SILACFilter Class Reference

Filter to use for SILACFiltering. More...

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

List of all members.

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
std::vector< DoubleReal >	getPeakPositions ()
	gets the m/z values of all peaks , which belong the last identified feature
const std::vector< DoubleReal > &	getExpectedMzShifts ()
	gets the m/z shifts relative to mono-isotopic peak of unlabelled peptide
std::vector< SILACPattern > &	getElements ()
	returns all identified elements
Int	getCharge ()
	returns the charge of the filter
std::vector< DoubleReal > &	getMassSeparations ()
	returns the mass shifts of the filter in [Da]
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.
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.
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.
bool	extractMzShiftsAndIntensitiesPicked_ (const MSSpectrum< Peak1D > &, DoubleReal mz, const SILACFiltering &)
	Extracts mass shifts and intensities from the picked data.
bool	extractMzShiftsAndIntensitiesPickedToPattern_ (const MSSpectrum< Peak1D > &, DoubleReal mz, const SILACFiltering &, SILACPattern &pattern)
	Extracts mass shifts and intensities from the picked data and returns pattern information.
bool	intensityFilter_ ()
	Checks all peaks against intensity cutoff.
bool	correlationFilter1_ (const SILACFiltering::SpectrumInterpolation &, DoubleReal mz, const SILACFiltering &)
	Checks peak form correlation between peaks of one isotope.
bool	correlationFilter2_ (const SILACFiltering::SpectrumInterpolation &, DoubleReal mz, const SILACFiltering &)
	Checks peak form correlation between peaks of different isotopes.
bool	averageneFilter_ (DoubleReal mz)
	Checks peak intensities against the averagine model.
Private Attributes
std::vector< DoubleReal >	mass_separations_
	mass shift(s) in [Da] to search for
Int	charge_
	charge of the ions to search for
DoubleReal	model_deviation_
	maximal value of which a predicted SILAC feature may deviate from the averagine model
Size	isotopes_per_peptide_
	number of peaks per peptide to search for
DoubleReal	intensity_cutoff_
	minimal intensity of SILAC features
DoubleReal	intensity_correlation_
	minimal intensity correlation between regions of different peaks
bool	allow_missing_peaks_
	flag for missing peaks
Size	number_of_peptides_
	number of peptides [i.e. number of labelled peptides +1, e.g. for SILAC triplet =3]
std::vector< DoubleReal >	peak_positions_
	peak positions of SILAC pattern
std::vector< DoubleReal >	mz_peptide_separations_
	m/z separtion between individual peptides [e.g. {0 Th, 4 Th, 5 Th}]
std::vector< DoubleReal >	expected_mz_shifts_
	m/z shifts relative to mono-isotopic peak of unlabelled peptide
DoubleReal	isotope_distance_
	distance between isotopic peaks of a peptide in [Th]
std::vector< SILACPattern >	elements_
	holds the recognized features
DoubleReal	current_mz_
	m/z at which the filter is currently applied to
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)
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
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
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)
Static Private Attributes
static IsotopeDistributionCache *	isotope_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

typedef IsotopeDistributionCache::TheoreticalIsotopePattern TheoreticalIsotopePattern [private]

---

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_separations	all mass shifts of the filter
	charge	charge of the ions to search for
	model_deviation	maximum deviation from the averagine model
	isotopes_per_peptide	number of peaks per peptide to search for
	intensity_cutoff	...
	intensity_correlation	minimal intensity correlation between regions of different peaks
	allow_missing_peaks	flag 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:

	rt	RT value of the position
	mz	m/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_ [static, private]

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