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

static float	preScore (Size matched_alpha, Size ions_alpha)
	compute a simple and fast to compute pre-score for a mono-link spectrum match

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

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

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.

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.

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

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

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

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

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

[in]	theoretical_spec	theoretical spectrum, sorted by position
[in]	matched_size	number of matched peaks between experimental and theoretical spectra
[in]	fragment_mass_tolerance	the tolerance of the alignment
[in]	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

[in]	matched_spec_linear	alignment between linear alpha or beta ions and linear experimental peaks
[in]	matched_spec_xlinks	alignment between xlink alpha or beta ions and xlink experimental peaks
[in]	spectrum_linear_peaks	experimental linear ion spectrum
[in]	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

[in]	theoretical_spec	theoretical spectrum, sorted by position
[in]	matched_size	alignment between the theoretical and the experimental spectra
[in]	fragment_mass_tolerance	fragment mass tolerance of the alignment
[in]	fragment_mass_tolerance_unit_ppm	fragment mass tolerance unit of the alignment, true = ppm, false = Da
[in]	is_xlink_spectrum	type of cross-link, true = cross-link, false = mono-link
[in]	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

[in]	matched_alpha	number of experimental peaks matched to theoretical linear ions from the alpha peptide
[in]	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

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

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

[in]	alpha_size	sequence length of alpha peptide
[in]	beta_size	sequence length of beta peptide
[in]	intsum_alpha	intensity sum of matched peaks from alpha peptide
[in]	intsum_beta	intensity sum of matched peaks from beta peptide
[in]	total_current	Sum of peak intensities of the experimental spectrum
[in]	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

[in]	alpha_size	sequence length of alpha peptide
[in]	beta_size	sequence length of beta peptide
[in]	intsum_alpha	intensity sum of matched peaks from alpha peptide
[in]	intsum_beta	intensity sum of matched peaks from beta peptide
[in]	total_current	sum of peak intensities of the experimental spectrum
[in]	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

[in]	spec1	first spectrum
[in]	spec2	second spectrum
[in]	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.
[in]	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

[in]	spec1	first spectrum
[in]	spec2	second spectrum
[in]	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()