AScore Class Reference

Implementation of the Ascore For a given Peptidesequence and its MS^2 spectrum it is tried to identify the most probable phosphorylation-site(s). For each phosphorylation site a score is calculated, which is an indicator for the probability that this site is phosphorylated. The algorithm is implemented according to Beausoleil et al. More...

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

List of all members.

Public Member Functions
	AScore ()
	Default constructor.
	~AScore ()
	Destructor.
PeptideHit	compute (PeptideHit &hit, RichPeakSpectrum &real_spectrum, DoubleReal fmt, Int number_of_phospho_sites)
	Computes the AScore and returns all computed phospho-sites. The safed sequences contain only phospho informations. All other modifications are dropped due to simplicity.
DoubleReal	computeCumulativeScore (UInt N, UInt n, DoubleReal p)
	Computes the cumulative binomial probabilities.
void	computeHighestPeptides (std::vector< std::vector< DoubleReal > > &peptide_site_scores, std::vector< ProbablePhosphoSites > &sites, std::vector< std::vector< Size > > &permutations)
	Finds the peptides with the highest PeptideScores and outputs all informations for computing the AScore.
void	compute_site_determining_ions (std::vector< RichPeakSpectrum > &th_spectra, ProbablePhosphoSites &candidates, Int charge, std::vector< RichPeakSpectrum > &site_determining_ions)
	Computes the site determing_ions for the given AS and sequences in candidates.
std::vector< Size >	computeTupel_ (AASequence &without_phospho)
	helperfunction
std::vector< std::vector< Size > >	computePermutations_ (std::vector< Size > tupel, Int number_of_phospho_sites)
	helper function
Private Member Functions
Int	numberOfMatchedIons_ (const RichPeakSpectrum &th, const RichPeakSpectrum &windows, Size depth, DoubleReal fmt)
	computes number of matched ions between windows and the given spectrum. All spectra have to be sorted by Position!
DoubleReal	peptideScore_ (std::vector< DoubleReal > &scores)
	computes the peptide score according to Beausoleil et al. page 1291

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Detailed Description

Implementation of the Ascore For a given Peptidesequence and its MS^2 spectrum it is tried to identify the most probable phosphorylation-site(s). For each phosphorylation site a score is calculated, which is an indicator for the probability that this site is phosphorylated. The algorithm is implemented according to Beausoleil et al.

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Constructor & Destructor Documentation

AScore

(

)

Default constructor.

~AScore

(

)

Destructor.

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Member Function Documentation

PeptideHit compute	(	PeptideHit &	hit,
		RichPeakSpectrum &	real_spectrum,
		DoubleReal	fmt,
		Int	number_of_phospho_sites
	)

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

Parameters:

	hit	a PeptideHit
	real_spectrum	spectrum mapped to hit
	fmt	fragment_mass_tolarence, when comparing real_spectrum to a theoretical spectrum of the amino acid seqeunce of hit.
	number_of_phospho_sites	which directs the method to search for this number of phosphorylated sites.

Note:

the original sequence is safed in the PeptideHits as MetaValue Search_engine_sequence.

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

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

DoubleReal computeCumulativeScore	(	UInt	N,
		UInt	n,
		DoubleReal	p
	)

Computes the cumulative binomial probabilities.

void computeHighestPeptides	(	std::vector< std::vector< DoubleReal > > &	peptide_site_scores,
		std::vector< ProbablePhosphoSites > &	sites,
		std::vector< std::vector< Size > > &	permutations
	)

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

Note:

This function assumes that there are more permutations than the assumed number of phosphorylations!

std::vector<std::vector<Size> > computePermutations_	(	std::vector< Size >	tupel,
		Int	number_of_phospho_sites
	)

helper function

std::vector<Size> computeTupel_

(

AASequence &

without_phospho

)

helperfunction

Int numberOfMatchedIons_	(	const RichPeakSpectrum &	th,
		const RichPeakSpectrum &	windows,
		Size	depth,
		DoubleReal	fmt
	)			[private]

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

DoubleReal peptideScore_

(

std::vector< DoubleReal > &

scores

)

[private]

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