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_ppm	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

matched_spec_linear	alignment between linear alpha or beta ions and linear experimental peaks
matched_spec_xlinks	alignment between xlink alpha or beta ions and xlink experimental peaks
spectrum_linear_peaks	experimental linear ion spectrum
spectrum_xlink_peaks	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_spec	theoretical spectrum, sorted by position
matched_size	alignment between the theoretical and the experimental spectra
fragment_mass_tolerance	fragment mass tolerance of the alignment
fragment_mass_tolerance_unit_ppm	fragment mass tolerance unit of the alignment, true = ppm, false = Da
is_xlink_spectrum	type of cross-link, true = cross-link, false = mono-link
n_charges	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

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

matched_alpha	number of experimental peaks matched to theoretical linear ions from the alpha peptide
ions_alpha	number of theoretical ions from the alpha peptide
matched_beta	number of experimental peaks matched to theoretical linear ions from the beta peptide
ions_beta	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

matched_spec_linear_alpha	alignment between linear alpha ions and linear experimental peaks
matched_spec_linear_beta	alignment between linear beta ions and linear experimental peaks
matched_spec_xlinks_alpha	alignment between xlink alpha ions and xlink experimental peaks
matched_spec_xlinks_beta	alignment between xlink beta ions and xlink experimental peaks
spectrum_linear_peaks	experimental linear ion spectrum
spectrum_xlink_peaks	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

alpha_size	sequence length of alpha peptide
beta_size	sequence length of beta peptide
intsum_alpha	intensity sum of matched peaks from alpha peptide
intsum_beta	intensity sum of matched peaks from beta peptide
total_current	Sum of peak intensities of the experimental spectrum
type_is_cross_link	Type of cross-link, true = cross-link, false = mono-link

Returns: 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

alpha_size	sequence length of alpha peptide
beta_size	sequence length of beta peptide
intsum_alpha	intensity sum of matched peaks from alpha peptide
intsum_beta	intensity sum of matched peaks from beta peptide
total_current	sum of peak intensities of the experimental spectrum
type_is_cross_link	type of cross-link, true = cross-link, false = mono-link

Returns: 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

spec1	first spectrum
spec2	second spectrum
maxshift	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()