/// <summary>
/// Add the parent ion, or associate the fragmentation scan with an existing parent ion
/// </summary>
/// <param name="scanList"></param>
/// <param name="surveyScanIndex"></param>
/// <param name="parentIonMZ"></param>
/// <param name="fragScanIndex"></param>
/// <param name="spectraCache"></param>
/// <param name="sicOptions"></param>
public void AddUpdateParentIons(
clsScanList scanList,
int surveyScanIndex,
double parentIonMZ,
int fragScanIndex,
clsSpectraCache spectraCache,
clsSICOptions sicOptions)
{
AddUpdateParentIons(scanList, surveyScanIndex, parentIonMZ, 0, 0, fragScanIndex, spectraCache, sicOptions);
}
/// <summary>
/// Check whether the scan number is within the range specified by sicOptions
/// </summary>
/// <param name="scanNumber"></param>
/// <param name="sicOptions"></param>
/// <returns>True if filtering is disabled, or if scanNumber is within the limits</returns>
public bool CheckScanInRange(
int scanNumber,
clsSICOptions sicOptions)
{
if (sicOptions.ScanRangeStart >= 0 && sicOptions.ScanRangeEnd > sicOptions.ScanRangeStart)
{
if (scanNumber < sicOptions.ScanRangeStart || scanNumber > sicOptions.ScanRangeEnd)
{
return(false);
}
}
return(true);
}
/// <summary>
/// Add the parent ion, or associate the fragmentation scan with an existing parent ion
/// </summary>
/// <param name="scanList"></param>
/// <param name="surveyScanIndex"></param>
/// <param name="parentIonMZ"></param>
/// <param name="mrmInfo"></param>
/// <param name="spectraCache"></param>
/// <param name="sicOptions"></param>
public void AddUpdateParentIons(
clsScanList scanList,
int surveyScanIndex,
double parentIonMZ,
clsMRMScanInfo mrmInfo,
clsSpectraCache spectraCache,
clsSICOptions sicOptions)
{
for (var mrmIndex = 0; mrmIndex < mrmInfo.MRMMassCount; mrmIndex++)
{
var mrmDaughterMZ = mrmInfo.MRMMassList[mrmIndex].CentralMass;
var mrmToleranceHalfWidth = Math.Round((mrmInfo.MRMMassList[mrmIndex].EndMass - mrmInfo.MRMMassList[mrmIndex].StartMass) / 2, 6);
if (mrmToleranceHalfWidth < 0.001)
{
mrmToleranceHalfWidth = 0.001;
}
AddUpdateParentIons(scanList, surveyScanIndex, parentIonMZ, mrmDaughterMZ, mrmToleranceHalfWidth, scanList.FragScans.Count - 1, spectraCache, sicOptions);
}
}
/// <summary>
/// Check whether the scan number and elution time are within the ranges specified by sicOptions
/// </summary>
/// <param name="scanNumber"></param>
/// <param name="elutionTime"></param>
/// <param name="sicOptions"></param>
/// <returns>True if filtering is disabled, or if scanNumber and elutionTime are within the limits</returns>
public bool CheckScanInRange(
int scanNumber,
double elutionTime,
clsSICOptions sicOptions)
{
if (!CheckScanInRange(scanNumber, sicOptions))
{
return(false);
}
if (sicOptions.RTRangeStart >= 0 && sicOptions.RTRangeEnd > sicOptions.RTRangeStart)
{
if (elutionTime < sicOptions.RTRangeStart || elutionTime > sicOptions.RTRangeEnd)
{
return(false);
}
}
return(true);
}
/// <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));
}
/// <summary>
/// Add the parent ion, or associate the fragmentation scan with an existing parent ion
///
/// Checks to see if the parent ion specified by surveyScanIndex and parentIonMZ exists in .ParentIons()
/// If mrmDaughterMZ is > 0, also considers that value when determining uniqueness
///
/// If the parent ion entry already exists, adds an entry to .FragScanIndices()
/// If it does not exist, adds a new entry to .ParentIons()
/// </summary>
/// <param name="scanList"></param>
/// <param name="surveyScanIndex">
/// If this is less than 0 the first MS2 scan(s) in the file occurred before we encountered a survey scan
/// In this case, we cannot properly associate the fragmentation scan with a survey scan
/// </param>
/// <param name="parentIonMZ"></param>
/// <param name="mrmDaughterMZ"></param>
/// <param name="mrmToleranceHalfWidth"></param>
/// <param name="fragScanIndex">This is typically equal to scanList.FragScans.Count - 1</param>
/// <param name="spectraCache"></param>
/// <param name="sicOptions"></param>
private void AddUpdateParentIons(
clsScanList scanList,
int surveyScanIndex,
double parentIonMZ,
double mrmDaughterMZ,
double mrmToleranceHalfWidth,
int fragScanIndex,
clsSpectraCache spectraCache,
clsSICOptions sicOptions)
{
const double MINIMUM_TOLERANCE_PPM = 0.01;
const double MINIMUM_TOLERANCE_DA = 0.0001;
var parentIonIndex = 0;
double parentIonTolerance;
if (sicOptions.SICToleranceIsPPM)
{
parentIonTolerance = sicOptions.SICTolerance / sicOptions.CompressToleranceDivisorForPPM;
if (parentIonTolerance < MINIMUM_TOLERANCE_PPM)
{
parentIonTolerance = MINIMUM_TOLERANCE_PPM;
}
}
else
{
parentIonTolerance = sicOptions.SICTolerance / sicOptions.CompressToleranceDivisorForDa;
if (parentIonTolerance < MINIMUM_TOLERANCE_DA)
{
parentIonTolerance = MINIMUM_TOLERANCE_DA;
}
}
// See if an entry exists yet in .ParentIons for the parent ion for this fragmentation scan
var matchFound = false;
if (mrmDaughterMZ > 0)
{
if (sicOptions.SICToleranceIsPPM)
{
// Force the tolerances to 0.01 m/z units
parentIonTolerance = MINIMUM_TOLERANCE_PPM;
}
else
{
// Force the tolerances to 0.01 m/z units
parentIonTolerance = MINIMUM_TOLERANCE_DA;
}
}
if (parentIonMZ > 0)
{
var parentIonToleranceDa = GetParentIonToleranceDa(sicOptions, parentIonMZ, parentIonTolerance);
for (parentIonIndex = scanList.ParentIons.Count - 1; parentIonIndex >= 0; parentIonIndex += -1)
{
if (scanList.ParentIons[parentIonIndex].SurveyScanIndex >= surveyScanIndex)
{
if (Math.Abs(scanList.ParentIons[parentIonIndex].MZ - parentIonMZ) <= parentIonToleranceDa)
{
if (mrmDaughterMZ < double.Epsilon ||
Math.Abs(scanList.ParentIons[parentIonIndex].MRMDaughterMZ - mrmDaughterMZ) <= parentIonToleranceDa)
{
matchFound = true;
break;
}
}
}
else
{
break;
}
}
}
if (!matchFound)
{
// Add a new parent ion entry to .ParentIons(), but only if surveyScanIndex is non-negative
if (surveyScanIndex < 0)
{
return;
}
var newParentIon = new clsParentIonInfo(parentIonMZ)
{
SurveyScanIndex = surveyScanIndex,
CustomSICPeak = false,
MRMDaughterMZ = mrmDaughterMZ,
MRMToleranceHalfWidth = mrmToleranceHalfWidth
};
newParentIon.FragScanIndices.Add(fragScanIndex);
newParentIon.OptimalPeakApexScanNumber = scanList.SurveyScans[surveyScanIndex].ScanNumber; // Was: .FragScans(fragScanIndex).ScanNumber
newParentIon.PeakApexOverrideParentIonIndex = -1;
scanList.FragScans[fragScanIndex].FragScanInfo.ParentIonInfoIndex = scanList.ParentIons.Count;
// Look for .MZ in the survey scan, using a tolerance of parentIonTolerance
// If found, then update the mass to the matched ion
// This is done to determine the parent ion mass more precisely
if (sicOptions.RefineReportedParentIonMZ)
{
if (FindClosestMZ(spectraCache, scanList.SurveyScans, surveyScanIndex, parentIonMZ, parentIonTolerance, out var parentIonMZMatch))
{
newParentIon.UpdateMz(parentIonMZMatch);
}
}
scanList.ParentIons.Add(newParentIon);
return;
}
// Add a new entry to .FragScanIndices() for the matching parent ion
// However, do not add a new entry if this is an MRM scan
if (mrmDaughterMZ < double.Epsilon)
{
scanList.ParentIons[parentIonIndex].FragScanIndices.Add(fragScanIndex);
scanList.FragScans[fragScanIndex].FragScanInfo.ParentIonInfoIndex = parentIonIndex;
}
}
