Extracts individual channels from MS/MS spectra for isobaric labeling experiments. More...
#include <OpenMS/ANALYSIS/QUANTITATION/IsobaricChannelExtractor.h>
Public Member Functions | |
IsobaricChannelExtractor (const IsobaricQuantitationMethod *const quant_method) | |
C'tor to create a new channel extractor for the given quantitation method. More... | |
IsobaricChannelExtractor (const IsobaricChannelExtractor &other) | |
Copy c'tor. More... | |
IsobaricChannelExtractor & | operator= (const IsobaricChannelExtractor &rhs) |
Assignment operator. More... | |
void | extractChannels (const MSExperiment< Peak1D > &ms_exp_data, ConsensusMap &consensus_map) |
Extracts the isobaric channels from the tandem MS data and stores intensity values in a consensus map. More... | |
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DefaultParamHandler (const String &name) | |
Constructor with name that is displayed in error messages. More... | |
DefaultParamHandler (const DefaultParamHandler &rhs) | |
Copy constructor. More... | |
virtual | ~DefaultParamHandler () |
Destructor. More... | |
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
Assignment operator. More... | |
virtual bool | operator== (const DefaultParamHandler &rhs) const |
Equality operator. More... | |
void | setParameters (const Param ¶m) |
Sets the parameters. More... | |
const Param & | getParameters () const |
Non-mutable access to the parameters. More... | |
const Param & | getDefaults () const |
Non-mutable access to the default parameters. More... | |
const String & | getName () const |
Non-mutable access to the name. More... | |
void | setName (const String &name) |
Mutable access to the name. More... | |
const std::vector< String > & | getSubsections () const |
Non-mutable access to the registered subsections. More... | |
Protected Member Functions | |
void | setDefaultParams_ () |
implemented for DefaultParamHandler More... | |
void | updateMembers_ () |
implemented for DefaultParamHandler More... | |
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void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Private Member Functions | |
void | registerChannelsInOutputMap_ (ConsensusMap &consensus_map) |
add channel information to the map after it has been filled More... | |
bool | isValidPrecursor_ (const Precursor &precursor) const |
Checks if the given precursor fulfills all constraints for extractions. More... | |
bool | hasLowIntensityReporter_ (const ConsensusFeature &cf) const |
Checks wether the given ConsensusFeature contains a channel that is below the given intensity threshold. More... | |
DoubleReal | computePrecursorPurity_ (const MSExperiment<>::ConstIterator &ms2_spec, const MSExperiment<>::ConstIterator &precursor) const |
Computes the purity of the precursor given an iterator pointing to the MS/MS spectrum and one to the precursor spectrum. More... | |
DoubleReal | sumPotentialIsotopePeaks_ (const MSExperiment< Peak1D >::ConstIterator &precursor, const Peak1D::CoordinateType &lower_mz_bound, const Peak1D::CoordinateType &upper_mz_bound, Peak1D::CoordinateType theoretical_mz, const Peak1D::CoordinateType isotope_offset) const |
Computes the sum of all isotopic peak intensities in the window defined by (lower|upper)_mz_bound beginning from theoretical_isotope_mz. More... | |
Private Attributes | |
const IsobaricQuantitationMethod * | quant_method_ |
The used quantitation method (itraq4plex, tmt6plex,..). More... | |
String | selected_activation_ |
Used to select only specific types of spectra for the channel extraction. More... | |
Peak2D::CoordinateType | reporter_mass_shift_ |
Allowed deviation between the expected and observed reporter ion m/z. More... | |
Peak2D::IntensityType | min_precursor_intensity_ |
Minimum intensity of the precursor to be considered for quantitation. More... | |
bool | keep_unannotated_precursor_ |
Flag if precursor with missing intensity value or missing precursor spectrum should be included or not. More... | |
Peak2D::IntensityType | min_reporter_intensity_ |
Minimum reporter ion intensity to be considered for quantitation. More... | |
bool | remove_low_intensity_quantifications_ |
Flag if complete qunatification should be discarded if a single reporter ion has an intensity below the threshold given in IsobaricChannelExtractor::min_reporter_intensity_ . More... | |
DoubleReal | min_precursor_purity_ |
Minimum precursor purity to accept the spectrum for quantitation. More... | |
DoubleReal | max_precursor_isotope_deviation_ |
Max. allowed deviation between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precursor. More... | |
Additional Inherited Members | |
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Param | param_ |
Container for current parameters. More... | |
Param | defaults_ |
Container for default parameters. This member should be filled in the constructor of derived classes! More... | |
std::vector< String > | subsections_ |
Container for registered subsections. This member should be filled in the constructor of derived classes! More... | |
String | error_name_ |
Name that is displayed in error messages during the parameter checking. More... | |
bool | check_defaults_ |
If this member is set to false no checking if parameters in done;. More... | |
bool | warn_empty_defaults_ |
If this member is set to false no warning is emitted when defaults are empty;. More... | |
Extracts individual channels from MS/MS spectra for isobaric labeling experiments.
Parameters of this class are:Name | Type | Default | Restrictions | Description |
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select_activation | string | High-energy collision-induced dissociation | Collision-induced dissociation, Post-source decay, Plasma desorption, Surface-induced dissociation, Blackbody infrared radiative dissociation, Electron capture dissociation, Infrared multiphoton dissociation, Sustained off-resonance irradiation, High-energy collision-induced dissociation, Low-energy collision-induced dissociation, Photodissociation, Electron transfer dissociation, | Operate only on MSn scans where any of its precursors features a certain activation method (e.g., usually HCD for iTRAQ). Set to empty string if you want to disable filtering. |
reporter_mass_shift | float | 0.1 | min: 1e-08 max: 0.5 | Allowed shift (left to right) in Da from the expected position. |
min_precursor_intensity | float | 1 | min: 0 | Minimum intensity of the precursor to be extracted. MS/MS scans having a precursor with a lower intensity will not be considered for quantitation. |
keep_unannotated_precursor | string | true | true, false | Flag if precursor with missing intensity value or missing precursor spectrum should be included or not. |
min_reporter_intensity | float | 0 | min: 0 | Minimum intenesity of the individual reporter ions to be used extracted. |
discard_low_intensity_quantifications | string | false | true, false | Remove all reporter intensities if a single reporter is below the threshold given in min_reporter_intensity. |
min_precursor_purity | float | 0 | min: 0 max: 1 | Minimum fraction of the total intensity in the isolation window of the precursor spectrum attributable to the selected precursor. |
precursor_isotope_deviation | float | 0.02 | min: 0 | Maximum allowed deviation between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precursor. |
IsobaricChannelExtractor | ( | const IsobaricQuantitationMethod *const | quant_method | ) |
C'tor to create a new channel extractor for the given quantitation method.
quant_method | IsobaricQuantitationMethod providing the necessery information which channels should be extracted. |
IsobaricChannelExtractor | ( | const IsobaricChannelExtractor & | other | ) |
Copy c'tor.
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private |
Computes the purity of the precursor given an iterator pointing to the MS/MS spectrum and one to the precursor spectrum.
ms2_spec | Iterator pointing to the ms2 spectrum. |
precursor | Iterator pointing to the precursor spectrum of ms2_spec. |
void extractChannels | ( | const MSExperiment< Peak1D > & | ms_exp_data, |
ConsensusMap & | consensus_map | ||
) |
Extracts the isobaric channels from the tandem MS data and stores intensity values in a consensus map.
ms_exp_data | Raw data to search for isobaric quantitation channels. |
consensus_map | Output map containing the identified channels and the corresponding intensities. |
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Checks wether the given ConsensusFeature contains a channel that is below the given intensity threshold.
cf | The ConsensusFeature to check. |
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Checks if the given precursor fulfills all constraints for extractions.
precursor | The precursor to test. |
IsobaricChannelExtractor& operator= | ( | const IsobaricChannelExtractor & | rhs | ) |
Assignment operator.
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private |
add channel information to the map after it has been filled
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protected |
implemented for DefaultParamHandler
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private |
Computes the sum of all isotopic peak intensities in the window defined by (lower|upper)_mz_bound beginning from theoretical_isotope_mz.
precursor | Iterator pointing to the precursor spectrum used for extracting the peaks. |
lower_mz_bound | Lower bound of the isolation window to analyze. |
upper_mz_bound | Upper bound of the isolation window to analyze. |
theoretical_mz | The start position for the search. Note that the intensity at this position will not included in the sum. |
isotope_offset | The offset with which the isolation window should be searched (i.e., +/- NEUTRON_MASS/precursor_charge, +/- determines if it scans from left or right from the theoretical_isotope_mz). |
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protectedvirtual |
implemented for DefaultParamHandler
Reimplemented from DefaultParamHandler.
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private |
Flag if precursor with missing intensity value or missing precursor spectrum should be included or not.
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private |
Max. allowed deviation between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precursor.
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private |
Minimum intensity of the precursor to be considered for quantitation.
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private |
Minimum precursor purity to accept the spectrum for quantitation.
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private |
Minimum reporter ion intensity to be considered for quantitation.
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private |
The used quantitation method (itraq4plex, tmt6plex,..).
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private |
Flag if complete qunatification should be discarded if a single reporter ion has an intensity below the threshold given in IsobaricChannelExtractor::min_reporter_intensity_ .
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private |
Allowed deviation between the expected and observed reporter ion m/z.
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private |
Used to select only specific types of spectra for the channel extraction.
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5 |