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 Size matched_size, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool is_xlink_spectrum=false, 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	matchOddsScoreSimpleSpec (const std::vector< SimpleTSGXLMS::SimplePeak > &theoretical_spec, const Size matched_size, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool is_xlink_spectrum=false, Size n_charges=1)

static double	logOccupancyProb (const PeakSpectrum &theoretical_spec, const Size matched_size, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm)
	compute the logOccupancyProb score, similar to the match_odds, 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_linear, const std::vector< std::pair< Size, Size > > &matched_spec_xlinks, const PeakSpectrum &spectrum_linear_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_linear_alpha, const std::vector< std::pair< Size, Size > > &matched_spec_linear_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_linear_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...

static double	xCorrelationPrescore (const PeakSpectrum &spec1, const PeakSpectrum &spec2, double tolerance)
	computes a crude dot product 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

◆ logOccupancyProb()

static double logOccupancyProb	(	const PeakSpectrum &	theoretical_spec,
		const Size	matched_size,
		double	fragment_mass_tolerance,
		bool	fragment_mass_tolerance_unit_ppm
	)

static

compute the logOccupancyProb score, similar to the match_odds, a score based on the probability of getting the given number of matched peaks by chance

Parameters

theoretical_spec	theoretical spectrum, sorted by position
matched_size	number of matched peaks between experimental and theoretical spectra
fragment_mass_tolerance	the tolerance of the alignment
fragment_mass_tolerance_unit	the tolerance unit of the alignment, true = ppm, false = Da

◆ matchedCurrentChain()

static double matchedCurrentChain	(	const std::vector< std::pair< Size, Size > > &	matched_spec_linear,
		const std::vector< std::pair< Size, Size > > &	matched_spec_xlinks,
		const PeakSpectrum &	spectrum_linear_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 linear alpha or beta ions and linear experimental peaks
alignment	between xlink alpha or beta ions and xlink experimental peaks
experimental	linear ion spectrum
experimental	xlink spectrum

◆ matchOddsScore()

static double matchOddsScore	(	const PeakSpectrum &	theoretical_spec,
		const Size	matched_size,
		double	fragment_mass_tolerance,
		bool	fragment_mass_tolerance_unit_ppm,
		bool	is_xlink_spectrum = `false`,
		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

◆ matchOddsScoreSimpleSpec()

static double matchOddsScoreSimpleSpec	(	const std::vector< SimpleTSGXLMS::SimplePeak > &	theoretical_spec,
		const Size	matched_size,
		double	fragment_mass_tolerance,
		bool	fragment_mass_tolerance_unit_ppm,
		bool	is_xlink_spectrum = `false`,
		Size	n_charges = `1`
	)

static

◆ preScore() [1/2]

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 linear ions from the alpha peptide
number	of theoretical ions from the alpha peptide

◆ preScore() [2/2]

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

◆ totalMatchedCurrent()

static double totalMatchedCurrent	(	const std::vector< std::pair< Size, Size > > &	matched_spec_linear_alpha,
		const std::vector< std::pair< Size, Size > > &	matched_spec_linear_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_linear_peaks,
		const PeakSpectrum &	spectrum_xlink_peaks
	)

static

computes sum of peak intensities of all matched peaks

Parameters

alignment	between linear alpha ions and linear experimental peaks
alignment	between linear beta ions and linear experimental peaks
alignment	between xlink alpha ions and xlink experimental peaks
alignment	between xlink beta ions and xlink experimental peaks
experimental	linear 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

◆ xCorrelationPrescore()

static double xCorrelationPrescore	(	const PeakSpectrum &	spec1,
		const PeakSpectrum &	spec2,
		double	tolerance
	)

static

computes a crude dot product 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

spec1	first spectrum
spec2	second spectrum
tolerance	tolerance or binsize in Da

Static Public Member Functions

Detailed Description

Member Function Documentation

◆ logOccupancyProb()

◆ matchedCurrentChain()

◆ matchOddsScore()

◆ matchOddsScoreSimpleSpec()

◆ preScore() [1/2]

◆ preScore() [2/2]

◆ totalMatchedCurrent()

◆ weightedTICScore()

◆ weightedTICScoreXQuest()

◆ xCorrelation()

◆ xCorrelationPrescore()