| OpenMS 2.5.0

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_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,
|  | 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

## ◆ preScore() [2/2]

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

## ◆ 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