan number var scanFilter = rawFile.GetFilterForScanNumber(scanNumber); // Get the scan event for this scan number var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber); // Only consider MS2 spectra if (scanFilter.MSOrder == MSOrderType.Ms2) { if (scanEvent.ScanData == ScanDataType.Centroid || (scanEvent.ScanData == ScanDataType.Profile && !ParseInput.ExcludeProfileData)) { Writer.WriteLine("BEGIN IONS"); Writer.WriteLine($"TITLE={ConstructSpectrumTitle(scanNumber)}"); Writer.WriteLine($"SCAN={scanNumber}"); Writer.WriteLine($"RTINSECONDS={time * 60}"); // Get the reaction information for the first precursor try { var reaction = scanEvent.GetReaction(0); var precursorMass = reaction.PrecursorMass; Writer.WriteLine($"PEPMASS={precursorMass:F7}"); } catch (ArgumentOutOfRangeException exception) { Log.Warn("No reaction found for scan " + scanNumber); } // trailer extra data list var trailerData = rawFile.GetTrailerExtraInformation(scanNumber); for (var i = 0; i < trailerData.Length; i++) { if (trailerData.Labels[i] == "Charge State:") { if (Convert.ToInt32(trailerData.Values[i]) > 0) { Writer.WriteLine($"CHARGE={trailerData.Values[i]}+"); } } } // Check if the scan has a centroid stream if (scan.HasCentroidStream) { var centroidStream = rawFile.GetCentroidStream(scanNumber, false); if (scan.CentroidScan.Length > 0) { for (var i = 0; i < centroidStream.Length; i++) { Writer.WriteLine( $"{centroidStream.Masses[i]:F7} {centroidStream.Intensities[i]:F10}"); } } } // Otherwise take the profile data else { // Get the scan statistics from the RAW file for this scan number var scanStatistics = rawFile.GetScanStatsForScanNumber(scanNumber); // Get the segmented (low res and profile) scan data var segmentedScan = rawFile.GetSegmentedScanFromScanNumber(scanNumber, scanStatistics); for (var i = 0; i < segmentedScan.Positions.Length; i++) { Writer.WriteLine( $"{segmentedScan.Positions[i]:F7} {segmentedScan.Intensities[i]:F10}"); } } Writer.WriteLine("END IONS"); } } } } }
/// <inheritdoc /> public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastScanNumber) { ConfigureWriter(".mgf"); using (Writer) { for (var scanNumber = firstScanNumber; scanNumber <= lastScanNumber; scanNumber++) { // Get each scan from the RAW file var scan = Scan.FromFile(rawFile, scanNumber); // Check to see if the RAW file contains label (high-res) data and if it is present // then look for any data that is out of order var time = rawFile.RetentionTimeFromScanNumber(scanNumber); // Get the scan filter for this scan number var scanFilter = rawFile.GetFilterForScanNumber(scanNumber); // Get the scan event for this scan number var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber); switch (scanFilter.MSOrder) { case MSOrderType.Ms: // Keep track of scan number for precursor reference _precursorScanNumber = scanNumber; break; case MSOrderType.Ms2: { if (scanEvent.ScanData == ScanDataType.Centroid || (scanEvent.ScanData == ScanDataType.Profile && (scan.HasCentroidStream || ParseInput.OutputFormat != OutputFormat.MGFNoProfileData))) { Writer.WriteLine("BEGIN IONS"); Writer.WriteLine($"TITLE={ConstructSpectrumTitle(scanNumber)}"); Writer.WriteLine($"SCANS={scanNumber}"); Writer.WriteLine($"RTINSECONDS={(time * 60).ToString(CultureInfo.InvariantCulture)}"); // Get the reaction information for the first precursor try { var reaction = scanEvent.GetReaction(0); var precursorMass = reaction.PrecursorMass; Writer.WriteLine("PEPMASS=" + precursorMass.ToString("0.0000000", CultureInfo.InvariantCulture)); //var precursorIntensity = 0.0; //GetPrecursorIntensity(rawFile, _precursorScanNumber, precursorMass); //Writer.WriteLine(precursorIntensity != null // ? $"PEPMASS={precursorMass:F7} {precursorIntensity}" // : $"PEPMASS={precursorMass:F7}"); } catch (ArgumentOutOfRangeException exception) { Log.Warn("No reaction found for scan " + scanNumber); } // trailer extra data list var trailerData = rawFile.GetTrailerExtraInformation(scanNumber); for (var i = 0; i < trailerData.Length; i++) { if (trailerData.Labels[i] == "Charge State:") { if (Convert.ToInt32(trailerData.Values[i]) > 0) { Writer.WriteLine($"CHARGE={trailerData.Values[i]}+"); } } } // write the filter string //Writer.WriteLine($"SCANEVENT={scanEvent.ToString()}"); // Check if the scan has a centroid stream if (scan.HasCentroidStream) { var centroidStream = rawFile.GetCentroidStream(scanNumber, false); if (scan.CentroidScan.Length > 0) { for (var i = 0; i < centroidStream.Length; i++) { Writer.WriteLine( centroidStream.Masses[i].ToString("0.0000000", CultureInfo.InvariantCulture) + " " + centroidStream.Intensities[i].ToString("0.0000000", CultureInfo.InvariantCulture)); } } } // Otherwise take the profile data else { // Get the scan statistics from the RAW file for this scan number var scanStatistics = rawFile.GetScanStatsForScanNumber(scanNumber); // Get the segmented (low res and profile) scan data var segmentedScan = rawFile.GetSegmentedScanFromScanNumber(scanNumber, scanStatistics); for (var i = 0; i < segmentedScan.Positions.Length; i++) { Writer.WriteLine( segmentedScan.Positions[i].ToString("0.0000000", CultureInfo.InvariantCulture) + " " + segmentedScan.Intensities[i].ToString("0.0000000000", CultureInfo.InvariantCulture)); } } Writer.WriteLine("END IONS"); } break; } } } } }
public static void ExtractAll(this RawDataCollection rawData, IRawDataPlus rawFile) { Log.Information("Beginning extraction of all possible data"); rawFile.SelectInstrument(Device.MS, 1); rawData.ExtractPrecursorScans(rawFile); ProgressIndicator P = new ProgressIndicator(rawData.scanIndex.allScans.Count(), "Extracting raw data"); TrailerExtraIndices indices = new TrailerExtraIndices(rawFile); for (int i = 1; i <= rawData.scanIndex.allScans.Count(); i++) { try { // first get out the mass spectrum if (rawData.scanIndex.allScans[i].MassAnalyzer == MassAnalyzerType.MassAnalyzerFTMS) { rawData.centroidStreams.Add(i, new CentroidStreamData(rawFile.GetCentroidStream(i, false))); } else { rawData.segmentedScans.Add(i, new SegmentedScanData(rawFile.GetSegmentedScanFromScanNumber(i, null))); } // add the trailer extra data rawData.trailerExtras.Add(i, TrailerExtras.ExtractTrailerExtra(rawData, rawFile, i, indices)); rawData.Performed.Add(Operations.TrailerExtras); // add the retention time rawData.retentionTimes.Add(i, rawFile.RetentionTimeFromScanNumber(i)); rawData.Performed.Add(Operations.RetentionTimes); // add the precursor mass PrecursorMasses.ExtractPrecursorMasses(rawData, rawFile, i); rawData.Performed.Add(Operations.PrecursorMasses); P.Update(); } catch (Exception e) { Log.Error("Extraction failed on scan {Scan}", i); throw e; } } if (rawData.methodData.AnalysisOrder == MSOrderType.Ms2 | rawData.methodData.AnalysisOrder == MSOrderType.Ms3) { rawData.Performed.Add(Operations.Ms1CentroidStreams); if (rawData.methodData.MassAnalyzers[MSOrderType.Ms2] == MassAnalyzerType.MassAnalyzerFTMS) { rawData.Performed.Add(Operations.Ms2CentroidStreams); } else { rawData.Performed.Add(Operations.Ms2SegmentedScans); } } if (rawData.methodData.AnalysisOrder == MSOrderType.Ms3) { if (rawData.methodData.MassAnalyzers[MSOrderType.Ms3] == MassAnalyzerType.MassAnalyzerFTMS) { rawData.Performed.Add(Operations.Ms3CentroidStreams); } else { rawData.Performed.Add(Operations.Ms3SegmentedScans); } } P.Done(); }
} } writer.Flush(); startNum += 1; } writer.Close(); } public static void getMSdataFromRT(double startRT, int endRT, string filePath, double lowMS = 0.00, double highMS = 0.00) { IRawDataPlus plus = RawFileReaderAdapter.FileFactory(filePath); plus.SelectInstrument(Device.MS, 1); if (highMS - 0.00 <= 0.01) { highMS = plus.RunHeaderEx.HighMass; } int startNum = plus.ScanNumberFromRetentionTime(startRT); int endNum = plus.ScanNumberFromRetentionTime(endRT); int maxNum = plus.RunHeaderEx.LastSpectrum > endNum ? endNum : plus.RunHeaderEx.LastSpectrum; string fileName = DateTime.Now.ToLocalTime().ToString().Replace("/", "").Replace(":", "").Replace(" ", "_") + ".csv"; FileStream stream = new FileStream(fileName, FileMode.Create, FileAccess.Write); StreamWriter writer = new StreamWriter(stream, Encoding.UTF8); writer.WriteLine("ScanNumber, RT, Mass, Resolution, Intensity, Noise, Filter"); while (startNum <= endNum) { Scan scan = Scan.FromFile(plus, startNum); string filter = plus.GetFilterForScanNumber(startNum).ToString(); int cnt = 0; while (cnt < scan.PreferredMasses.Length) { if (lowMS < scan.PreferredMasses[cnt] && scan.PreferredMasses[cnt] < highMS) { double rt = plus.RetentionTimeFromScanNumber(startNum); double msval = scan.PreferredMasses[cnt]; double resolution = (scan.PreferredResolutions.Length == 0) ? 0.0 : scan.PreferredResolutions[cnt]; double intensity = (scan.PreferredIntensities.Length == 0) ? 0.0 : scan.PreferredIntensities[cnt]; double noise = (scan.PreferredNoises.Length == 0) ? 0.0 : scan.PreferredNoises[cnt]; //writer.WriteLine("{0},{1},{2},{3},{4},{5},{6}", startNum.ToString(), rt.ToString(), msval.ToString(), resolution.ToString(), intensity.ToString(), noise.ToString(), filter.ToString()); writer.WriteLine("{0},{1},{2},{3}", startNum.ToString(), rt.ToString(), msval.ToString(), intensity.ToString()); } cnt += 1; } startNum += 1; } writer.Close(); } public static void getSRMIacdMZ(string filePath, double valMS,int recVal) { IRawDataPlus plus = RawFileReaderAdapter.FileFactory(filePath); ////////////////////////////////// plus.SelectInstrument(Device.MS, 1); ///////////////////////////////// var startNum = plus.RunHeaderEx.FirstSpectrum; var endNum = plus.RunHeaderEx.LastSpectrum; string fileName = DateTime.Now.ToLocalTime().ToString().Replace("/", "").Replace(":", "").Replace(" ", "_") + ".csv"; FileStream stream = new FileStream(fileName, FileMode.Create, FileAccess.Write); StreamWriter writer = new StreamWriter(stream, Encoding.UTF8); double[] masses = null; double[] intensities = null; writer.WriteLine("ScanNumber, RT, Mass, Intensity"); while (startNum <= endNum) { double rt = plus.RetentionTimeFromScanNumber(startNum); IScanFilter scanFilter = plus.GetFilterForScanNumber(startNum); if (scanFilter.MSOrder == MSOrderType.Ms) { Scan scan = Scan.FromFile(plus, startNum); IScanEvent scanEvent = plus.GetScanEventForScanNumber(startNum); if (scan.HasCentroidStream && (scanEvent.ScanData == ScanDataType.Centroid || scanEvent.ScanData == ScanDataType.Profile)) { var centroidStream = plus.GetCentroidStream(startNum, false); if (scan.CentroidScan.Length > 0) { masses = centroidStream.Masses; intensities = centroidStream.Intensities; } } else { // Get the scan statistics from the RAW file for this scan number var scanStatistics = plus.GetScanStatsForScanNumber(startNum); // Get the segmented (low res and profile) scan data var segmentedScan = plus.GetSegmentedScanFromScanNumber(startNum, scanStatistics); if (segmentedScan.Positions.Length > 0) { masses = segmentedScan.Positions; intensities = segmentedScan.Intensities; } } for(int i = 0; i < masses.Length; ++ i) { masses[i] = Double.Parse(masses[i].ToString("n4")); } int front = 0; int rear = masses.Length - 1; int mid = front + ((rear - front) >> 1); bool findVal = false; while(front <= rear) { if (Double.Equals(masses[mid],valMS)) { findVal = true; break; } else if(masses[mid] < valMS) { front = mid + 1; } else { rear = mid - 1; } mid = front + ((rear - front) >> 1); } if(findVal && intensities[mid] >= recVal) { writer.WriteLine("{0},{1},{2},{3}",startNum.ToString(), rt.ToString(), masses[mid].ToString(), intensities[mid].ToString()); } } writer.Flush(); startNum += 1; } writer.Close(); } } }