Simulate iTRAQ experiments. More...
#include <OpenMS/SIMULATION/LABELING/ITRAQLabeler.h>
 
  
 | Public Types | |
| typedef ItraqConstants::ChannelInfo | ChannelInfo | 
| typedef ItraqConstants::ChannelMapType | ChannelMapType | 
| typedef ItraqConstants::IsotopeMatrices | IsotopeMatrices | 
| Public Member Functions | |
| ITRAQLabeler () | |
| default constructor  More... | |
| virtual | ~ITRAQLabeler () | 
| destructor  More... | |
| void | preCheck (Param ¶m) const | 
| Checks the (simulation) params passed if they are consistent with the labeling technique.  More... | |
| void | setUpHook (FeatureMapSimVector &) | 
| Hook to prepare the simulation process.  More... | |
| void | postDigestHook (FeatureMapSimVector &) | 
| Labeling between digestion and rt simulation.  More... | |
| void | postRTHook (FeatureMapSimVector &) | 
| Labeling after rt simulation.  More... | |
| void | postDetectabilityHook (FeatureMapSimVector &) | 
| Labeling after detectability simulation.  More... | |
| void | postIonizationHook (FeatureMapSimVector &) | 
| Labeling after ionization.  More... | |
| void | postRawMSHook (FeatureMapSimVector &) | 
| Labeling after raw signal generation.  More... | |
| void | postRawTandemMSHook (FeatureMapSimVector &, MSSimExperiment &) | 
| Labeling after Tandem MS (e.g. iTRAQ)  More... | |
|  Public Member Functions inherited from BaseLabeler | |
| BaseLabeler () | |
| constructor  More... | |
| virtual | ~BaseLabeler () | 
| destructor  More... | |
| virtual Param | getDefaultParameters () const | 
| Returns the default parameters. Re-implement.  More... | |
| virtual void | setRnd (const SimRandomNumberGenerator &rng) | 
| Set the random number generator.  More... | |
| ConsensusMap & | getConsensus () | 
| const String & | getDescription () const | 
| Get short description of the labeler (e.g., channels used)  More... | |
| String | getChannelIntensityName (const Size channel_index) const | 
| to ensure standardized meta value names across labelers for channel intensity  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... | |
| Static Public Member Functions | |
| static BaseLabeler * | create () | 
| create new object (needed by Factory)  More... | |
| static const String | getProductName () | 
| name of the model (needed by Factory)  More... | |
|  Static Public Member Functions inherited from BaseLabeler | |
| static void | registerChildren () | 
| register all derived classes here (implemented in file BaseLabeler_impl.h)  More... | |
| Protected Member Functions | |
| void | addModificationToPeptideHit_ (Feature &feature, const String &modification, const Size &pos) const | 
| Modify the first peptide hit of the feature with a modification at pos.  More... | |
| void | labelPeptide_ (const Feature &feature, FeatureMapSim &result) const | 
| tag a feature with iTRAQ modifications  More... | |
| Feature | mergeFeatures_ (Feature &labeled_channel_feature, const AASequence &unmodified_sequence, std::map< AASequence, Feature > &unlabeled_features_index) const | 
| void | updateMembers_ () | 
| Synchronize members with param class.  More... | |
| DoubleReal | getRTProfileIntensity_ (const Feature &f, const DoubleReal MS2_RT_time) const | 
| Matrix< SimIntensityType > | getItraqIntensity_ (const Feature &f, const DoubleReal MS2_RT_time) const | 
| convert meta information from feature into intensity values for iTRAQ  More... | |
|  Protected Member Functions inherited from BaseLabeler | |
| FeatureMapSim | mergeProteinIdentificationsMaps_ (const FeatureMapSimVector &maps) | 
| Creates an empty FeatureMap with the merged ProteinIdentifications from all FeatureMaps contained in maps.  More... | |
| void | mergeProteinAccessions_ (Feature &target, const Feature &source) const | 
| join all protein references of two features  More... | |
| void | recomputeConsensus_ (const FeatureMapSim &simulated_features) | 
| Based on the stored consensus recompute the associations for the passed features, assuming that the features where derived from the features stored in the consensus.  More... | |
|  Protected Member Functions inherited from DefaultParamHandler | |
| void | defaultsToParam_ () | 
| Updates the parameters after the defaults have been set in the constructor.  More... | |
| Protected Attributes | |
| Int | itraq_type_ | 
| set to either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX  More... | |
| ChannelMapType | channel_map_ | 
| IsotopeMatrices | isotope_corrections_ | 
| Matrices with isotope correction values (one for each plex-type)  More... | |
| DoubleReal | y_labeling_efficiency_ | 
| efficiency of "Y" labeling  More... | |
|  Protected Attributes inherited from BaseLabeler | |
| ConsensusMap | consensus_ | 
| SimRandomNumberGenerator const * | rng_ | 
| String | channel_description_ | 
|  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... | |
Simulate iTRAQ experiments.
Adds reporter ion intensities to MS/MS scans. Supports custom channel allocation and isotope matrices.
Parameters of this class are:| Name | Type | Default | Restrictions | Description | 
|---|---|---|---|---|
| iTRAQ | string | 4plex | 4plex, 8plex | 4plex or 8plex iTRAQ? | 
| reporter_mass_shift | float | 0.1 | min: 0 max: 0.5 | Allowed shift (uniformly distributed - left to right) in Da from the expected position (of e.g. 114.1, 115.1) | 
| channel_active_4plex | string list | [114:myReference] | Four-plex only: Each channel that was used in the experiment and its description (114-117) in format | |
| channel_active_8plex | string list | [113:myReference] | Eight-plex only: Each channel that was used in the experiment and its description (113-121) in format | |
| isotope_correction_values_4plex | string list | [114:0/1/5.9/0.2, 115:0/2/5.6/0.1, 116:0/3/4.5/0.1, 117:0.1/4/3.5/0.1] | override default values (see Documentation); use the following format: | |
| isotope_correction_values_8plex | string list | [113:0/0/6.89/0.22, 114:0/0.94/5.9/0.16, 115:0/1.88/4.9/0.1, 116:0/2.82/3.9/0.07, 117:0.06/3.77/2.99/0, 118:0.09/4.71/1.88/0, 119:0.14/5.66/0.87/0, 121:0.27/7.44/0.18/0] | override default values (see Documentation); use the following format: | |
| Y_contamination | float | 0.3 | min: 0 max: 1 | Efficiency of labeling tyrosine ('Y') residues. 0=off, 1=full labeling | 
| ITRAQLabeler | ( | ) | 
default constructor
| 
 | virtual | 
destructor
| 
 | protected | 
Modify the first peptide hit of the feature with a modification at pos. 
| 
 | inlinestatic | 
create new object (needed by Factory)
Referenced by BaseLabeler::registerChildren().
| 
 | protected | 
convert meta information from feature into intensity values for iTRAQ
| 
 | inlinestatic | 
name of the model (needed by Factory)
Referenced by BaseLabeler::registerChildren().
| 
 | protected | 
| 
 | protected | 
tag a feature with iTRAQ modifications
This might produce several features, due to incomplete labeling of "Y" residues. The resulting features are exact copies, except for their intensity and modification state.
| 
 | protected | 
| 
 | virtual | 
Labeling after detectability simulation.
Implements BaseLabeler.
| 
 | virtual | 
Labeling between digestion and rt simulation.
Implements BaseLabeler.
| 
 | virtual | 
Labeling after ionization.
Implements BaseLabeler.
| 
 | virtual | 
Labeling after raw signal generation.
Implements BaseLabeler.
| 
 | virtual | 
Labeling after Tandem MS (e.g. iTRAQ)
Implements BaseLabeler.
| 
 | virtual | 
Labeling after rt simulation.
Implements BaseLabeler.
| 
 | virtual | 
Checks the (simulation) params passed if they are consistent with the labeling technique.
| param | Param object containing the simulation parameters | 
| Exception::InvalidParameter | if the given parameters are not consistent with the labeling technique | 
Implements BaseLabeler.
| 
 | virtual | 
Hook to prepare the simulation process.
Implements BaseLabeler.
| 
 | protectedvirtual | 
Synchronize members with param class.
Reimplemented from DefaultParamHandler.
| 
 | protected | 
map the channel-name (e.g. 114) onto its description and the centroid mass the channel-name is also the id-string in the mapList section of the ConsensusMap
| 
 | protected | 
Matrices with isotope correction values (one for each plex-type)
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 | protected | 
set to either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX
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 | protected | 
efficiency of "Y" labeling
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:33 using doxygen 1.8.5 |