XQuestScores Class Reference

An implementation of the scores for cross-link identification from the xQuest algorithm (O. Rinner et al., 2008, "Identification of cross-linked peptides from large sequence databases") More...

#include <OpenMS/ANALYSIS/XLMS/XQuestScores.h>

Static Public Member Functions
static float	preScore (Size matched_alpha, Size ions_alpha, Size matched_beta, Size ions_beta)
	compute a simple and fast to compute pre-score for a cross-link spectrum match More...
static float	preScore (Size matched_alpha, Size ions_alpha)
	compute a simple and fast to compute pre-score for a mono-link spectrum match More...
static double	matchOddsScore (const PeakSpectrum &theoretical_spec, const std::vector< std::pair< Size, Size > > &matched_spec, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool is_xlink_spectrum, Size n_charges=1)
	compute the match-odds score, a score based on the probability of getting the given number of matched peaks by chance More...
static double	weightedTICScoreXQuest (Size alpha_size, Size beta_size, double intsum_alpha, double intsum_beta, double total_current, bool type_is_cross_link)
	compute the weighted total ion current score for a cross-link. Reimplementation from xQuest. More...
static double	weightedTICScore (Size alpha_size, Size beta_size, double intsum_alpha, double intsum_beta, double total_current, bool type_is_cross_link)
	compute the weighted total ion current score for a cross-link. Scaling changed from original xQuest. More...
static double	matchedCurrentChain (const std::vector< std::pair< Size, Size > > &matched_spec_common, const std::vector< std::pair< Size, Size > > &matched_spec_xlinks, const PeakSpectrum &spectrum_common_peaks, const PeakSpectrum &spectrum_xlink_peaks)
	computes sum of peak intensities of matched peaks for either the alpha or the beta peptide More...
static double	totalMatchedCurrent (const std::vector< std::pair< Size, Size > > &matched_spec_common_alpha, const std::vector< std::pair< Size, Size > > &matched_spec_common_beta, const std::vector< std::pair< Size, Size > > &matched_spec_xlinks_alpha, const std::vector< std::pair< Size, Size > > &matched_spec_xlinks_beta, const PeakSpectrum &spectrum_common_peaks, const PeakSpectrum &spectrum_xlink_peaks)
	computes sum of peak intensities of all matched peaks More...
static std::vector< double >	xCorrelation (const PeakSpectrum &spec1, const PeakSpectrum &spec2, Int maxshift, double tolerance)
	computes a crude cross-correlation between two spectra. Crude, because it uses a static binsize based on a tolerance in Da and it uses equal intensities for all peaks More...

Detailed Description

An implementation of the scores for cross-link identification from the xQuest algorithm (O. Rinner et al., 2008, "Identification of cross-linked peptides from large sequence databases")

Member Function Documentation

matchedCurrentChain()

static double matchedCurrentChain ( const std::vector< std::pair< Size, Size > > &  matched_spec_common, const std::vector< std::pair< Size, Size > > &  matched_spec_xlinks, const PeakSpectrum &  spectrum_common_peaks, const PeakSpectrum &  spectrum_xlink_peaks  )

static

computes sum of peak intensities of matched peaks for either the alpha or the beta peptide

Parameters

alignment	between common alpha or beta ions and common experimental peaks
alignment	between xlink alpha or beta ions and xlink experimental peaks
experimental	common ion spectrum
experimental	xlink spectrum

matchOddsScore()

static double matchOddsScore ( const PeakSpectrum &  theoretical_spec, const std::vector< std::pair< Size, Size > > &  matched_spec, double  fragment_mass_tolerance, bool  fragment_mass_tolerance_unit_ppm, bool  is_xlink_spectrum, Size  n_charges = 1  )

static

compute the match-odds score, a score based on the probability of getting the given number of matched peaks by chance

Parameters

theoretical	spectrum, sorted by position
alignment	between the theoretical and the experimental spectra
fragment	mass tolerance of the alignment
fragment	mass tolerance unit of the alignment, true = ppm, false = Da
type	of cross-link, true = cross-link, false = mono-link
number	of considered charges in the theoretical spectrum

preScore() [1/2]

static float preScore ( Size  matched_alpha, Size  ions_alpha, Size  matched_beta, Size  ions_beta  )

static

compute a simple and fast to compute pre-score for a cross-link spectrum match

Parameters

number	of experimental peaks matched to theoretical common ions from the alpha peptide
number	of theoretical ions from the alpha peptide
number	of experimental peaks matched to theoretical common ions from the beta peptide
number	of theoretical ions from the beta peptide

preScore() [2/2]

static float preScore ( Size  matched_alpha, Size  ions_alpha  )

static

compute a simple and fast to compute pre-score for a mono-link spectrum match

Parameters

number	of experimental peaks matched to theoretical common ions from the alpha peptide
number	of theoretical ions from the alpha peptide

totalMatchedCurrent()

static double totalMatchedCurrent ( const std::vector< std::pair< Size, Size > > &  matched_spec_common_alpha, const std::vector< std::pair< Size, Size > > &  matched_spec_common_beta, const std::vector< std::pair< Size, Size > > &  matched_spec_xlinks_alpha, const std::vector< std::pair< Size, Size > > &  matched_spec_xlinks_beta, const PeakSpectrum &  spectrum_common_peaks, const PeakSpectrum &  spectrum_xlink_peaks  )

static

computes sum of peak intensities of all matched peaks

Parameters

alignment	between common alpha ions and common experimental peaks
alignment	between common beta ions and common experimental peaks
alignment	between xlink alpha ions and xlink experimental peaks
alignment	between xlink beta ions and xlink experimental peaks
experimental	common ion spectrum
experimental	xlink spectrum

weightedTICScore()

static double weightedTICScore ( Size  alpha_size, Size  beta_size, double  intsum_alpha, double  intsum_beta, double  total_current, bool  type_is_cross_link  )

static

compute the weighted total ion current score for a cross-link. Scaling changed from original xQuest.

Parameters

sequence	length of alpha peptide
sequence	length of beta peptide
intensity	sum of matched peaks from alpha peptide
intensity	sum of matched peaks from beta peptide
type	of cross-link, true = cross-link, false = mono-link
sum	of peak intensities of the experimental spectrum
true	= cross-link, false = mono-link. in case of a mono-link, beta_size and intsum_beta should be 0

weightedTICScoreXQuest()

static double weightedTICScoreXQuest ( Size  alpha_size, Size  beta_size, double  intsum_alpha, double  intsum_beta, double  total_current, bool  type_is_cross_link  )

static

compute the weighted total ion current score for a cross-link. Reimplementation from xQuest.

Parameters

sequence	length of alpha peptide
sequence	length of beta peptide
intensity	sum of matched peaks from alpha peptide
intensity	sum of matched peaks from beta peptide
type	of cross-link, true = cross-link, false = mono-link
sum	of peak intensities of the experimental spectrum
true	= cross-link, false = mono-link. in case of a mono-link, beta_size and intsum_beta should be 0

xCorrelation()

static std::vector< double > xCorrelation ( const PeakSpectrum &  spec1, const PeakSpectrum &  spec2, Int  maxshift, double  tolerance  )

static

computes a crude cross-correlation between two spectra. Crude, because it uses a static binsize based on a tolerance in Da and it uses equal intensities for all peaks

Parameters

first	spectrum
second	spectrum
number	of bins, that should be considered for shifting the second spectrum. the second spectrum is shifted from -maxshift to +maxshift of tolerance bins and a correlation is computed for each position.
tolerance	or binsize in Da