private float CompareFragSpectraForParentIons(
clsScanList scanList,
clsSpectraCache spectraCache,
int parentIonIndex1,
int parentIonIndex2,
clsBinningOptions binningOptions,
MASICPeakFinder.clsBaselineNoiseOptions noiseThresholdOptions,
DataInput.clsDataImport dataImportUtilities)
{
// Compare the fragmentation spectra for the two parent ions
// Returns the highest similarity score (ranging from 0 to 1)
// Returns 0 if no similarity or no spectra to compare
// Returns -1 if an error
float highestSimilarityScore;
try
{
if (scanList.ParentIons[parentIonIndex1].CustomSICPeak || scanList.ParentIons[parentIonIndex2].CustomSICPeak)
{
// Custom SIC values do not have fragmentation spectra; nothing to compare
highestSimilarityScore = 0;
}
else if (scanList.ParentIons[parentIonIndex1].MRMDaughterMZ > 0 || scanList.ParentIons[parentIonIndex2].MRMDaughterMZ > 0)
{
// MRM Spectra should not be compared
highestSimilarityScore = 0;
}
else
{
highestSimilarityScore = 0;
foreach (var fragSpectrumIndex1 in scanList.ParentIons[parentIonIndex1].FragScanIndices)
{
if (!spectraCache.GetSpectrum(scanList.FragScans[fragSpectrumIndex1].ScanNumber, out var spectrum1, false))
{
SetLocalErrorCode(clsMASIC.eMasicErrorCodes.ErrorUncachingSpectrum);
return(-1);
}
// ReSharper disable once ConditionIsAlwaysTrueOrFalse
if (!clsMASIC.DISCARD_LOW_INTENSITY_MSMS_DATA_ON_LOAD)
#pragma warning disable 162
// ReSharper disable HeuristicUnreachableCode
{
dataImportUtilities.DiscardDataBelowNoiseThreshold(spectrum1, scanList.FragScans[fragSpectrumIndex1].BaselineNoiseStats.NoiseLevel, 0, 0, noiseThresholdOptions);
}
// ReSharper restore HeuristicUnreachableCode
#pragma warning restore 162
foreach (var fragSpectrumIndex2 in scanList.ParentIons[parentIonIndex2].FragScanIndices)
{
if (!spectraCache.GetSpectrum(scanList.FragScans[fragSpectrumIndex2].ScanNumber, out var spectrum2, false))
{
SetLocalErrorCode(clsMASIC.eMasicErrorCodes.ErrorUncachingSpectrum);
return(-1);
}
// ReSharper disable once ConditionIsAlwaysTrueOrFalse
if (!clsMASIC.DISCARD_LOW_INTENSITY_MSMS_DATA_ON_LOAD)
#pragma warning disable 162
// ReSharper disable HeuristicUnreachableCode
{
dataImportUtilities.DiscardDataBelowNoiseThreshold(spectrum2, scanList.FragScans[fragSpectrumIndex2].BaselineNoiseStats.NoiseLevel, 0, 0, noiseThresholdOptions);
}
// ReSharper restore HeuristicUnreachableCode
#pragma warning restore 162
var similarityScore = CompareSpectra(spectrum1, spectrum2, binningOptions);
if (similarityScore > highestSimilarityScore)
{
highestSimilarityScore = similarityScore;
}
}
}
}
}
catch (Exception ex)
{
ReportError("Error in CompareFragSpectraForParentIons", ex);
return(-1);
}
return(highestSimilarityScore);
}
/// <summary>
/// Discard data below the noise threshold
/// </summary>
/// <param name="msSpectrum"></param>
/// <param name="noiseThresholdIntensity"></param>
/// <param name="mzIgnoreRangeStart"></param>
/// <param name="mzIgnoreRangeEnd"></param>
/// <param name="noiseThresholdOptions"></param>
public void DiscardDataBelowNoiseThreshold(
clsMSSpectrum msSpectrum,
double noiseThresholdIntensity,
double mzIgnoreRangeStart,
double mzIgnoreRangeEnd,
MASICPeakFinder.clsBaselineNoiseOptions noiseThresholdOptions)
{
var ionCountNew = 0;
try
{
switch (noiseThresholdOptions.BaselineNoiseMode)
{
case MASICPeakFinder.clsMASICPeakFinder.eNoiseThresholdModes.AbsoluteThreshold:
if (noiseThresholdOptions.BaselineNoiseLevelAbsolute > 0)
{
ionCountNew = 0;
for (var ionIndex = 0; ionIndex < msSpectrum.IonCount; ionIndex++)
{
// Always keep points in the m/z ignore range
// If CheckPointInMZIgnoreRange returns true, set pointPassesFilter to true
var pointPassesFilter = clsUtilities.CheckPointInMZIgnoreRange(msSpectrum.IonsMZ[ionIndex], mzIgnoreRangeStart, mzIgnoreRangeEnd);
if (!pointPassesFilter)
{
// Check the point's intensity against .BaselineNoiseLevelAbsolute
if (msSpectrum.IonsIntensity[ionIndex] >= noiseThresholdOptions.BaselineNoiseLevelAbsolute)
{
pointPassesFilter = true;
}
}
if (pointPassesFilter)
{
msSpectrum.IonsMZ[ionCountNew] = msSpectrum.IonsMZ[ionIndex];
msSpectrum.IonsIntensity[ionCountNew] = msSpectrum.IonsIntensity[ionIndex];
ionCountNew += 1;
}
}
}
else
{
ionCountNew = msSpectrum.IonCount;
}
break;
case MASICPeakFinder.clsMASICPeakFinder.eNoiseThresholdModes.TrimmedMeanByAbundance:
case MASICPeakFinder.clsMASICPeakFinder.eNoiseThresholdModes.TrimmedMeanByCount:
case MASICPeakFinder.clsMASICPeakFinder.eNoiseThresholdModes.TrimmedMedianByAbundance:
if (noiseThresholdOptions.MinimumSignalToNoiseRatio > 0)
{
ionCountNew = 0;
for (var ionIndex = 0; ionIndex < msSpectrum.IonCount; ionIndex++)
{
// Always keep points in the m/z ignore range
// If CheckPointInMZIgnoreRange returns true, set pointPassesFilter to true
var pointPassesFilter = clsUtilities.CheckPointInMZIgnoreRange(msSpectrum.IonsMZ[ionIndex], mzIgnoreRangeStart, mzIgnoreRangeEnd);
if (!pointPassesFilter)
{
// Check the point's intensity against .BaselineNoiseLevelAbsolute
if (MASICPeakFinder.clsMASICPeakFinder.ComputeSignalToNoise(msSpectrum.IonsIntensity[ionIndex], noiseThresholdIntensity) >= noiseThresholdOptions.MinimumSignalToNoiseRatio)
{
pointPassesFilter = true;
}
}
if (pointPassesFilter)
{
msSpectrum.IonsMZ[ionCountNew] = msSpectrum.IonsMZ[ionIndex];
msSpectrum.IonsIntensity[ionCountNew] = msSpectrum.IonsIntensity[ionIndex];
ionCountNew += 1;
}
}
}
else
{
ionCountNew = msSpectrum.IonCount;
}
break;
default:
ReportError("Unknown BaselineNoiseMode encountered in DiscardDataBelowNoiseThreshold: " +
noiseThresholdOptions.BaselineNoiseMode.ToString());
break;
}
if (ionCountNew < msSpectrum.IonCount)
{
msSpectrum.ShrinkArrays(ionCountNew);
}
}
catch (Exception ex)
{
ReportError("Error discarding data below the noise threshold", ex, clsMASIC.eMasicErrorCodes.UnspecifiedError);
}
}
