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< 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...

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

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.

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.