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AScore Class Reference

Implementation of the Ascore For a given peptide sequence 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>

Public Member Functions

 AScore ()
 Default constructor. More...
 
 ~AScore ()
 Destructor. More...
 
PeptideHit compute (PeptideHit &hit, RichPeakSpectrum &real_spectrum, DoubleReal fmt, Int number_of_phospho_sites)
 Computes the AScore and returns all computed phospho-sites. The saved sequences contain only phospho informations. All other modifications are dropped due to simplicity. More...
 
DoubleReal computeCumulativeScore (UInt N, UInt n, DoubleReal p)
 Computes the cumulative binomial probabilities. More...
 
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. More...
 
void compute_site_determining_ions (std::vector< RichPeakSpectrum > &th_spectra, ProbablePhosphoSites &candidates, Int charge, std::vector< RichPeakSpectrum > &site_determining_ions)
 Computes the site determining_ions for the given AS and sequences in candidates. More...
 
std::vector< SizecomputeTupel_ (AASequence &without_phospho)
 helperfunction More...
 
std::vector< std::vector< Size > > computePermutations_ (std::vector< Size > tupel, Int number_of_phospho_sites)
 helper function More...
 

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! More...
 
DoubleReal peptideScore_ (std::vector< DoubleReal > &scores)
 computes the peptide score according to Beausoleil et al. page 1291 More...
 

Detailed Description

Implementation of the Ascore For a given peptide sequence 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.

Constructor & Destructor Documentation

AScore ( )

Default constructor.

~AScore ( )

Destructor.

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 saved sequences contain only phospho informations. All other modifications are dropped due to simplicity.

Parameters
hita PeptideHit
real_spectrumspectrum mapped to hit
fmtfragment_mass_tolerance, when comparing real_spectrum to a theoretical spectrum of the amino acid sequence of hit.
number_of_phospho_siteswhich 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.
void compute_site_determining_ions ( std::vector< RichPeakSpectrum > &  th_spectra,
ProbablePhosphoSites candidates,
Int  charge,
std::vector< RichPeakSpectrum > &  site_determining_ions 
)

Computes the site determining_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


OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5