Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
Public Member Functions | List of all members
AScore Class Reference

Implementation of the Ascore For a given peptide sequence and its MS/MS spectrum it identifies the most probable phosphorylation-site(s). For each phosphorylation site a probability score is calculated. The algorithm is implemented according to Beausoleil et al. More...

#include <OpenMS/ANALYSIS/ID/AScore.h>

Public Member Functions

 AScore ()
 Default constructor. More...
 
 ~AScore ()
 Destructor. More...
 
PeptideHit compute (PeptideHit &hit, RichPeakSpectrum &real_spectrum, double fragment_mass_tolerance, bool fragment_mass_unit_ppm) const
 Computes the AScore and returns all computed phospho-sites. The saved sequences contain only phospho information. All other modifications are dropped due to simplicity. More...
 
void computeSiteDeterminingIons (std::vector< RichPeakSpectrum > &th_spectra, ProbablePhosphoSites &candidates, Int charge, std::vector< RichPeakSpectrum > &site_determining_ions) const
 Computes the site determining_ions for the given AS and sequences in candidates. More...
 
std::vector< SizegetSites (AASequence &without_phospho) const
 return all phospho sites More...
 
std::vector< std::vector< Size > > computePermutations (std::vector< Size > sites, Int n_phosphorylation_events) const
 calculate all n_phosphorylation_events sized sets of phospho sites (all versions of the peptides with exactly n_phosphorylation_events) More...
 
Size numberOfMatchedIons (const RichPeakSpectrum &th, const RichPeakSpectrum &windows, Size depth, double fragment_mass_tolerance, bool fragment_mass_tolerance_ppm=false) const
 Computes number of matched ions between windows and the given spectrum. All spectra have to be sorted by position! More...
 
double peptideScore (const std::vector< double > &scores) const
 Computes the peptide score according to Beausoleil et al. page 1291. More...
 
void determineHighestScoringPermutations (const std::vector< std::vector< double > > &peptide_site_scores, std::vector< ProbablePhosphoSites > &sites, const std::vector< std::vector< Size > > &permutations) const
 Finds the peptides with the highest PeptideScores and outputs all information for computing the AScore. More...
 
double computeCumulativeScore (Size N, Size n, double p) const
 Computes the cumulative binomial probabilities. More...
 

Detailed Description

Implementation of the Ascore For a given peptide sequence and its MS/MS spectrum it identifies the most probable phosphorylation-site(s). For each phosphorylation site a probability score is calculated. The algorithm is implemented according to Beausoleil et al.

Constructor & Destructor Documentation

AScore ( )

Default constructor.

~AScore ( )

Destructor.

Member Function Documentation

PeptideHit compute ( PeptideHit hit,
RichPeakSpectrum real_spectrum,
double  fragment_mass_tolerance,
bool  fragment_mass_unit_ppm 
) const

Computes the AScore and returns all computed phospho-sites. The saved sequences contain only phospho information. All other modifications are dropped due to simplicity.

Parameters
hita PeptideHit
real_spectrumspectrum mapped to hit
fmtfragment_mass_tolerance, when comparing real_spectrum to a theoretical spectrum of the amino acid sequence of hit.
number_of_phospho_siteswhich directs the method to search for this number of phosphorylated sites.
Note
the original sequence is saved in the PeptideHits as MetaValue Search_engine_sequence.
double computeCumulativeScore ( Size  N,
Size  n,
double  p 
) const

Computes the cumulative binomial probabilities.

std::vector<std::vector<Size> > computePermutations ( std::vector< Size sites,
Int  n_phosphorylation_events 
) const

calculate all n_phosphorylation_events sized sets of phospho sites (all versions of the peptides with exactly n_phosphorylation_events)

void computeSiteDeterminingIons ( std::vector< RichPeakSpectrum > &  th_spectra,
ProbablePhosphoSites candidates,
Int  charge,
std::vector< RichPeakSpectrum > &  site_determining_ions 
) const

Computes the site determining_ions for the given AS and sequences in candidates.

void determineHighestScoringPermutations ( const std::vector< std::vector< double > > &  peptide_site_scores,
std::vector< ProbablePhosphoSites > &  sites,
const std::vector< std::vector< Size > > &  permutations 
) const

Finds the peptides with the highest PeptideScores and outputs all information for computing the AScore.

Note
This function assumes that there are more permutations than the assumed number of phosphorylations!
std::vector<Size> getSites ( AASequence without_phospho) const

return all phospho sites

Size numberOfMatchedIons ( const RichPeakSpectrum th,
const RichPeakSpectrum windows,
Size  depth,
double  fragment_mass_tolerance,
bool  fragment_mass_tolerance_ppm = false 
) const

Computes number of matched ions between windows and the given spectrum. All spectra have to be sorted by position!

double peptideScore ( const std::vector< double > &  scores) const

Computes the peptide score according to Beausoleil et al. page 1291.


OpenMS / TOPP release 2.0.0 Documentation generated on Thu Aug 20 2015 01:44:32 using doxygen 1.8.9.1