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< DoubleReal > | getPeakPositions () |
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< DoubleReal > | mass_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< DoubleReal > | peak_positions_ |
peak positions of SILAC pattern More... | |
std::vector< DoubleReal > | mz_peptide_separations_ |
m/z separtion between individual peptides [e.g. {0 Th, 4 Th, 5 Th}] More... | |
std::vector< DoubleReal > | expected_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< SILACPattern > | elements_ |
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 IsotopeDistributionCache * | isotope_distribution_ |
Friends | |
class | SILACFiltering |
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.
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
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 |
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Checks peak intensities against the averagine model.
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Checks peak form correlation between peaks of one isotope.
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Checks peak form correlation between peaks of different isotopes.
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Extracts mass shifts and intensities from the raw (interpolated) data.
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Extracts mass shifts and intensities from the picked data.
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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
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private |
Checks all peaks against intensity cutoff.
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private |
Checks if there exists a SILAC feature at the given position in the raw (interpolated) data, which corresponds to the filter's properties.
rt | RT value of the position |
mz | m/z value of the position |
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Checks if there exists a SILAC feature at the given position in the picked data.
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friend |
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flag for missing peaks
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charge of the ions to search for
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m/z at which the filter is currently applied to
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holds the recognized features
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intensities at mz + exact_shifts in a SILAC pattern, where mz is the m/z of the mono-isotopic peak of light peptide
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m/z positions mz + exact_shifts in a SILAC pattern, where mz is the m/z of the mono-isotopic peak of light peptide
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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)
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m/z shifts relative to mono-isotopic peak of unlabelled peptide
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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)
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minimal intensity correlation between regions of different peaks
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minimal intensity of SILAC features
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distance between isotopic peaks of a peptide in [Th]
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Isotope distributions
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number of peaks per peptide to search for
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mass shift(s) in [Da] to search for
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maximal value of which a predicted SILAC feature may deviate from the averagine model
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m/z separtion between individual peptides [e.g. {0 Th, 4 Th, 5 Th}]
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number of peptides [i.e. number of labelled peptides +1, e.g. for SILAC triplet =3]
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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 |