PScore

class pyopenms.PScore

Bases: object

Cython implementation of _PScore

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1PScore.html

__init__()

  • Cython signature: void PScore()

  • Cython signature: void PScore(PScore &)

Methods

__init__

  • Cython signature: void PScore()

calculateIntensityRankInMZWindow

Cython signature: libcpp_vector[size_t] calculateIntensityRankInMZWindow(libcpp_vector[double] & mz, libcpp_vector[double] & intensities, double mz_window)

calculatePeakLevelSpectra

Cython signature: libcpp_map[size_t,MSSpectrum] calculatePeakLevelSpectra(MSSpectrum & spec, libcpp_vector[size_t] & ranks, size_t min_level, size_t max_level)

calculateRankMap

Cython signature: libcpp_vector[libcpp_vector[size_t]] calculateRankMap(MSExperiment & peak_map, double mz_window)

computePScore

  • Cython signature: double computePScore(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, libcpp_map[size_t,MSSpectrum] & peak_level_spectra, libcpp_vector[MSSpectrum] & theo_spectra, double mz_window)
calculateIntensityRankInMZWindow()

Cython signature: libcpp_vector[size_t] calculateIntensityRankInMZWindow(libcpp_vector[double] & mz, libcpp_vector[double] & intensities, double mz_window)

The peak rank is defined as the number of neighboring peaks in +/- (mz_window/2) that have higher intensity The result can be used to efficiently filter spectra for top 1..n peaks in mass windows —– :param mz: The m/z positions of the peaks :param intensities: The intensities of the peaks :param mz_window: The window in Thomson centered at each peak

calculatePeakLevelSpectra()

Cython signature: libcpp_map[size_t,MSSpectrum] calculatePeakLevelSpectra(MSSpectrum & spec, libcpp_vector[size_t] & ranks, size_t min_level, size_t max_level)

A spectrum of peak level n retains the (n+1) top intensity peaks in a sliding mz_window centered at each peak

calculateRankMap()

Cython signature: libcpp_vector[libcpp_vector[size_t]] calculateRankMap(MSExperiment & peak_map, double mz_window)

Parameters

  • peak_map – Fragment spectra used for rank calculation. Typically a peak map after removal of all MS1 spectra

  • mz_window – Window in Thomson centered at each peak

computePScore()

  • Cython signature: double computePScore(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, libcpp_map[size_t,MSSpectrum] & peak_level_spectra, libcpp_vector[MSSpectrum] & theo_spectra, double mz_window)

Similar to Andromeda, a vector of theoretical spectra can be provided that e.g. contain loss spectra or higher charge spectra depending on the sequence. The best score obtained by scoring all those theoretical spectra against the experimental ones is returned —– :param fragment_mass_tolerance: Mass tolerance for matching peaks :param fragment_mass_tolerance_unit_ppm: Whether Thomson or ppm is used :param peak_level_spectra: Spectra for different peak levels (=filtered by maximum rank). :param theo_spectra: Theoretical spectra as obtained e.g. from TheoreticalSpectrumGenerator :param mz_window: Window in Thomson centered at each peak

  • Cython signature: double computePScore(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, libcpp_map[size_t,MSSpectrum] & peak_level_spectra, MSSpectrum & theo_spectrum, double mz_window)

Parameters

  • fragment_mass_tolerance – Mass tolerance for matching peaks

  • fragment_mass_tolerance_unit_ppm – Whether Thomson or ppm is used

  • peak_level_spectra – Spectra for different peak levels (=filtered by maximum rank)

  • theo_spectra – Theoretical spectra as obtained e.g. from TheoreticalSpectrumGenerator

  • mz_window – Window in Thomson centered at each peak