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... | |
|  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 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... | |
|  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 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 | |
|  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< 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 | 
|---|---|---|---|---|
| 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.
| 
 | 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. | 
| 
 | private | 
Checks wether the given ConsensusFeature contains a channel that is below the given intensity threshold.
| cf | The ConsensusFeature to check. | 
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 | private | 
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
| 
 | 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). | 
| 
 | 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.
| 
 | private | 
Minimum intensity of the precursor to be considered for quantitation.
| 
 | private | 
Minimum precursor purity to accept the spectrum for quantitation.
| 
 | private | 
Minimum reporter ion intensity to be considered for quantitation.
| 
 | private | 
The used quantitation method (itraq4plex, tmt6plex,..).
| 
 | 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_ .
| 
 | 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 |