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
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virtual |
destructor
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protected |
Modify the first peptide hit of the feature with a modification at pos.
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inlinestatic |
create new object (needed by Factory)
Referenced by BaseLabeler::registerChildren().
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protected |
convert meta information from feature into intensity values for iTRAQ
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inlinestatic |
name of the model (needed by Factory)
Referenced by BaseLabeler::registerChildren().
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protected |
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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.
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protected |
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virtual |
Labeling after detectability simulation.
Implements BaseLabeler.
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virtual |
Labeling between digestion and rt simulation.
Implements BaseLabeler.
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virtual |
Labeling after ionization.
Implements BaseLabeler.
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virtual |
Labeling after raw signal generation.
Implements BaseLabeler.
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virtual |
Labeling after Tandem MS (e.g. iTRAQ)
Implements BaseLabeler.
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virtual |
Labeling after rt simulation.
Implements BaseLabeler.
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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.
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virtual |
Hook to prepare the simulation process.
Implements BaseLabeler.
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protectedvirtual |
Synchronize members with param class.
Reimplemented from DefaultParamHandler.
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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
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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 |