/// <summary>
/// Constructor
/// </summary>
public clsMRMProcessing(clsMASICOptions masicOptions, clsDataOutput dataOutputHandler)
{
mOptions = masicOptions;
mDataAggregation = new clsDataAggregation();
RegisterEvents(mDataAggregation);
mDataOutputHandler = dataOutputHandler;
}
/// <summary>
/// Looks for the reporter ion peaks using FindReporterIonsWork
/// </summary>
/// <param name="scanList"></param>
/// <param name="spectraCache"></param>
/// <param name="inputFilePathFull">Full path to the input file</param>
/// <param name="outputDirectoryPath"></param>
/// <returns></returns>
/// <remarks></remarks>
public bool FindReporterIons(
clsScanList scanList,
clsSpectraCache spectraCache,
string inputFilePathFull,
string outputDirectoryPath)
{
const char TAB_DELIMITER = '\t';
var outputFilePath = "??";
try
{
// Use Xraw to read the .Raw files
var readerOptions = new ThermoReaderOptions()
{
LoadMSMethodInfo = false,
LoadMSTuneInfo = false
};
var rawFileReader = new XRawFileIO(readerOptions);
RegisterEvents(rawFileReader);
var includeFtmsColumns = false;
if (inputFilePathFull.ToUpper().EndsWith(DataInput.clsDataImport.THERMO_RAW_FILE_EXTENSION.ToUpper()))
{
// Processing a thermo .Raw file
// Check whether any of the frag scans has IsFTMS true
for (var masterOrderIndex = 0; masterOrderIndex < scanList.MasterScanOrderCount; masterOrderIndex++)
{
var scanPointer = scanList.MasterScanOrder[masterOrderIndex].ScanIndexPointer;
if (scanList.MasterScanOrder[masterOrderIndex].ScanType == clsScanList.eScanTypeConstants.SurveyScan)
{
// Skip survey scans
continue;
}
if (scanList.FragScans[scanPointer].IsFTMS)
{
includeFtmsColumns = true;
break;
}
}
if (includeFtmsColumns)
{
rawFileReader.OpenRawFile(inputFilePathFull);
}
}
if (mOptions.ReporterIons.ReporterIonList.Count == 0)
{
// No reporter ions defined; default to ITraq
mOptions.ReporterIons.SetReporterIonMassMode(clsReporterIons.eReporterIonMassModeConstants.ITraqFourMZ);
}
// Populate array reporterIons, which we will sort by m/z
var reporterIons = new clsReporterIonInfo[mOptions.ReporterIons.ReporterIonList.Count];
var reporterIonIndex = 0;
foreach (var reporterIon in mOptions.ReporterIons.ReporterIonList)
{
reporterIons[reporterIonIndex] = reporterIon;
reporterIonIndex += 1;
}
Array.Sort(reporterIons, new clsReportIonInfoComparer());
outputFilePath = clsDataOutput.ConstructOutputFilePath(
Path.GetFileName(inputFilePathFull),
outputDirectoryPath,
clsDataOutput.eOutputFileTypeConstants.ReporterIonsFile);
using (var writer = new StreamWriter(outputFilePath))
{
// Write the file headers
var reporterIonMZsUnique = new SortedSet <string>();
var headerColumns = new List <string>(7 + reporterIons.Length + 1)
{
"Dataset",
"ScanNumber",
"Collision Mode",
"ParentIonMZ",
"BasePeakIntensity",
"BasePeakMZ",
"ReporterIonIntensityMax"
};
var obsMZHeaders = new List <string>(reporterIons.Length);
var uncorrectedIntensityHeaders = new List <string>(reporterIons.Length);
var ftmsSignalToNoise = new List <string>(reporterIons.Length);
var ftmsResolution = new List <string>(reporterIons.Length);
//var ftmsLabelDataMz = new List<string>(reporterIons.Length);
var saveUncorrectedIntensities =
mOptions.ReporterIons.ReporterIonApplyAbundanceCorrection && mOptions.ReporterIons.ReporterIonSaveUncorrectedIntensities;
var dataAggregation = new clsDataAggregation();
RegisterEvents(dataAggregation);
foreach (var reporterIon in reporterIons)
{
if (!reporterIon.ContaminantIon || saveUncorrectedIntensities)
{
// Construct the reporter ion intensity header
// We skip contaminant ions, unless saveUncorrectedIntensities is True, then we include them
string mzValue;
if (mOptions.ReporterIons.ReporterIonMassMode == clsReporterIons.eReporterIonMassModeConstants.TMTTenMZ ||
mOptions.ReporterIons.ReporterIonMassMode == clsReporterIons.eReporterIonMassModeConstants.TMTElevenMZ ||
mOptions.ReporterIons.ReporterIonMassMode == clsReporterIons.eReporterIonMassModeConstants.TMTSixteenMZ)
{
mzValue = reporterIon.MZ.ToString("#0.000");
}
else
{
mzValue = ((int)Math.Round(reporterIon.MZ, 0)).ToString();
}
if (reporterIonMZsUnique.Contains(mzValue))
{
// Uniquify the m/z value
mzValue += "_" + reporterIonIndex;
}
try
{
reporterIonMZsUnique.Add(mzValue);
}
catch (Exception ex)
{
// Error updating the SortedSet;
// this shouldn't happen based on the .ContainsKey test above
}
// Append the reporter ion intensity title to the headers
headerColumns.Add("Ion_" + mzValue);
// This string will only be included in the header line if mOptions.ReporterIons.ReporterIonSaveObservedMasses is true
obsMZHeaders.Add("Ion_" + mzValue + "_ObsMZ");
// This string will be included in the header line if saveUncorrectedIntensities is true
uncorrectedIntensityHeaders.Add("Ion_" + mzValue + "_OriginalIntensity");
// This string will be included in the header line if includeFtmsColumns is true
ftmsSignalToNoise.Add("Ion_" + mzValue + "_SignalToNoise");
ftmsResolution.Add("Ion_" + mzValue + "_Resolution");
// Uncomment to include the label data m/z value in the _ReporterIons.txt file
// This string will only be included in the header line if mOptions.ReporterIons.ReporterIonSaveObservedMasses is true
//ftmsLabelDataMz.Add("Ion_" + mzValue + "_LabelDataMZ");
}
}
headerColumns.Add("Weighted Avg Pct Intensity Correction");
if (mOptions.ReporterIons.ReporterIonSaveObservedMasses)
{
headerColumns.AddRange(obsMZHeaders);
}
if (saveUncorrectedIntensities)
{
headerColumns.AddRange(uncorrectedIntensityHeaders);
}
if (includeFtmsColumns)
{
headerColumns.AddRange(ftmsSignalToNoise);
headerColumns.AddRange(ftmsResolution);
// Uncomment to include the label data m/z value in the _ReporterIons.txt file
// If mOptions.ReporterIons.ReporterIonSaveObservedMasses Then
// headerColumns.AddRange(ftmsLabelDataMz)
// End If
}
// Write the headers to the output file, separated by tabs
writer.WriteLine(string.Join(TAB_DELIMITER.ToString(), headerColumns));
UpdateProgress(0, "Searching for reporter ions");
for (var masterOrderIndex = 0; masterOrderIndex < scanList.MasterScanOrderCount; masterOrderIndex++)
{
var scanPointer = scanList.MasterScanOrder[masterOrderIndex].ScanIndexPointer;
if (scanList.MasterScanOrder[masterOrderIndex].ScanType == clsScanList.eScanTypeConstants.SurveyScan)
{
// Skip Survey Scans
continue;
}
FindReporterIonsWork(
rawFileReader,
dataAggregation,
includeFtmsColumns,
mOptions.SICOptions,
scanList,
spectraCache,
scanList.FragScans[scanPointer],
writer,
reporterIons,
TAB_DELIMITER,
saveUncorrectedIntensities,
mOptions.ReporterIons.ReporterIonSaveObservedMasses);
if (scanList.MasterScanOrderCount > 1)
{
UpdateProgress((short)(masterOrderIndex / (double)(scanList.MasterScanOrderCount - 1) * 100));
}
else
{
UpdateProgress(0);
}
UpdateCacheStats(spectraCache);
if (mOptions.AbortProcessing)
{
break;
}
}
}
if (includeFtmsColumns)
{
// Close the handle to the data file
rawFileReader.CloseRawFile();
}
return(true);
}
catch (Exception ex)
{
ReportError("Error writing the reporter ions to: " + outputFilePath, ex, clsMASIC.eMasicErrorCodes.OutputFileWriteError);
return(false);
}
}
/// <summary>
/// Looks for the reporter ion m/z values, +/- a tolerance
/// Calls AggregateIonsInRange with returnMax = True, meaning we're reporting the maximum ion abundance for each reporter ion m/z
/// </summary>
/// <param name="rawFileReader"></param>
/// <param name="dataAggregation"></param>
/// <param name="includeFtmsColumns"></param>
/// <param name="sicOptions"></param>
/// <param name="scanList"></param>
/// <param name="spectraCache"></param>
/// <param name="currentScan"></param>
/// <param name="writer"></param>
/// <param name="reporterIons"></param>
/// <param name="delimiter"></param>
/// <param name="saveUncorrectedIntensities"></param>
/// <param name="saveObservedMasses"></param>
/// <remarks></remarks>
private void FindReporterIonsWork(
XRawFileIO rawFileReader,
clsDataAggregation dataAggregation,
bool includeFtmsColumns,
clsSICOptions sicOptions,
clsScanList scanList,
clsSpectraCache spectraCache,
clsScanInfo currentScan,
TextWriter writer,
IList <clsReporterIonInfo> reporterIons,
char delimiter,
bool saveUncorrectedIntensities,
bool saveObservedMasses)
{
const bool USE_MAX_ABUNDANCE_IN_WINDOW = true;
// The following will be a value between 0 and 100
// Using Absolute Value of percent change to avoid averaging both negative and positive values
double parentIonMZ;
if (currentScan.FragScanInfo.ParentIonInfoIndex >= 0 && currentScan.FragScanInfo.ParentIonInfoIndex < scanList.ParentIons.Count)
{
parentIonMZ = scanList.ParentIons[currentScan.FragScanInfo.ParentIonInfoIndex].MZ;
}
else
{
parentIonMZ = 0;
}
if (!spectraCache.GetSpectrum(currentScan.ScanNumber, out var spectrum, true))
{
SetLocalErrorCode(clsMASIC.eMasicErrorCodes.ErrorUncachingSpectrum);
return;
}
// Initialize the arrays used to track the observed reporter ion values
var reporterIntensities = new double[reporterIons.Count];
var reporterIntensitiesCorrected = new double[reporterIons.Count];
var closestMZ = new double[reporterIons.Count];
// Initialize the output variables
var dataColumns = new List <string>()
{
sicOptions.DatasetID.ToString(),
currentScan.ScanNumber.ToString(),
currentScan.FragScanInfo.CollisionMode,
StringUtilities.DblToString(parentIonMZ, 2),
StringUtilities.DblToString(currentScan.BasePeakIonIntensity, 2),
StringUtilities.DblToString(currentScan.BasePeakIonMZ, 4)
};
var reporterIntensityList = new List <string>(reporterIons.Count);
var obsMZList = new List <string>(reporterIons.Count);
var uncorrectedIntensityList = new List <string>(reporterIons.Count);
var ftmsSignalToNoise = new List <string>(reporterIons.Count);
var ftmsResolution = new List <string>(reporterIons.Count);
//var ftmsLabelDataMz = new List<string>(reporterIons.Count);
double reporterIntensityMax = 0;
// Find the reporter ion intensities
// Also keep track of the closest m/z for each reporter ion
// Note that we're using the maximum intensity in the range (not the sum)
for (var reporterIonIndex = 0; reporterIonIndex < reporterIons.Count; reporterIonIndex++)
{
var ion = reporterIons[reporterIonIndex];
// Search for the reporter ion MZ in this mass spectrum
reporterIntensities[reporterIonIndex] = dataAggregation.AggregateIonsInRange(
spectrum,
ion.MZ,
ion.MZToleranceDa,
out _,
out closestMZ[reporterIonIndex],
USE_MAX_ABUNDANCE_IN_WINDOW);
ion.SignalToNoise = 0;
ion.Resolution = 0;
ion.LabelDataMZ = 0;
}
if (includeFtmsColumns && currentScan.IsFTMS)
{
// Retrieve the label data for this spectrum
rawFileReader.GetScanLabelData(currentScan.ScanNumber, out var ftLabelData);
// Find each reporter ion in ftLabelData
for (var reporterIonIndex = 0; reporterIonIndex < reporterIons.Count; reporterIonIndex++)
{
var mzToFind = reporterIons[reporterIonIndex].MZ;
var mzToleranceDa = reporterIons[reporterIonIndex].MZToleranceDa;
var highestIntensity = 0.0;
var udtBestMatch = new udtFTLabelInfoType();
var matchFound = false;
foreach (var labelItem in ftLabelData)
{
// Compare labelItem.Mass (which is m/z of the ion in labelItem) to the m/z of the current reporter ion
if (Math.Abs(mzToFind - labelItem.Mass) > mzToleranceDa)
{
continue;
}
// m/z is within range
if (labelItem.Intensity > highestIntensity)
{
udtBestMatch = labelItem;
highestIntensity = labelItem.Intensity;
matchFound = true;
}
}
if (matchFound)
{
reporterIons[reporterIonIndex].SignalToNoise = udtBestMatch.SignalToNoise;
reporterIons[reporterIonIndex].Resolution = udtBestMatch.Resolution;
reporterIons[reporterIonIndex].LabelDataMZ = udtBestMatch.Mass;
}
}
}
// Populate reporterIntensitiesCorrected with the data in reporterIntensities
Array.Copy(reporterIntensities, reporterIntensitiesCorrected, reporterIntensities.Length);
if (mOptions.ReporterIons.ReporterIonApplyAbundanceCorrection)
{
if (mOptions.ReporterIons.ReporterIonMassMode == clsReporterIons.eReporterIonMassModeConstants.ITraqFourMZ ||
mOptions.ReporterIons.ReporterIonMassMode == clsReporterIons.eReporterIonMassModeConstants.ITraqEightMZHighRes ||
mOptions.ReporterIons.ReporterIonMassMode == clsReporterIons.eReporterIonMassModeConstants.ITraqEightMZLowRes ||
mOptions.ReporterIons.ReporterIonMassMode == clsReporterIons.eReporterIonMassModeConstants.TMTTenMZ ||
mOptions.ReporterIons.ReporterIonMassMode == clsReporterIons.eReporterIonMassModeConstants.TMTElevenMZ ||
mOptions.ReporterIons.ReporterIonMassMode == clsReporterIons.eReporterIonMassModeConstants.TMTSixteenMZ)
{
// Correct the reporter ion intensities using the Reporter Ion Intensity Corrector class
if (intensityCorrector.ReporterIonMode != mOptions.ReporterIons.ReporterIonMassMode ||
intensityCorrector.ITraq4PlexCorrectionFactorType != mOptions.ReporterIons.ReporterIonITraq4PlexCorrectionFactorType)
{
intensityCorrector.UpdateReporterIonMode(
mOptions.ReporterIons.ReporterIonMassMode,
mOptions.ReporterIons.ReporterIonITraq4PlexCorrectionFactorType);
}
// Count the number of non-zero data points in reporterIntensitiesCorrected()
var positiveCount = 0;
for (var reporterIonIndex = 0; reporterIonIndex < reporterIons.Count; reporterIonIndex++)
{
if (reporterIntensitiesCorrected[reporterIonIndex] > 0)
{
positiveCount += 1;
}
}
// Apply the correction if 2 or more points are non-zero
if (positiveCount >= 2)
{
intensityCorrector.ApplyCorrection(reporterIntensitiesCorrected);
}
}
}
// Now construct the string of intensity values, delimited by delimiter
// Will also compute the percent change in intensities
// Initialize the variables used to compute the weighted average percent change
double pctChangeSum = 0;
double originalIntensitySum = 0;
for (var reporterIonIndex = 0; reporterIonIndex < reporterIons.Count; reporterIonIndex++)
{
if (!reporterIons[reporterIonIndex].ContaminantIon)
{
// Update the PctChange variables and the IntensityMax variable only if this is not a Contaminant Ion
originalIntensitySum += reporterIntensities[reporterIonIndex];
if (reporterIntensities[reporterIonIndex] > 0)
{
// Compute the percent change, then update pctChangeSum
var pctChange =
(reporterIntensitiesCorrected[reporterIonIndex] - reporterIntensities[reporterIonIndex]) /
reporterIntensities[reporterIonIndex];
// Using Absolute Value here to prevent negative changes from cancelling out positive changes
pctChangeSum += Math.Abs(pctChange * reporterIntensities[reporterIonIndex]);
}
if (reporterIntensitiesCorrected[reporterIonIndex] > reporterIntensityMax)
{
reporterIntensityMax = reporterIntensitiesCorrected[reporterIonIndex];
}
}
if (!reporterIons[reporterIonIndex].ContaminantIon || saveUncorrectedIntensities)
{
// Append the reporter ion intensity to reporterIntensityList
// We skip contaminant ions, unless saveUncorrectedIntensities is True, then we include them
reporterIntensityList.Add(StringUtilities.DblToString(reporterIntensitiesCorrected[reporterIonIndex], 2));
if (saveObservedMasses)
{
// Append the observed reporter mass value to obsMZList
obsMZList.Add(StringUtilities.DblToString(closestMZ[reporterIonIndex], 3));
}
if (saveUncorrectedIntensities)
{
// Append the original, uncorrected intensity value
uncorrectedIntensityList.Add(StringUtilities.DblToString(reporterIntensities[reporterIonIndex], 2));
}
if (includeFtmsColumns)
{
if (Math.Abs(reporterIons[reporterIonIndex].SignalToNoise) < float.Epsilon &&
Math.Abs(reporterIons[reporterIonIndex].Resolution) < float.Epsilon &&
Math.Abs(reporterIons[reporterIonIndex].LabelDataMZ) < float.Epsilon)
{
// A match was not found in the label data; display blanks (not zeroes)
ftmsSignalToNoise.Add(string.Empty);
ftmsResolution.Add(string.Empty);
//ftmsLabelDataMz.Add(string.Empty);
}
else
{
ftmsSignalToNoise.Add(StringUtilities.DblToString(reporterIons[reporterIonIndex].SignalToNoise, 2));
ftmsResolution.Add(StringUtilities.DblToString(reporterIons[reporterIonIndex].Resolution, 2));
//ftmsLabelDataMz.Add(StringUtilities.DblToString(reporterIons(reporterIonIndex).LabelDataMZ, 4));
}
}
}
}
// Compute the weighted average percent intensity correction value
float weightedAvgPctIntensityCorrection;
if (originalIntensitySum > 0)
{
weightedAvgPctIntensityCorrection = (float)(pctChangeSum / originalIntensitySum * 100);
}
else
{
weightedAvgPctIntensityCorrection = 0;
}
// Resize the target list capacity to large enough to hold all data.
dataColumns.Capacity = reporterIntensityList.Count + 3 + obsMZList.Count + uncorrectedIntensityList.Count +
ftmsSignalToNoise.Count + ftmsResolution.Count;
// Append the maximum reporter ion intensity then the individual reporter ion intensities
dataColumns.Add(StringUtilities.DblToString(reporterIntensityMax, 2));
dataColumns.AddRange(reporterIntensityList);
// Append the weighted average percent intensity correction
if (weightedAvgPctIntensityCorrection < float.Epsilon)
{
dataColumns.Add("0");
}
else
{
dataColumns.Add(StringUtilities.DblToString(weightedAvgPctIntensityCorrection, 1));
}
if (saveObservedMasses)
{
dataColumns.AddRange(obsMZList);
}
if (saveUncorrectedIntensities)
{
dataColumns.AddRange(uncorrectedIntensityList);
}
if (includeFtmsColumns)
{
dataColumns.AddRange(ftmsSignalToNoise);
dataColumns.AddRange(ftmsResolution);
// Uncomment to include the label data m/z value in the _ReporterIons.txt file
//if (saveObservedMasses)
// dataColumns.AddRange(ftmsLabelDataMz)
}
writer.WriteLine(string.Join(delimiter.ToString(), dataColumns));
}
