private int GetScanData(XRawFileIO reader, clsScanInfo scanInfo, out double[] mzList, out double[] intensityList)
{
if (scanInfo.IsFTMS)
{
var labelDataCount = reader.GetScanLabelData(scanInfo.ScanNumber, out var labelData);
if (labelDataCount > 0)
{
mzList = new double[labelDataCount];
intensityList = new double[labelDataCount];
for (var i = 0; i < labelDataCount; i++)
{
mzList[i] = labelData[i].Mass;
intensityList[i] = labelData[i].Intensity;
}
return(labelDataCount);
}
}
var dataPointCount = reader.GetScanData(scanInfo.ScanNumber, out mzList, out intensityList, 0, true);
return(dataPointCount);
}
private static void TestReader(string rawFilePath, bool centroid = false, bool testSumming = false, int scanStart = 0, int scanEnd = 0)
{
try
{
var rawFile = ResolveDataFile(rawFilePath);
if (rawFile == null)
{
return;
}
var options = new ThermoReaderOptions {
LoadMSMethodInfo = mLoadMethods
};
using (var reader = new XRawFileIO(rawFile.FullName, options, mTraceMode))
{
RegisterEvents(reader);
var numScans = reader.GetNumScans();
var collisionEnergyList = string.Empty;
ShowMethod(reader);
var scanStep = 1;
if (scanStart < 1)
{
scanStart = 1;
}
if (scanEnd < 1)
{
scanEnd = numScans;
scanStep = 21;
}
else
{
if (scanEnd < scanStart)
{
scanEnd = scanStart;
}
}
if (scanEnd > numScans)
{
scanEnd = numScans;
}
var msLevelStats = new Dictionary <int, int>();
Console.WriteLine();
Console.WriteLine("Reading data for scans {0} to {1}, step {2}", scanStart, scanEnd, scanStep);
for (var scanNum = scanStart; scanNum <= scanEnd; scanNum += scanStep)
{
if (scanNum > reader.ScanEnd)
{
ConsoleMsgUtils.ShowWarning("Exiting for loop since scan number {0} is greater than the max scan number, {1}", scanNum, reader.ScanEnd);
break;
}
if (mOnlyLoadMSLevelInfo)
{
var msLevel = reader.GetMSLevel(scanNum);
if (msLevelStats.TryGetValue(msLevel, out var msLevelObsCount))
{
msLevelStats[msLevel] = msLevelObsCount + 1;
}
else
{
msLevelStats.Add(msLevel, 1);
}
if (mScanInfoInterval <= 0 || scanNum % mScanInfoInterval == 0)
{
Console.WriteLine("Scan " + scanNum);
}
continue;
}
var success = reader.GetScanInfo(scanNum, out clsScanInfo scanInfo);
if (!success)
{
continue;
}
if (mScanInfoInterval <= 0 || scanNum % mScanInfoInterval == 0)
{
Console.WriteLine("Scan " + scanNum + " at " + scanInfo.RetentionTime.ToString("0.00") + " minutes: " + scanInfo.FilterText);
}
if (mLoadCollisionEnergies)
{
var collisionEnergies = reader.GetCollisionEnergy(scanNum);
if (collisionEnergies.Count == 0)
{
collisionEnergyList = string.Empty;
}
else if (collisionEnergies.Count >= 1)
{
collisionEnergyList = collisionEnergies[0].ToString("0.0");
if (collisionEnergies.Count > 1)
{
for (var index = 1; index <= collisionEnergies.Count - 1; index++)
{
collisionEnergyList += ", " + collisionEnergies[index].ToString("0.0");
}
}
}
if (string.IsNullOrEmpty(collisionEnergyList))
{
Console.WriteLine();
}
else
{
Console.WriteLine("; CE " + collisionEnergyList);
}
}
if (mGetScanEvents)
{
if (scanInfo.TryGetScanEvent("Monoisotopic M/Z:", out var monoMZ))
{
Console.WriteLine("Monoisotopic M/Z: " + monoMZ);
}
if (scanInfo.TryGetScanEvent("Charge State", out var chargeState, true))
{
Console.WriteLine("Charge State: " + chargeState);
}
if (scanInfo.TryGetScanEvent("MS2 Isolation Width", out var isolationWidth, true))
{
Console.WriteLine("MS2 Isolation Width: " + isolationWidth);
}
}
if (!mLoadScanData || (scanNum % 50 != 0 && scanEnd - scanStart > 50))
{
continue;
}
// Get the data for scan scanNum
Console.WriteLine();
Console.WriteLine("Spectrum for scan " + scanNum);
reader.GetScanData(scanNum, out var mzList, out var intensityList, 0, centroid);
var mzDisplayStepSize = 50;
if (centroid)
{
mzDisplayStepSize = 1;
}
for (var i = 0; i <= mzList.Length - 1; i += mzDisplayStepSize)
{
Console.WriteLine(" " + mzList[i].ToString("0.000") + " mz " + intensityList[i].ToString("0"));
}
Console.WriteLine();
const int scansToSum = 15;
if (scanNum + scansToSum < numScans && testSumming)
{
// Get the data for scan scanNum through scanNum + 15
#pragma warning disable 618
reader.GetScanDataSumScans(scanNum, scanNum + scansToSum, out var massIntensityPairs, 0, centroid);
#pragma warning restore 618
Console.WriteLine("Summed spectrum, scans " + scanNum + " through " + (scanNum + scansToSum));
for (var i = 0; i <= massIntensityPairs.GetLength(1) - 1; i += 50)
{
Console.WriteLine(" " + massIntensityPairs[0, i].ToString("0.000") + " mz " +
massIntensityPairs[1, i].ToString("0"));
}
Console.WriteLine();
}
if (!scanInfo.IsFTMS)
{
continue;
}
var dataCount = reader.GetScanLabelData(scanNum, out var ftLabelData);
Console.WriteLine();
Console.WriteLine("{0,12}{1,12}{2,12}{3,12}{4,12}{5,12}", "Mass", "Intensity", "Resolution", "Baseline", "Noise", "Charge");
for (var i = 0; i <= dataCount - 1; i += 50)
{
Console.WriteLine("{0,12:F3}{1,12:0}{2,12:0}{3,12:F1}{4,12:0}{5,12:0}",
ftLabelData[i].Mass,
ftLabelData[i].Intensity,
ftLabelData[i].Resolution,
ftLabelData[i].Baseline,
ftLabelData[i].Noise,
ftLabelData[i].Charge);
}
dataCount = reader.GetScanPrecisionData(scanNum, out var ftPrecisionData);
Console.WriteLine();
Console.WriteLine("{0,12}{1,12}{2,12}{3,12}{4,12}", "Mass", "Intensity", "AccuracyMMU", "AccuracyPPM", "Resolution");
for (var i = 0; i <= dataCount - 1; i += 50)
{
Console.WriteLine("{0,12:F3}{1,12:0}{2,12:F3}{3,12:F3}{4,12:0}",
ftPrecisionData[i].Mass,
ftPrecisionData[i].Intensity, ftPrecisionData[i].AccuracyMMU,
ftPrecisionData[i].AccuracyPPM,
ftPrecisionData[i].Resolution);
}
}
if (mOnlyLoadMSLevelInfo)
{
Console.WriteLine();
Console.WriteLine("{0,-10} {1}", "MSLevel", "Scans");
foreach (var item in msLevelStats)
{
Console.WriteLine("{0, -10} {1}", item.Key, item.Value);
}
}
}
}
catch (Exception ex)
{
ShowError("Error in TestReader: " + ex.Message, ex);
}
}
/// <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));
}