private static void WritePScans(string fileName, IRawDataPlus raw, List <PScan> scans) { var enumerator = raw.GetFilteredScanEnumerator(" "); foreach (var scanNumber in enumerator) // note in my tests serial is faster than Parallel.Foreach() (this involves disk access, so it makes sense) { //trailer iinformation is extracted via index var trailers = raw.GetTrailerExtraValues(scanNumber); var trailerLabels = raw.GetTrailerExtraInformation(scanNumber); object chargeState = 0; for (int i = 0; i < trailerLabels.Labels.Length; i++) { if (trailerLabels.Labels[i] == "Charge State:") { chargeState = raw.GetTrailerExtraValue(scanNumber, i); break; } } var scanFilter = raw.GetFilterForScanNumber(scanNumber); var scanStats = raw.GetScanStatsForScanNumber(scanNumber); CentroidStream centroidStream = new CentroidStream(); //check for FT mass analyzer data if (scanFilter.MassAnalyzer == MassAnalyzerType.MassAnalyzerFTMS) { centroidStream = raw.GetCentroidStream(scanNumber, false); } //check for IT mass analyzer data if (scanFilter.MassAnalyzer == MassAnalyzerType.MassAnalyzerITMS) { var scanData = raw.GetSimplifiedScan(scanNumber); centroidStream.Masses = scanData.Masses; centroidStream.Intensities = scanData.Intensities; } var msOrder = raw.GetScanEventForScanNumber(scanNumber).MSOrder; if (msOrder == MSOrderType.Ms) { var pscan = GetPScan(scanStats, centroidStream, 1, fileName, Convert.ToInt32(chargeState)); scans.Add(pscan); } if (msOrder == MSOrderType.Ms2) { var precursorMz = raw.GetScanEventForScanNumber(scanNumber).GetReaction(0).PrecursorMass; var pscan = GetPScan(scanStats, centroidStream, 2, fileName, precursorMz, Convert.ToInt32(chargeState)); scans.Add(pscan); } var t = raw.GetTrailerExtraValues(scanNumber); } WriteScans(scans, fileName); }