PScore Struct Reference

Implementation of the PScore PSM scoring algorithm. More...

#include <OpenMS/ANALYSIS/RNPXL/PScore.h>

Static Public Member Functions
static std::vector< Size >	calculateIntensityRankInMZWindow (const std::vector< double > &mz, const std::vector< double > &intensities, double mz_window)
	calculate local (windowed) peak ranks. More...
static std::vector< std::vector< Size > >	calculateRankMap (const PeakMap &peak_map, double mz_window=100)
	precalculated, windowed peak ranks for a whole experiment. More...
static std::map< Size, PeakSpectrum >	calculatePeakLevelSpectra (const PeakSpectrum &spec, const std::vector< Size > &ranks, Size min_level=1, Size max_level=9)
	Calculates spectra for peak level between min_level to max_level and stores them in the map A spectrum of peak level n retains the (n+1) top intensity peaks in a sliding mz_window centered at each peak. More...
static double	computePScore (double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const std::map< Size, PeakSpectrum > &peak_level_spectra, const std::vector< PeakSpectrum > &theo_spectra, double mz_window=100.0)
	Computes the PScore for a vector of theoretical spectra. More...
static double	computePScore (double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const std::map< Size, PeakSpectrum > &peak_level_spectra, const PeakSpectrum &theo_spectrum, double mz_window=100.0)
	Computes the PScore for a single theoretical spectrum. More...
static double	massCorrectionTerm (double mass)
static double	cleavageCorrectionTerm (Size cleavages, bool consecutive_cleavage)
static double	modificationCorrectionTerm (Size modifications)

Detailed Description

Implementation of the PScore PSM scoring algorithm.

Member Function Documentation

calculateIntensityRankInMZWindow()

static std::vector<Size> calculateIntensityRankInMZWindow ( const std::vector< double > &  mz, const std::vector< double > &  intensities, double  mz_window  )

static

calculate local (windowed) peak ranks.

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

Note

ranks are zero based (highest intensity peak in window has rank 0)

Parameters

mz	m/z positions of the peaks
intensities	of the peaks
mz_window	window in Thomson centered at each peak

calculatePeakLevelSpectra()

static std::map<Size, PeakSpectrum > calculatePeakLevelSpectra ( const PeakSpectrum &  spec, const std::vector< Size > &  ranks, Size  min_level = 1, Size  max_level = 9  )

static

Calculates spectra for peak level between min_level to max_level and stores them in the map A spectrum of peak level n retains the (n+1) top intensity peaks in a sliding mz_window centered at each peak.

Note

levels are zero based (level 0 has only the top intensity peaks for each window, level 1 the top and second most intensive one)

min and max level are taken from the Andromeda publication but are similar to the AScore publication

calculateRankMap()

static std::vector<std::vector<Size> > calculateRankMap ( const PeakMap &  peak_map, double  mz_window = 100  )

static

precalculated, windowed peak ranks for a whole experiment.

The peak rank is defined as the number of neighboring peaks in +/- (mz_window/2) that have higher intensity

1. Each spectrum is subdivided into windows of size mz_window.
2. For each window, peak ranks are assigned using calculateIntensityRankInMZWindow().
3. A rank map is returned

Note

ranks are zero based (top element has rank 0)

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

cleavageCorrectionTerm()

static double cleavageCorrectionTerm ( Size  cleavages, bool  consecutive_cleavage  )

static

correction term for type of cleavage. For reference see the Andromeda source code.

Note

constants used in the correction term might be instrument dependent

computePScore() [1/2]

static double computePScore ( double  fragment_mass_tolerance, bool  fragment_mass_tolerance_unit_ppm, const std::map< Size, PeakSpectrum > &  peak_level_spectra, const PeakSpectrum &  theo_spectrum, double  mz_window = 100.0  )

static

Computes the PScore for a single theoretical spectrum.

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

computePScore() [2/2]

static double computePScore ( double  fragment_mass_tolerance, bool  fragment_mass_tolerance_unit_ppm, const std::map< Size, PeakSpectrum > &  peak_level_spectra, const std::vector< PeakSpectrum > &  theo_spectra, double  mz_window = 100.0  )

static

Computes the PScore for a vector of theoretical spectra.

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.

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

massCorrectionTerm()

static double massCorrectionTerm ( double  mass )

static

additive correction terms used by Andromeda (pscore + massC + cleaveC + modC - 100). For reference see the Andromeda source code.

Note

constants used in the correction term might be instrument dependent

modificationCorrectionTerm()

static double modificationCorrectionTerm ( Size  modifications )

static

correction term for modification. For reference see the Andromeda source code.

Note

constants used in the correction term might be instrument dependent