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 (const PeptideHit &hit, PeakSpectrum &real_spectrum, double fragment_mass_tolerance, bool fragment_mass_unit_ppm, Size max_peptide_len=60, Size max_num_perm=16384)
	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...

Protected Member Functions
int	compareMZ_ (double mz1, double mz2, double fragment_mass_tolerance, bool fragment_mass_unit_ppm) const

template<class InputIterator1 , class InputIterator2 , class OutputIterator >
OutputIterator	getSpectrumDifference_ (InputIterator1 first1, InputIterator1 last1, InputIterator2 first2, InputIterator2 last2, OutputIterator result, double fragment_mass_tolerance, bool fragment_mass_unit_ppm) const

void	computeSiteDeterminingIons_ (const std::vector< PeakSpectrum > &th_spectra, const ProbablePhosphoSites &candidates, std::vector< PeakSpectrum > &site_determining_ions, double fragment_mass_tolerance, bool fragment_mass_unit_ppm) const
	Computes the site determining_ions for the given AS and sequences in candidates. More...

std::vector< Size >	getSites_ (const AASequence &without_phospho) const
	return all phospho sites More...

std::vector< std::vector< Size > >	computePermutations_ (const 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 PeakSpectrum &th, const PeakSpectrum &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, std::multimap< double, Size > &ranking) 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...

Size	numberOfPhosphoEvents_ (const String sequence) const
	Computes number of phospho events in a sequence. More...

AASequence	removePhosphositesFromSequence_ (const String sequence) const
	Create variant of the peptide with all phosphorylations removed. More...

std::vector< PeakSpectrum >	createTheoreticalSpectra_ (const std::vector< std::vector< Size > > &permutations, const AASequence &seq_without_phospho) const
	Create theoretical spectra with all combinations with the number of phosphorylation events. More...

std::vector< PeakSpectrum >	peakPickingPerWindowsInSpectrum_ (PeakSpectrum &real_spectrum) const
	Pick top 10 intensity peaks for each 100 Da windows. More...

std::vector< std::vector< double > >	calculatePermutationPeptideScores_ (std::vector< PeakSpectrum > &th_spectra, const std::vector< PeakSpectrum > &windows_top10, double fragment_mass_tolerance, bool fragment_mass_unit_ppm) const
	Create 10 scores for each theoretical spectrum (permutation), according to Beausoleil et al. Figure 3 b. More...

std::multimap< double, Size >	rankWeightedPermutationPeptideScores_ (const std::vector< std::vector< double > > &peptide_site_scores) const
	Rank weighted permutation scores ascending. More...

Friends
struct	PScore

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()

AScore ( )

Default constructor.

◆ ~AScore()

~AScore ( )

Destructor.

Member Function Documentation

◆ calculatePermutationPeptideScores_()

std::vector<std::vector<double> > calculatePermutationPeptideScores_	(	std::vector< PeakSpectrum > &	th_spectra,
		const std::vector< PeakSpectrum > &	windows_top10,
		double	fragment_mass_tolerance,
		bool	fragment_mass_unit_ppm
	)		const

protected

Create 10 scores for each theoretical spectrum (permutation), according to Beausoleil et al. Figure 3 b.

◆ compareMZ_()

int compareMZ_	(	double	mz1,
		double	mz2,
		double	fragment_mass_tolerance,
		bool	fragment_mass_unit_ppm
	)		const

protected

◆ compute()

PeptideHit compute	(	const PeptideHit &	hit,
		PeakSpectrum &	real_spectrum,
		double	fragment_mass_tolerance,
		bool	fragment_mass_unit_ppm,
		Size	max_peptide_len = `60`,
		Size	max_num_perm = `16384`
	)

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.

◆ computeCumulativeScore_()

double computeCumulativeScore_	(	Size	N,
		Size	n,
		double	p
	)		const

protected

Computes the cumulative binomial probabilities.

◆ computePermutations_()

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

protected

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

◆ computeSiteDeterminingIons_()

void computeSiteDeterminingIons_	(	const std::vector< PeakSpectrum > &	th_spectra,
		const ProbablePhosphoSites &	candidates,
		std::vector< PeakSpectrum > &	site_determining_ions,
		double	fragment_mass_tolerance,
		bool	fragment_mass_unit_ppm
	)		const

protected

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

◆ createTheoreticalSpectra_()

std::vector<PeakSpectrum> createTheoreticalSpectra_	(	const std::vector< std::vector< Size > > &	permutations,
		const AASequence &	seq_without_phospho
	)		const

protected

Create theoretical spectra with all combinations with the number of phosphorylation events.

◆ determineHighestScoringPermutations_()

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

protected

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!

◆ getSites_()

std::vector<Size> getSites_ ( const AASequence & without_phospho ) const

protected

return all phospho sites

◆ getSpectrumDifference_()

OutputIterator getSpectrumDifference_	(	InputIterator1	first1,
		InputIterator1	last1,
		InputIterator2	first2,
		InputIterator2	last2,
		OutputIterator	result,
		double	fragment_mass_tolerance,
		bool	fragment_mass_unit_ppm
	)		const

inlineprotected

getSpectrumDifference_ works similar as the method std::set_difference (http://en.cppreference.com/w/cpp/algorithm/set_difference). set_difference was reimplemented, because it was necessary to overwrite the compare operator to be able to compare the m/z values. not implemented as "operator<", because using tolerances for comparison does not imply total ordering

◆ numberOfMatchedIons_()

Size numberOfMatchedIons_	(	const PeakSpectrum &	th,
		const PeakSpectrum &	windows,
		Size	depth,
		double	fragment_mass_tolerance,
		bool	fragment_mass_tolerance_ppm = `false`
	)		const

protected

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

◆ numberOfPhosphoEvents_()

Size numberOfPhosphoEvents_ ( const String sequence ) const

protected

Computes number of phospho events in a sequence.

◆ peakPickingPerWindowsInSpectrum_()

std::vector<PeakSpectrum> peakPickingPerWindowsInSpectrum_ ( PeakSpectrum & real_spectrum ) const

protected

Pick top 10 intensity peaks for each 100 Da windows.

◆ peptideScore_()

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

protected

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

◆ rankWeightedPermutationPeptideScores_()

std::multimap<double, Size> rankWeightedPermutationPeptideScores_ ( const std::vector< std::vector< double > > & peptide_site_scores ) const

protected

Rank weighted permutation scores ascending.

◆ removePhosphositesFromSequence_()

AASequence removePhosphositesFromSequence_ ( const String sequence ) const

protected

Create variant of the peptide with all phosphorylations removed.

Friends And Related Function Documentation

◆ PScore

friend struct PScore

friend

Public Member Functions

Protected Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

◆ AScore()

◆ ~AScore()

Member Function Documentation

◆ calculatePermutationPeptideScores_()

◆ compareMZ_()

◆ compute()

◆ computeCumulativeScore_()

◆ computePermutations_()

◆ computeSiteDeterminingIons_()

◆ createTheoreticalSpectra_()

◆ determineHighestScoringPermutations_()

◆ getSites_()

◆ getSpectrumDifference_()

◆ numberOfMatchedIons_()

◆ numberOfPhosphoEvents_()

◆ peakPickingPerWindowsInSpectrum_()

◆ peptideScore_()

◆ rankWeightedPermutationPeptideScores_()

◆ removePhosphositesFromSequence_()

Friends And Related Function Documentation

◆ PScore