private void ComputeNoiseLevelForMassSpectrum(
clsScanInfo scanInfo,
clsMSSpectrum msSpectrum,
clsBaselineNoiseOptions noiseThresholdOptions)
{
const bool IGNORE_NON_POSITIVE_DATA = true;
scanInfo.BaselineNoiseStats = clsMASICPeakFinder.InitializeBaselineNoiseStats(0, noiseThresholdOptions.BaselineNoiseMode);
if (noiseThresholdOptions.BaselineNoiseMode == clsMASICPeakFinder.eNoiseThresholdModes.AbsoluteThreshold)
{
scanInfo.BaselineNoiseStats.NoiseLevel = noiseThresholdOptions.BaselineNoiseLevelAbsolute;
scanInfo.BaselineNoiseStats.PointsUsed = 1;
}
else if (msSpectrum.IonCount > 0)
{
mPeakFinder.ComputeTrimmedNoiseLevel(
msSpectrum.IonsIntensity, 0, msSpectrum.IonCount - 1,
noiseThresholdOptions, IGNORE_NON_POSITIVE_DATA,
out var newBaselineNoiseStats);
scanInfo.BaselineNoiseStats = newBaselineNoiseStats;
}
}
private bool LoadSpectraForThermoRawFile(
XRawFileIO xcaliburAccessor,
clsSpectraCache spectraCache,
clsScanInfo scanInfo,
clsBaselineNoiseOptions noiseThresholdOptions,
bool discardLowIntensityData,
bool compressSpectraData,
double msDataResolution,
bool keepRawSpectrum)
{
var lastKnownLocation = "Start";
try
{
// Load the ions for this scan
lastKnownLocation = "xcaliburAccessor.GetScanData for scan " + scanInfo.ScanNumber;
// Retrieve the m/z and intensity values for the given scan
// We retrieve the profile-mode data, since that's required for determining spectrum noise
scanInfo.IonCountRaw = xcaliburAccessor.GetScanData(scanInfo.ScanNumber, out var mzList, out var intensityList);
if (scanInfo.IonCountRaw > 0)
{
var ionCountVerified = VerifyDataSorted(scanInfo.ScanNumber, scanInfo.IonCountRaw, mzList, intensityList);
if (ionCountVerified != scanInfo.IonCountRaw)
{
scanInfo.IonCountRaw = ionCountVerified;
}
}
scanInfo.IonCount = scanInfo.IonCountRaw;
lastKnownLocation = "Instantiate new clsMSSpectrum";
var msSpectrum = new clsMSSpectrum(scanInfo.ScanNumber, mzList, intensityList, scanInfo.IonCountRaw);
lastKnownLocation = "Manually determine the base peak m/z and base peak intensity";
// ReSharper disable once CommentTypo
// Regarding BPI, comparison of data read via the ThermoRawFileReader vs.
// that read from the .mzML file for dataset QC_Shew_18_02-run1_02Mar19_Arwen_18-11-02
// showed that 25% of the spectra had incorrect BPI values
double totalIonIntensity = 0;
double basePeakIntensity = 0;
double basePeakMz = 0;
for (var ionIndex = 0; ionIndex < scanInfo.IonCountRaw; ionIndex++)
{
totalIonIntensity += intensityList[ionIndex];
if (intensityList[ionIndex] > basePeakIntensity)
{
basePeakIntensity = intensityList[ionIndex];
basePeakMz = mzList[ionIndex];
}
}
if (Math.Abs(scanInfo.BasePeakIonMZ - basePeakMz) > 0.1)
{
mBpiUpdateCount += 1;
if (mBpiUpdateCount < 10)
{
ConsoleMsgUtils.ShowDebug("Updating BPI in scan {0} from {1:F3} m/z to {2:F3} m/z, and BPI Intensity from {3:F0} to {4:F0}",
scanInfo.ScanNumber, scanInfo.BasePeakIonMZ, basePeakMz, scanInfo.BasePeakIonIntensity, basePeakIntensity);
}
scanInfo.BasePeakIonMZ = basePeakMz;
scanInfo.BasePeakIonIntensity = basePeakIntensity;
}
// Determine the minimum positive intensity in this scan
lastKnownLocation = "Call mMASICPeakFinder.FindMinimumPositiveValue";
scanInfo.MinimumPositiveIntensity = mPeakFinder.FindMinimumPositiveValue(msSpectrum.IonsIntensity, 0);
if (msSpectrum.IonCount > 0)
{
if (scanInfo.TotalIonIntensity < float.Epsilon)
{
scanInfo.TotalIonIntensity = totalIonIntensity;
}
}
else
{
scanInfo.TotalIonIntensity = 0;
}
bool discardLowIntensityDataWork;
bool compressSpectraDataWork;
if (scanInfo.MRMScanType == MRMScanTypeConstants.NotMRM)
{
discardLowIntensityDataWork = discardLowIntensityData;
compressSpectraDataWork = compressSpectraData;
}
else
{
discardLowIntensityDataWork = false;
compressSpectraDataWork = false;
}
lastKnownLocation = "Call ProcessAndStoreSpectrum";
mScanTracking.ProcessAndStoreSpectrum(
scanInfo, this,
spectraCache, msSpectrum,
noiseThresholdOptions,
discardLowIntensityDataWork,
compressSpectraDataWork,
msDataResolution,
keepRawSpectrum);
}
catch (Exception ex)
{
ReportError("Error in LoadSpectraForThermoRawFile (LastKnownLocation: " + lastKnownLocation + ")", ex, clsMASIC.eMasicErrorCodes.InputFileDataReadError);
return(false);
}
return(true);
}
public bool ProcessAndStoreSpectrum(
clsScanInfo scanInfo,
DataInput.clsDataImport dataImportUtilities,
clsSpectraCache spectraCache,
clsMSSpectrum msSpectrum,
clsBaselineNoiseOptions noiseThresholdOptions,
bool discardLowIntensityData,
bool compressData,
double msDataResolution,
bool keepRawSpectrum)
{
var lastKnownLocation = "Start";
try
{
// Determine the noise threshold intensity for this spectrum
// Stored in scanInfo.BaselineNoiseStats
lastKnownLocation = "Call ComputeNoiseLevelForMassSpectrum";
ComputeNoiseLevelForMassSpectrum(scanInfo, msSpectrum, noiseThresholdOptions);
if (!keepRawSpectrum)
{
return(true);
}
// Discard low intensity data, but not for MRM scans
if (discardLowIntensityData && scanInfo.MRMScanType == ThermoRawFileReader.MRMScanTypeConstants.NotMRM)
{
// Discard data below the noise level or below the minimum S/N level
// If we are searching for Reporter ions, then it is important to not discard any of the ions in the region of the reporter ion m/z values
lastKnownLocation = "Call DiscardDataBelowNoiseThreshold";
dataImportUtilities.DiscardDataBelowNoiseThreshold(msSpectrum,
scanInfo.BaselineNoiseStats.NoiseLevel,
mReporterIons.MZIntensityFilterIgnoreRangeStart,
mReporterIons.MZIntensityFilterIgnoreRangeEnd,
noiseThresholdOptions);
scanInfo.IonCount = msSpectrum.IonCount;
}
if (compressData)
{
lastKnownLocation = "Call CompressSpectraData";
// Again, if we are searching for Reporter ions, then it is important to not discard any of the ions in the region of the reporter ion m/z values
CompressSpectraData(msSpectrum, msDataResolution,
mReporterIons.MZIntensityFilterIgnoreRangeStart,
mReporterIons.MZIntensityFilterIgnoreRangeEnd);
}
if (msSpectrum.IonCount > MAX_ALLOWABLE_ION_COUNT)
{
// Do not keep more than 50,000 ions
lastKnownLocation = "Call DiscardDataToLimitIonCount";
mSpectraFoundExceedingMaxIonCount += 1;
// Display a message at the console the first 10 times we encounter spectra with over MAX_ALLOWABLE_ION_COUNT ions
// In addition, display a new message every time a new max value is encountered
if (mSpectraFoundExceedingMaxIonCount <= 10 || msSpectrum.IonCount > mMaxIonCountReported)
{
Console.WriteLine();
Console.WriteLine(
"Note: Scan " + scanInfo.ScanNumber + " has " + msSpectrum.IonCount + " ions; " +
"will only retain " + MAX_ALLOWABLE_ION_COUNT + " (trimmed " +
mSpectraFoundExceedingMaxIonCount.ToString() + " spectra)");
mMaxIonCountReported = msSpectrum.IonCount;
}
dataImportUtilities.DiscardDataToLimitIonCount(msSpectrum,
mReporterIons.MZIntensityFilterIgnoreRangeStart,
mReporterIons.MZIntensityFilterIgnoreRangeEnd,
MAX_ALLOWABLE_ION_COUNT);
scanInfo.IonCount = msSpectrum.IonCount;
}
lastKnownLocation = "Call AddSpectrumToPool";
var success = spectraCache.AddSpectrumToPool(msSpectrum, scanInfo.ScanNumber);
return(success);
}
catch (Exception ex)
{
ReportError("Error in ProcessAndStoreSpectrum (LastKnownLocation: " + lastKnownLocation + ")", ex, clsMASIC.eMasicErrorCodes.InputFileDataReadError);
return(false);
}
}
