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SILACFilter Class Reference

Filter to use for SILACFiltering. More...

#include <OpenMS/FILTERING/DATAREDUCTION/SILACFilter.h>

Public Member Functions

 SILACFilter (std::vector< DoubleReal > mass_separations, Int charge, DoubleReal model_deviation, Int isotopes_per_peptide, DoubleReal intensity_cutoff, DoubleReal intensity_correlation, bool allow_missing_peaks)
 detailed constructor for SILAC pair filtering More...
 
std::vector< DoubleRealgetPeakPositions ()
 gets the m/z values of all peaks , which belong the last identified feature More...
 
const std::vector< DoubleReal > & getExpectedMzShifts ()
 gets the m/z shifts relative to mono-isotopic peak of unlabelled peptide More...
 
std::vector< SILACPattern > & getElements ()
 returns all identified elements More...
 
Int getCharge ()
 returns the charge of the filter More...
 
std::vector< DoubleReal > & getMassSeparations ()
 returns the mass shifts of the filter in [Da] More...
 

Private Types

typedef
IsotopeDistributionCache::TheoreticalIsotopePattern 
TheoreticalIsotopePattern
 

Private Member Functions

bool isSILACPattern_ (const MSSpectrum< Peak1D > &, const SILACFiltering::SpectrumInterpolation &, DoubleReal mz, DoubleReal picked_mz, const SILACFiltering &, MSSpectrum< Peak1D > &debug, SILACPattern &pattern)
 Checks if there exists a SILAC feature at the given position in the raw (interpolated) data, which corresponds to the filter's properties. More...
 
bool isSILACPatternPicked_ (const MSSpectrum< Peak1D > &, DoubleReal mz, const SILACFiltering &, MSSpectrum< Peak1D > &debug)
 Checks if there exists a SILAC feature at the given position in the picked data. More...
 
bool extractMzShiftsAndIntensities_ (const MSSpectrum< Peak1D > &, const SILACFiltering::SpectrumInterpolation &, DoubleReal mz, DoubleReal picked_mz, const SILACFiltering &)
 Extracts mass shifts and intensities from the raw (interpolated) data. More...
 
bool extractMzShiftsAndIntensitiesPicked_ (const MSSpectrum< Peak1D > &, DoubleReal mz, const SILACFiltering &)
 Extracts mass shifts and intensities from the picked data. More...
 
bool extractMzShiftsAndIntensitiesPickedToPattern_ (const MSSpectrum< Peak1D > &, DoubleReal mz, const SILACFiltering &, SILACPattern &pattern)
 Extracts mass shifts and intensities from the picked data and returns pattern information. More...
 
bool intensityFilter_ ()
 Checks all peaks against intensity cutoff. More...
 
bool correlationFilter1_ (const SILACFiltering::SpectrumInterpolation &, DoubleReal mz, const SILACFiltering &)
 Checks peak form correlation between peaks of one isotope. More...
 
bool correlationFilter2_ (const SILACFiltering::SpectrumInterpolation &, DoubleReal mz, const SILACFiltering &)
 Checks peak form correlation between peaks of different isotopes. More...
 
bool averageneFilter_ (DoubleReal mz)
 Checks peak intensities against the averagine model. More...
 

Private Attributes

std::vector< DoubleRealmass_separations_
 mass shift(s) in [Da] to search for More...
 
Int charge_
 charge of the ions to search for More...
 
DoubleReal model_deviation_
 maximal value of which a predicted SILAC feature may deviate from the averagine model More...
 
Size isotopes_per_peptide_
 number of peaks per peptide to search for More...
 
DoubleReal intensity_cutoff_
 minimal intensity of SILAC features More...
 
DoubleReal intensity_correlation_
 minimal intensity correlation between regions of different peaks More...
 
bool allow_missing_peaks_
 flag for missing peaks More...
 
Size number_of_peptides_
 number of peptides [i.e. number of labelled peptides +1, e.g. for SILAC triplet =3] More...
 
std::vector< DoubleRealpeak_positions_
 peak positions of SILAC pattern More...
 
std::vector< DoubleRealmz_peptide_separations_
 m/z separtion between individual peptides [e.g. {0 Th, 4 Th, 5 Th}] More...
 
std::vector< DoubleRealexpected_mz_shifts_
 m/z shifts relative to mono-isotopic peak of unlabelled peptide More...
 
DoubleReal isotope_distance_
 distance between isotopic peaks of a peptide in [Th] More...
 
std::vector< SILACPatternelements_
 holds the recognized features More...
 
DoubleReal current_mz_
 m/z at which the filter is currently applied to More...
 
std::vector< std::vector
< DoubleReal > > 
exact_shifts_
 exact m/z shift of isotopic peaks in a SILAC pattern relative to the mono-isotopic peak of the light peptide, peptides (row) x isotope (column) More...
 
std::vector< std::vector
< DoubleReal > > 
exact_mz_positions_
 m/z positions mz + exact_shifts in a SILAC pattern, where mz is the m/z of the mono-isotopic peak of light peptide More...
 
std::vector< std::vector
< DoubleReal > > 
exact_intensities_
 intensities at mz + exact_shifts in a SILAC pattern, where mz is the m/z of the mono-isotopic peak of light peptide More...
 
std::vector< std::vector
< DoubleReal > > 
expected_shifts_
 expected m/z shift of isotopic peaks in a SILAC pattern relative to the mono-isotopic peak of the light peptide, peptides (row) x isotope (column) More...
 

Static Private Attributes

static IsotopeDistributionCacheisotope_distribution_
 

Friends

class SILACFiltering
 

Detailed Description

Filter to use for SILACFiltering.

A SILACFilter searches for SILAC patterns, which correspond to the defined mass shifts and charge. Only peaks are taken into account, which were not blacklisted by other filters before e.g. are not part of a SILAC pair yet.

See Also
SILACFiltering

Member Typedef Documentation

Constructor & Destructor Documentation

SILACFilter ( std::vector< DoubleReal mass_separations,
Int  charge,
DoubleReal  model_deviation,
Int  isotopes_per_peptide,
DoubleReal  intensity_cutoff,
DoubleReal  intensity_correlation,
bool  allow_missing_peaks 
)

detailed constructor for SILAC pair filtering

Parameters
mass_separationsall mass shifts of the filter
chargecharge of the ions to search for
model_deviationmaximum deviation from the averagine model
isotopes_per_peptidenumber of peaks per peptide to search for
intensity_cutoff...
intensity_correlationminimal intensity correlation between regions of different peaks
allow_missing_peaksflag for missing peaks

Member Function Documentation

bool averageneFilter_ ( DoubleReal  mz)
private

Checks peak intensities against the averagine model.

bool correlationFilter1_ ( const SILACFiltering::SpectrumInterpolation ,
DoubleReal  mz,
const SILACFiltering  
)
private

Checks peak form correlation between peaks of one isotope.

bool correlationFilter2_ ( const SILACFiltering::SpectrumInterpolation ,
DoubleReal  mz,
const SILACFiltering  
)
private

Checks peak form correlation between peaks of different isotopes.

bool extractMzShiftsAndIntensities_ ( const MSSpectrum< Peak1D > &  ,
const SILACFiltering::SpectrumInterpolation ,
DoubleReal  mz,
DoubleReal  picked_mz,
const SILACFiltering  
)
private

Extracts mass shifts and intensities from the raw (interpolated) data.

bool extractMzShiftsAndIntensitiesPicked_ ( const MSSpectrum< Peak1D > &  ,
DoubleReal  mz,
const SILACFiltering  
)
private

Extracts mass shifts and intensities from the picked data.

bool extractMzShiftsAndIntensitiesPickedToPattern_ ( const MSSpectrum< Peak1D > &  ,
DoubleReal  mz,
const SILACFiltering ,
SILACPattern pattern 
)
private

Extracts mass shifts and intensities from the picked data and returns pattern information.

Int getCharge ( )

returns the charge of the filter

std::vector<SILACPattern>& getElements ( )

returns all identified elements

const std::vector<DoubleReal>& getExpectedMzShifts ( )

gets the m/z shifts relative to mono-isotopic peak of unlabelled peptide

std::vector<DoubleReal>& getMassSeparations ( )

returns the mass shifts of the filter in [Da]

std::vector<DoubleReal> getPeakPositions ( )

gets the m/z values of all peaks , which belong the last identified feature

bool intensityFilter_ ( )
private

Checks all peaks against intensity cutoff.

bool isSILACPattern_ ( const MSSpectrum< Peak1D > &  ,
const SILACFiltering::SpectrumInterpolation ,
DoubleReal  mz,
DoubleReal  picked_mz,
const SILACFiltering ,
MSSpectrum< Peak1D > &  debug,
SILACPattern pattern 
)
private

Checks if there exists a SILAC feature at the given position in the raw (interpolated) data, which corresponds to the filter's properties.

Parameters
rtRT value of the position
mzm/z value of the position
bool isSILACPatternPicked_ ( const MSSpectrum< Peak1D > &  ,
DoubleReal  mz,
const SILACFiltering ,
MSSpectrum< Peak1D > &  debug 
)
private

Checks if there exists a SILAC feature at the given position in the picked data.

Friends And Related Function Documentation

friend class SILACFiltering
friend

Member Data Documentation

bool allow_missing_peaks_
private

flag for missing peaks

Int charge_
private

charge of the ions to search for

DoubleReal current_mz_
private

m/z at which the filter is currently applied to

std::vector<SILACPattern> elements_
private

holds the recognized features

std::vector<std::vector<DoubleReal> > exact_intensities_
private

intensities at mz + exact_shifts in a SILAC pattern, where mz is the m/z of the mono-isotopic peak of light peptide

std::vector<std::vector<DoubleReal> > exact_mz_positions_
private

m/z positions mz + exact_shifts in a SILAC pattern, where mz is the m/z of the mono-isotopic peak of light peptide

std::vector<std::vector<DoubleReal> > exact_shifts_
private

exact m/z shift of isotopic peaks in a SILAC pattern relative to the mono-isotopic peak of the light peptide, peptides (row) x isotope (column)

std::vector<DoubleReal> expected_mz_shifts_
private

m/z shifts relative to mono-isotopic peak of unlabelled peptide

std::vector<std::vector<DoubleReal> > expected_shifts_
private

expected m/z shift of isotopic peaks in a SILAC pattern relative to the mono-isotopic peak of the light peptide, peptides (row) x isotope (column)

DoubleReal intensity_correlation_
private

minimal intensity correlation between regions of different peaks

DoubleReal intensity_cutoff_
private

minimal intensity of SILAC features

DoubleReal isotope_distance_
private

distance between isotopic peaks of a peptide in [Th]

IsotopeDistributionCache* isotope_distribution_
staticprivate

Isotope distributions

Size isotopes_per_peptide_
private

number of peaks per peptide to search for

std::vector<DoubleReal> mass_separations_
private

mass shift(s) in [Da] to search for

DoubleReal model_deviation_
private

maximal value of which a predicted SILAC feature may deviate from the averagine model

std::vector<DoubleReal> mz_peptide_separations_
private

m/z separtion between individual peptides [e.g. {0 Th, 4 Th, 5 Th}]

Size number_of_peptides_
private

number of peptides [i.e. number of labelled peptides +1, e.g. for SILAC triplet =3]

std::vector<DoubleReal> peak_positions_
private

peak positions of SILAC pattern


OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:30 using doxygen 1.8.5