public static Spectrum GetMS1Spectrum(ref ThermoRawSpectrumReader reader, int scan, ref ISpectrum ms1) { // scan header Spectrum spectrum = new Spectrum { id = "scan=" + scan.ToString() }; double dLowMass = 0; double dHighMass = 0; double dTIC = 0; double dBasePeakMass = 0; double dBasePeakIntensity = 0; reader.GetScanHeaderInfoForScanNum(scan, ref dLowMass, ref dHighMass, ref dTIC, ref dBasePeakMass, ref dBasePeakIntensity); SetScanHeader(spectrum, dLowMass, dHighMass, dTIC, dBasePeakMass, dBasePeakIntensity); // binary data spectrum.binaryDataArrayList = new BinaryDataArrayList(); SetBinaryDataArrayHeader(spectrum.binaryDataArrayList); ms1 = reader.GetSpectrum(scan); //majorPeaks = picking.Process(ms1.GetPeaks()); spectrum.cvParam[0] = new Component.CVParam() { cvRef = "MS", accession = "MS:1000511", name = "ms level", value = "1", }; spectrum.binaryDataArrayList.binaryDataArray[0].binary = ms1.GetPeaks().SelectMany(p => BitConverter.GetBytes(p.GetMZ())).ToArray(); spectrum.binaryDataArrayList.binaryDataArray[1].binary = ms1.GetPeaks().SelectMany(p => BitConverter.GetBytes(p.GetIntensity())).ToArray(); spectrum.defaultArrayLength = ms1.GetPeaks().Count.ToString(); spectrum.binaryDataArrayList.binaryDataArray[0].encodedLength = Convert.ToBase64String(spectrum.binaryDataArrayList.binaryDataArray[0].binary).Length.ToString(); spectrum.binaryDataArrayList.binaryDataArray[1].encodedLength = Convert.ToBase64String(spectrum.binaryDataArrayList.binaryDataArray[1].binary).Length.ToString(); return(spectrum); }
public static Spectrum GetMS2Spectrum(ref ThermoRawSpectrumReader reader, int scan, AveragineType type, ChargerType chargerType, LocalMaximaPicking picking, IProcess process, ISpectrum ms1) { // scan header Spectrum spectrum = new Spectrum { id = "scan=" + scan.ToString() }; double dLowMass = 0; double dHighMass = 0; double dTIC = 0; double dBasePeakMass = 0; double dBasePeakIntensity = 0; reader.GetScanHeaderInfoForScanNum(scan, ref dLowMass, ref dHighMass, ref dTIC, ref dBasePeakMass, ref dBasePeakIntensity); SetScanHeader(spectrum, dLowMass, dHighMass, dTIC, dBasePeakMass, dBasePeakIntensity); // binary data spectrum.binaryDataArrayList = new BinaryDataArrayList(); SetBinaryDataArrayHeader(spectrum.binaryDataArrayList); spectrum.cvParam[0] = new Component.CVParam() { cvRef = "MS", accession = "MS:1000511", name = "ms level", value = "2", }; double mz = reader.GetPrecursorMass(scan, reader.GetMSnOrder(scan)); List <IPeak> ms1Peaks = FilterPeaks(ms1.GetPeaks(), mz, searchRange); if (ms1Peaks.Count() == 0) { return(null); } // insert pseudo peaks for large gaps List <IPeak> peaks = new List <IPeak>(); double precision = 0.02; double last = ms1Peaks.First().GetMZ(); foreach (IPeak peak in ms1Peaks) { if (peak.GetMZ() - last > precision) { peaks.Add(new GeneralPeak(last + precision / 2, 0)); peaks.Add(new GeneralPeak(peak.GetMZ() - precision / 2, 0)); } peaks.Add(peak); last = peak.GetMZ(); } List <IPeak> majorPeaks = picking.Process(peaks); ICharger charger = new Patterson(); if (chargerType == ChargerType.Fourier) { charger = new Fourier(); } else if (chargerType == ChargerType.Combined) { charger = new PattersonFourierCombine(); } int charge = charger.Charge(peaks, mz - searchRange, mz + searchRange); // find evelope cluster EnvelopeProcess envelope = new EnvelopeProcess(); var cluster = envelope.Cluster(majorPeaks, mz, charge); if (cluster.Count == 0) { return(null); } // find monopeak Averagine averagine = new Averagine(type); BrainCSharp braincs = new BrainCSharp(); MonoisotopicSearcher searcher = new MonoisotopicSearcher(averagine, braincs); MonoisotopicScore result = searcher.Search(mz, charge, cluster); // process spectrum ISpectrum ms2 = reader.GetSpectrum(scan); List <IPeak> ms2Peaks = process.Process(ms2).GetPeaks(); spectrum.binaryDataArrayList.binaryDataArray[0].binary = ms2Peaks.SelectMany(p => BitConverter.GetBytes(p.GetMZ())).ToArray(); spectrum.binaryDataArrayList.binaryDataArray[1].binary = ms2Peaks.SelectMany(p => BitConverter.GetBytes(p.GetIntensity())).ToArray(); spectrum.defaultArrayLength = ms2Peaks.Count.ToString(); spectrum.precursorList = new PrecursorList { count = "1", precursor = new Precursor[1] }; for (int i = 0; i < spectrum.precursorList.precursor.Length; i++) { spectrum.precursorList.precursor[i] = new Precursor(); } spectrum.precursorList.precursor[0].selectedIonList = new SelectedIonList { count = "1", selectedIon = new SelectedIon[1] }; for (int i = 0; i < spectrum.precursorList.precursor[0].selectedIonList.selectedIon.Length; i++) { spectrum.precursorList.precursor[0].selectedIonList.selectedIon[i] = new SelectedIon(); } spectrum.precursorList.precursor[0].selectedIonList.selectedIon[0].cvParam = new Component.CVParam[2]; spectrum.precursorList.precursor[0].selectedIonList.selectedIon[0].cvParam[0] = new Component.CVParam() { cvRef = "MS", accession = "MS:1000744", name = "selected ion m/z", value = result.GetMZ().ToString(), unitCvRef = "MS", unitAccession = "MS:1000040", unitName = "m/z" }; spectrum.precursorList.precursor[0].selectedIonList.selectedIon[0].cvParam[1] = new Component.CVParam() { cvRef = "MS", accession = "MS:1000041", name = "charge state", value = charge.ToString() }; spectrum.precursorList.precursor[0].activation = new Activation { cvParam = new Component.CVParam[1] }; spectrum.precursorList.precursor[0].activation.cvParam[0] = ActivationCVParam(reader.GetActivation(scan)); spectrum.binaryDataArrayList.binaryDataArray[0].encodedLength = Convert.ToBase64String(spectrum.binaryDataArrayList.binaryDataArray[0].binary).Length.ToString(); spectrum.binaryDataArrayList.binaryDataArray[1].encodedLength = Convert.ToBase64String(spectrum.binaryDataArrayList.binaryDataArray[1].binary).Length.ToString(); return(spectrum); }