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< Size > | getSites (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... | |
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.
AScore | ( | ) |
Default constructor.
~AScore | ( | ) |
Destructor.
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.
hit | a PeptideHit |
real_spectrum | spectrum mapped to hit |
fmt | fragment_mass_tolerance, when comparing real_spectrum to a theoretical spectrum of the amino acid sequence of hit. |
number_of_phospho_sites | which directs the method to search for this number of phosphorylated sites. |
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.
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!
OpenMS / TOPP release 2.0.0 | Documentation generated on Thu Aug 20 2015 01:44:32 using doxygen 1.8.9.1 |