/// <summary>
/// Initializes a new instance of the <see cref="ExtractedIonChromatogram"/> class.
/// Get the extracted ion chromatogram from the whole drift time scan range.
/// </summary>
/// <param name="uimfReader">
/// The UIMF reader.
/// </param>
/// <param name="frameNumber">
/// The frame number.
/// </param>
/// <param name="centerMz">
/// The MZ.
/// </param>
/// <param name="massToleranceInPpm">
/// The mass Tolerance In Ppm.
/// </param>
public ExtractedIonChromatogram(DataReader uimfReader, int frameNumber, double centerMz, double massToleranceInPpm)
{
FrameParams param = uimfReader.GetFrameParams(frameNumber);
this.IntensityPoints = uimfReader.GetXic(
centerMz,
massToleranceInPpm,
frameNumber,
frameNumber,
1,
param.Scans,
DataReader.FrameType.MS1,
DataReader.ToleranceType.PPM);
this.CenterMz = centerMz;
this.MassToleranceInPpm = massToleranceInPpm;
this.NumberOfMobilityScans = param.Scans;
}
/// <summary>
/// Initializes a new instance of the <see cref="ExtractedIonChromatogram"/> class.
/// Get the extracted ion chromatogram from the a particular drift time scan range.
/// </summary>
/// <param name="uimfReader">
/// The uimf reader.
/// </param>
/// <param name="frameNumber">
/// The frame number.
/// </param>
/// <param name="centerMz">
/// The center mz.
/// </param>
/// <param name="massToleranceInPpm">
/// The mass tolerance in ppm.
/// </param>
/// <param name="centerDriftTimeInMs">
/// The center drift time.
/// </param>
/// <param name="driftTimeErrorInMs">
/// The drift time error in ms.
/// </param>
public ExtractedIonChromatogram(DataReader uimfReader, int frameNumber, double centerMz, double massToleranceInPpm, double centerDriftTimeInMs, double driftTimeErrorInMs)
{
FrameParams param = uimfReader.GetFrameParams(frameNumber);
double driftTimeMin = centerDriftTimeInMs - driftTimeErrorInMs;
double driftTimeMax = centerDriftTimeInMs + driftTimeErrorInMs;
double scanWidthInSeconds = param.GetValueDouble(FrameParamKeyType.AverageTOFLength) / 1000000000;
int scanNumberMin = Metrics.DriftTimeInMsToNearestImsScanNumber(driftTimeMin, scanWidthInSeconds, param.Scans);
int scanNumberMax = Metrics.DriftTimeInMsToNearestImsScanNumber(driftTimeMax, scanWidthInSeconds, param.Scans);
this.IntensityPoints = uimfReader.GetXic(
centerMz,
massToleranceInPpm,
frameNumber,
frameNumber,
scanNumberMin,
scanNumberMax,
DataReader.FrameType.MS1,
DataReader.ToleranceType.PPM);
this.CenterMz = centerMz;
this.MassToleranceInPpm = massToleranceInPpm;
this.NumberOfMobilityScans = param.Scans;
}
/// <summary>
/// The score feature using isotopic profile.
/// </summary>
/// <param name="imsPeak">
/// The ims Peak.
/// </param>
/// <param name="reader">
/// The reader.
/// </param>
/// <param name="target">
/// The Target.
/// </param>
/// <param name="isotopicPeakList">
/// The isotopic peak list.
/// </param>
/// <param name="voltageGroup">
/// The voltage Group.
/// </param>
/// <param name="selectedMethod">
/// The selected Method.
/// </param>
/// <param name="globalMaxIntensities">
/// </param>
/// <returns>
/// The <see cref="double"/>.
/// </returns>
/// <exception cref="InvalidOperationException">
/// </exception>
public static double IsotopicProfileScore(StandardImsPeak imsPeak, DataReader reader, IImsTarget target, List<Peak> isotopicPeakList, VoltageGroup voltageGroup, IsotopicScoreMethod selectedMethod, double globalMaxIntensities, double totalScans)
{
// No need to move on if the isotopic profile is not found
// if (observedIsotopicProfile == null || observedIsotopicProfile.MonoIsotopicMass < 1)
// {
// result.AnalysisStatus = AnalysisStatus.IsotopicProfileNotFound;
// continue;
// }
// Find Isotopic Profile
// List<Peak> massSpectrumPeaks;
// IsotopicProfile observedIsotopicProfile = _msFeatureFinder.IterativelyFindMSFeature(massSpectrum, theoreticalIsotopicProfile, out massSpectrumPeaks);
if (target.CompositionWithoutAdduct == null)
{
throw new InvalidOperationException("Cannot score feature using isotopic profile for Ims Target without CompositionWithoutAdduct provided.");
}
// Bad Feature, so get out
if (imsPeak == null)
{
return 0;
}
// Get the scanWindow size
int scanNumberMax = imsPeak.PeakApex.DriftTimeFullWidthHalfMaxHigherBondInScanNumber;
int scanNumberMin = imsPeak.PeakApex.DriftTimeFullWidthHalfMaxLowerBondInScanNumber;
if ((scanNumberMin < 0) || (scanNumberMax > totalScans - 1))
{
return 0;
}
// Get the mass error from the observed feature peak from the Target theoretical peak
double mzOffset = imsPeak.PeakApex.MzCenterInDalton - target.MassWithAdduct;
List<double> observedIsotopicPeakList = new List<double>();
int totalIsotopicIndex = isotopicPeakList.Count;
int[] isotopicIndexMask = new int[totalIsotopicIndex];
// Find an unsaturated peak in the isotopic profile
for (int i = 0; i < totalIsotopicIndex; i++)
{
// Isotopic centerMz
double Mz = isotopicPeakList[i].XValue;
var peakList = reader.GetXic(Mz + mzOffset,
imsPeak.PeakApex.MzWindowToleranceInPpm,
voltageGroup.FirstFrameNumber,
voltageGroup.LastFrameNumber,
scanNumberMin,
scanNumberMax,
DataReader.FrameType.MS1,
DataReader.ToleranceType.PPM);
// Sum the intensities
double sumIntensities = 0;
foreach (var point in peakList)
{
sumIntensities += point.Intensity;
if (point.IsSaturated)
{
isotopicIndexMask[i] = 1;
}
}
sumIntensities /= voltageGroup.FrameAccumulationCount;
observedIsotopicPeakList.Add(sumIntensities);
}
// Return 0 if the intensity sum is really small
if (observedIsotopicPeakList.Sum() < globalMaxIntensities * 0.0003)
{
return 0;
}
// If the unsaturated isotopes are below a certain threshold
if (totalIsotopicIndex - isotopicIndexMask.Sum() <= 1)
{
return 0;
}
if (selectedMethod == IsotopicScoreMethod.Angle)
{
return IsotopicProfileScoreAngle(observedIsotopicPeakList, isotopicPeakList);
}
else if (selectedMethod == IsotopicScoreMethod.EuclideanDistance)
{
return IsotopicProfileScoreEuclidean(observedIsotopicPeakList, isotopicPeakList);
}
else if (selectedMethod == IsotopicScoreMethod.PearsonCorrelation)
{
return PearsonCorrelation(observedIsotopicPeakList, isotopicPeakList);
}
else if (selectedMethod == IsotopicScoreMethod.Bhattacharyya)
{
return BhattacharyyaDistance(observedIsotopicPeakList, isotopicPeakList);
}
else if (selectedMethod == IsotopicScoreMethod.EuclideanDistanceAlternative)
{
return EuclideanAlternative(observedIsotopicPeakList, isotopicPeakList);
}
else
{
throw new NotImplementedException();
}
}
