 |
OpenMS
2.7.0
|
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... | |
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")
|
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
| 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 |
|
static |
computes sum of peak intensities of matched peaks for either the alpha or the beta peptide
| 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 |
|
static |
compute the match-odds score, a score based on the probability of getting the given number of matched peaks by chance
| 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 |
|
static |
compute a simple and fast to compute pre-score for a mono-link spectrum match
| number | of experimental peaks matched to theoretical linear ions from the alpha peptide |
| number | of theoretical ions from the alpha peptide |
|
static |
compute a simple and fast to compute pre-score for a cross-link spectrum match
| 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 |
|
static |
computes sum of peak intensities of all matched peaks
| 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 |
|
static |
compute the weighted total ion current score for a cross-link. Scaling changed from original xQuest.
| 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 |
|
static |
compute the weighted total ion current score for a cross-link. Reimplementation from xQuest.
| 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 |
|
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
| 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 |
|
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
| spec1 | first spectrum |
| spec2 | second spectrum |
| tolerance | tolerance or binsize in Da |
1.9.1
