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 (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