OpenMS  2.8.0
Static Public Member Functions | List of all members
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 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_spectheoretical spectrum, sorted by position
matched_sizenumber of matched peaks between experimental and theoretical spectra
fragment_mass_tolerancethe tolerance of the alignment
fragment_mass_tolerance_unit_ppmthe 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_linearalignment between linear alpha or beta ions and linear experimental peaks
matched_spec_xlinksalignment between xlink alpha or beta ions and xlink experimental peaks
spectrum_linear_peaksexperimental linear ion spectrum
spectrum_xlink_peaksexperimental 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_spectheoretical spectrum, sorted by position
matched_sizealignment between the theoretical and the experimental spectra
fragment_mass_tolerancefragment mass tolerance of the alignment
fragment_mass_tolerance_unit_ppmfragment mass tolerance unit of the alignment, true = ppm, false = Da
is_xlink_spectrumtype of cross-link, true = cross-link, false = mono-link
n_chargesnumber 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_alphanumber of experimental peaks matched to theoretical linear ions from the alpha peptide
ions_alphanumber 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_alphanumber of experimental peaks matched to theoretical linear ions from the alpha peptide
ions_alphanumber of theoretical ions from the alpha peptide
matched_betanumber of experimental peaks matched to theoretical linear ions from the beta peptide
ions_betanumber 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_alphaalignment between linear alpha ions and linear experimental peaks
matched_spec_linear_betaalignment between linear beta ions and linear experimental peaks
matched_spec_xlinks_alphaalignment between xlink alpha ions and xlink experimental peaks
matched_spec_xlinks_betaalignment between xlink beta ions and xlink experimental peaks
spectrum_linear_peaksexperimental linear ion spectrum
spectrum_xlink_peaksexperimental 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_sizesequence length of alpha peptide
beta_sizesequence length of beta peptide
intsum_alphaintensity sum of matched peaks from alpha peptide
intsum_betaintensity sum of matched peaks from beta peptide
total_currentSum of peak intensities of the experimental spectrum
type_is_cross_linkType 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_sizesequence length of alpha peptide
beta_sizesequence length of beta peptide
intsum_alphaintensity sum of matched peaks from alpha peptide
intsum_betaintensity sum of matched peaks from beta peptide
total_currentsum of peak intensities of the experimental spectrum
type_is_cross_linktype 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
spec1first spectrum
spec2second spectrum
maxshiftNumber 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.
toleranceor 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
spec1first spectrum
spec2second spectrum
tolerancetolerance or binsize in Da