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IsobaricChannelExtractor Class Reference

Extracts individual channels from MS/MS spectra for isobaric labeling experiments. More...

#include <OpenMS/ANALYSIS/QUANTITATION/IsobaricChannelExtractor.h>

Inheritance diagram for IsobaricChannelExtractor:
DefaultParamHandler

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...
 
IsobaricChannelExtractoroperator= (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...
 
- Public Member Functions inherited from DefaultParamHandler
 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 DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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...
 
- Protected Member Functions inherited from DefaultParamHandler
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 IsobaricQuantitationMethodquant_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

- Protected Attributes inherited from DefaultParamHandler
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< Stringsubsections_
 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...
 

Detailed Description

Extracts individual channels from MS/MS spectra for isobaric labeling experiments.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
select_activation stringHigh-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 float0.1 min: 1e-08 max: 0.5Allowed shift (left to right) in Da from the expected position.
min_precursor_intensity float1 min: 0Minimum 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 stringtrue true, falseFlag if precursor with missing intensity value or missing precursor spectrum should be included or not.
min_reporter_intensity float0 min: 0Minimum intenesity of the individual reporter ions to be used extracted.
discard_low_intensity_quantifications stringfalse true, falseRemove all reporter intensities if a single reporter is below the threshold given in min_reporter_intensity.
min_precursor_purity float0 min: 0 max: 1Minimum fraction of the total intensity in the isolation window of the precursor spectrum attributable to the selected precursor.
precursor_isotope_deviation float0.02 min: 0Maximum allowed deviation between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precursor.

Note:

Constructor & Destructor Documentation

IsobaricChannelExtractor ( const IsobaricQuantitationMethod *const  quant_method)

C'tor to create a new channel extractor for the given quantitation method.

Parameters
quant_methodIsobaricQuantitationMethod providing the necessery information which channels should be extracted.

Copy c'tor.

Member Function Documentation

DoubleReal computePrecursorPurity_ ( const MSExperiment<>::ConstIterator &  ms2_spec,
const MSExperiment<>::ConstIterator &  precursor 
) const
private

Computes the purity of the precursor given an iterator pointing to the MS/MS spectrum and one to the precursor spectrum.

Parameters
ms2_specIterator pointing to the ms2 spectrum.
precursorIterator pointing to the precursor spectrum of ms2_spec.
Returns
Fraction of the total intensity in the isolation window of the precursor spectrum that was assigned to the precursor.
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.

Parameters
ms_exp_dataRaw data to search for isobaric quantitation channels.
consensus_mapOutput map containing the identified channels and the corresponding intensities.
bool hasLowIntensityReporter_ ( const ConsensusFeature cf) const
private

Checks wether the given ConsensusFeature contains a channel that is below the given intensity threshold.

Parameters
cfThe ConsensusFeature to check.
Returns
$true$ if a low intensity reporter is contained, $false$ otherwise.
bool isValidPrecursor_ ( const Precursor precursor) const
private

Checks if the given precursor fulfills all constraints for extractions.

Parameters
precursorThe precursor to test.
Returns
$true$ if the precursor can be used for extraction, $false$ otherwise.

Assignment operator.

void registerChannelsInOutputMap_ ( ConsensusMap consensus_map)
private

add channel information to the map after it has been filled

void setDefaultParams_ ( )
protected

implemented for DefaultParamHandler

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
private

Computes the sum of all isotopic peak intensities in the window defined by (lower|upper)_mz_bound beginning from theoretical_isotope_mz.

Parameters
precursorIterator pointing to the precursor spectrum used for extracting the peaks.
lower_mz_boundLower bound of the isolation window to analyze.
upper_mz_boundUpper bound of the isolation window to analyze.
theoretical_mzThe start position for the search. Note that the intensity at this position will not included in the sum.
isotope_offsetThe 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).
void updateMembers_ ( )
protectedvirtual

implemented for DefaultParamHandler

Reimplemented from DefaultParamHandler.

Member Data Documentation

bool keep_unannotated_precursor_
private

Flag if precursor with missing intensity value or missing precursor spectrum should be included or not.

DoubleReal max_precursor_isotope_deviation_
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.

Peak2D::IntensityType min_precursor_intensity_
private

Minimum intensity of the precursor to be considered for quantitation.

DoubleReal min_precursor_purity_
private

Minimum precursor purity to accept the spectrum for quantitation.

Peak2D::IntensityType min_reporter_intensity_
private

Minimum reporter ion intensity to be considered for quantitation.

const IsobaricQuantitationMethod* quant_method_
private

The used quantitation method (itraq4plex, tmt6plex,..).

bool remove_low_intensity_quantifications_
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_ .

Peak2D::CoordinateType reporter_mass_shift_
private

Allowed deviation between the expected and observed reporter ion m/z.

String selected_activation_
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