DoubleReal IsobaricChannelExtractor::sumPotentialIsotopePeaks_(const MSExperiment<Peak1D>::ConstIterator& precursor,
const Peak1D::CoordinateType& lower_mz_bound,
const Peak1D::CoordinateType& upper_mz_bound,
Peak1D::CoordinateType theoretical_mz,
const Peak1D::CoordinateType isotope_offset) const
{
DoubleReal intensity_contribution = 0.0;
// move theoretical_mz to first potential isotopic peak
theoretical_mz += isotope_offset;
// check if we are still in the isolation window
while (theoretical_mz > lower_mz_bound && theoretical_mz < upper_mz_bound)
{
Size potential_peak = precursor->findNearest(theoretical_mz);
// is isotopic ?
if (fabs(theoretical_mz - (*precursor)[potential_peak].getMZ()) < max_precursor_isotope_deviation_)
{
intensity_contribution += (*precursor)[potential_peak].getIntensity();
}
else
{
// we abort in case of missing peaks
break;
}
// update mz with the defined offset
theoretical_mz += isotope_offset;
}
return intensity_contribution;
}
DoubleReal IsobaricChannelExtractor::computePrecursorPurity_(const MSExperiment<Peak1D>::ConstIterator& ms2_spec, const MSExperiment<Peak1D>::ConstIterator& precursor) const
{
// we cannot analyze precursors without a charge
if (ms2_spec->getPrecursors()[0].getCharge() == 0)
return 1.0;
// compute boundaries
const MSExperiment<>::SpectrumType::ConstIterator isolation_lower_mz = precursor->MZBegin(ms2_spec->getPrecursors()[0].getMZ() - ms2_spec->getPrecursors()[0].getIsolationWindowLowerOffset());
const MSExperiment<>::SpectrumType::ConstIterator isolation_upper_mz = precursor->MZEnd(ms2_spec->getPrecursors()[0].getMZ() + ms2_spec->getPrecursors()[0].getIsolationWindowUpperOffset());
Peak1D::IntensityType total_intensity = 0;
// get total intensity
for (MSExperiment<>::SpectrumType::ConstIterator isolation_it = isolation_lower_mz;
isolation_it != isolation_upper_mz;
++isolation_it)
{
total_intensity += isolation_it->getIntensity();
}
// now get the intensity of the precursor .. we assume everything in the distance of 1/c to belong to the precursor
// for c == charge of precursor
// precursor mz
Size precursor_peak_idx = precursor->findNearest(ms2_spec->getPrecursors()[0].getMZ());
Peak1D precursor_peak = (*precursor)[precursor_peak_idx];
Peak1D::IntensityType precursor_intensity = precursor_peak.getIntensity();
// compute the
double charge_dist = Constants::NEUTRON_MASS_U / (double) ms2_spec->getPrecursors()[0].getCharge();
// search left of precursor for isotopic peaks
precursor_intensity += sumPotentialIsotopePeaks_(precursor, isolation_lower_mz->getMZ(), isolation_upper_mz->getMZ(), precursor_peak.getMZ(), -1 * charge_dist);
// search right of precursor for isotopic peaks
precursor_intensity += sumPotentialIsotopePeaks_(precursor, isolation_lower_mz->getMZ(), isolation_upper_mz->getMZ(), precursor_peak.getMZ(), charge_dist);
return precursor_intensity / total_intensity;
}
