OpenMS  2.8.0
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
ITRAQLabeler Class Reference

Simulate iTRAQ experiments. More...

#include <OpenMS/SIMULATION/LABELING/ITRAQLabeler.h>

Inheritance diagram for ITRAQLabeler:
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Collaboration diagram for ITRAQLabeler:
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Public Types

typedef ItraqConstants::ChannelInfo ChannelInfo
 
typedef ItraqConstants::ChannelMapType ChannelMapType
 
typedef ItraqConstants::IsotopeMatrices IsotopeMatrices
 

Public Member Functions

 ITRAQLabeler ()
 default constructor More...
 
 ~ITRAQLabeler () override
 destructor More...
 
void preCheck (Param &param) const override
 Checks the (simulation) params passed if they are consistent with the labeling technique. More...
 
void setUpHook (SimTypes::FeatureMapSimVector &) override
 Hook to prepare the simulation process. More...
 
void postDigestHook (SimTypes::FeatureMapSimVector &) override
 Labeling between digestion and rt simulation. More...
 
void postRTHook (SimTypes::FeatureMapSimVector &) override
 Labeling after rt simulation. More...
 
void postDetectabilityHook (SimTypes::FeatureMapSimVector &) override
 Labeling after detectability simulation. More...
 
void postIonizationHook (SimTypes::FeatureMapSimVector &) override
 Labeling after ionization. More...
 
void postRawMSHook (SimTypes::FeatureMapSimVector &) override
 Labeling after raw signal generation. More...
 
void postRawTandemMSHook (SimTypes::FeatureMapSimVector &, SimTypes::MSSimExperiment &) override
 Labeling after Tandem MS (e.g. iTRAQ) More...
 
- Public Member Functions inherited from BaseLabeler
 BaseLabeler ()
 constructor More...
 
 ~BaseLabeler () override
 destructor More...
 
virtual Param getDefaultParameters () const
 Returns the default parameters. Re-implement. More...
 
virtual void setRnd (SimTypes::MutableSimRandomNumberGeneratorPtr rng)
 Set the random number generator. More...
 
ConsensusMapgetConsensus ()
 
const StringgetDescription () 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 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...
 

Static Public Member Functions

static BaseLabelercreate ()
 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...
 
- Static Public Member Functions inherited from DefaultParamHandler
static void writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
 Writes all parameters to meta values. 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, SimTypes::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_ () override
 Synchronize members with param class. More...
 
double getRTProfileIntensity_ (const Feature &f, const double MS2_RT_time) const
 
EigenMatrixXdPtr getItraqIntensity_ (const Feature &f, const double MS2_RT_time) const
 convert meta information from feature into intensity values for iTRAQ More...
 
- Protected Member Functions inherited from BaseLabeler
SimTypes::FeatureMapSim mergeProteinIdentificationsMaps_ (const SimTypes::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 SimTypes::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...
 
double y_labeling_efficiency_
 efficiency of "Y" labeling More...
 
- Protected Attributes inherited from BaseLabeler
ConsensusMap consensus_
 
SimTypes::MutableSimRandomNumberGeneratorPtr 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< 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

Simulate iTRAQ experiments.

Adds reporter ion intensities to MS/MS scans. Supports custom channel allocation and isotope matrices.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
iTRAQ string4plex 4plex, 8plex4plex or 8plex iTRAQ?
reporter_mass_shift float0.1 min: 0.0 max: 0.5Allowed 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 :, e.g. "114:myref","115:liver".
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 :, e.g. "113:myref","115:liver","118:lung".
isotope_correction_values_4plex string list[114:0.0/1.0/5.9/0.2, 115:0.0/2.0/5.6/0.1, 116:0.0/3.0/4.5/0.1, 117:0.1/4.0/3.5/0.1]  override default values (see Documentation); use the following format: :<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'
isotope_correction_values_8plex string list[113:0.0/0.0/6.89/0.22, 114:0.0/0.94/5.9/0.16, 115:0.0/1.88/4.9/0.1, 116:0.0/2.82/3.9/0.07, 117:0.06/3.77/2.99/0.0, 118:0.09/4.71/1.88/0.0, 119:0.14/5.66/0.87/0.0, 121:0.27/7.44/0.18/0.0]  override default values (see Documentation); use the following format: :<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '113:0/0.3/4/0' , '116:0.1/0.3/3/0.2'
Y_contamination float0.3 min: 0.0 max: 1.0Efficiency of labeling tyrosine ('Y') residues. 0=off, 1=full labeling

Note:

Member Typedef Documentation

◆ ChannelInfo

◆ ChannelMapType

◆ IsotopeMatrices

Constructor & Destructor Documentation

◆ ITRAQLabeler()

default constructor

◆ ~ITRAQLabeler()

~ITRAQLabeler ( )
override

destructor

Member Function Documentation

◆ addModificationToPeptideHit_()

void addModificationToPeptideHit_ ( Feature feature,
const String modification,
const Size pos 
) const
protected

Modify the first peptide hit of the feature with a modification at pos.

◆ create()

static BaseLabeler* create ( )
inlinestatic

create new object (needed by Factory)

Referenced by BaseLabeler::registerChildren().

◆ getItraqIntensity_()

EigenMatrixXdPtr getItraqIntensity_ ( const Feature f,
const double  MS2_RT_time 
) const
protected

convert meta information from feature into intensity values for iTRAQ

◆ getProductName()

static const String getProductName ( )
inlinestatic

name of the model (needed by Factory)

Referenced by BaseLabeler::registerChildren().

◆ getRTProfileIntensity_()

double getRTProfileIntensity_ ( const Feature f,
const double  MS2_RT_time 
) const
protected

◆ labelPeptide_()

void labelPeptide_ ( const Feature feature,
SimTypes::FeatureMapSim result 
) const
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.

◆ mergeFeatures_()

Feature mergeFeatures_ ( Feature labeled_channel_feature,
const AASequence unmodified_sequence,
std::map< AASequence, Feature > &  unlabeled_features_index 
) const
protected

◆ postDetectabilityHook()

void postDetectabilityHook ( SimTypes::FeatureMapSimVector )
overridevirtual

Labeling after detectability simulation.

Implements BaseLabeler.

◆ postDigestHook()

void postDigestHook ( SimTypes::FeatureMapSimVector )
overridevirtual

Labeling between digestion and rt simulation.

Implements BaseLabeler.

◆ postIonizationHook()

void postIonizationHook ( SimTypes::FeatureMapSimVector )
overridevirtual

Labeling after ionization.

Implements BaseLabeler.

◆ postRawMSHook()

void postRawMSHook ( SimTypes::FeatureMapSimVector )
overridevirtual

Labeling after raw signal generation.

Implements BaseLabeler.

◆ postRawTandemMSHook()

void postRawTandemMSHook ( SimTypes::FeatureMapSimVector ,
SimTypes::MSSimExperiment  
)
overridevirtual

Labeling after Tandem MS (e.g. iTRAQ)

Implements BaseLabeler.

◆ postRTHook()

void postRTHook ( SimTypes::FeatureMapSimVector )
overridevirtual

Labeling after rt simulation.

Implements BaseLabeler.

◆ preCheck()

void preCheck ( Param param) const
overridevirtual

Checks the (simulation) params passed if they are consistent with the labeling technique.

Parameters
paramParam object containing the simulation parameters
Exceptions
Exception::InvalidParameterif the given parameters are not consistent with the labeling technique

Implements BaseLabeler.

◆ setUpHook()

void setUpHook ( SimTypes::FeatureMapSimVector )
overridevirtual

Hook to prepare the simulation process.

Implements BaseLabeler.

◆ updateMembers_()

void updateMembers_ ( )
overrideprotectedvirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ channel_map_

ChannelMapType channel_map_
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

◆ isotope_corrections_

IsotopeMatrices isotope_corrections_
protected

Matrices with isotope correction values (one for each plex-type)

◆ itraq_type_

Int itraq_type_
protected

◆ y_labeling_efficiency_

double y_labeling_efficiency_
protected

efficiency of "Y" labeling