Simulate iTRAQ experiments. More...

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

Inheritance diagram for ITRAQLabeler:

Collaboration diagram for ITRAQLabeler:

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...

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 &param)
	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...

Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &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< 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...

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:

Name	Type	Default	Restrictions	Description
iTRAQ	string	4plex	4plex, 8plex	4plex or 8plex iTRAQ?
reporter_mass_shift	float	0.1	min: 0.0 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 :, 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	float	0.3	min: 0.0 max: 1.0	Efficiency of labeling tyrosine ('Y') residues. 0=off, 1=full labeling

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Member Typedef Documentation

◆ ChannelInfo

typedef ItraqConstants::ChannelInfo ChannelInfo

◆ ChannelMapType

typedef ItraqConstants::ChannelMapType ChannelMapType

◆ IsotopeMatrices

typedef ItraqConstants::IsotopeMatrices IsotopeMatrices

Constructor & Destructor Documentation

◆ ITRAQLabeler()

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

param Param object containing the simulation parameters

Exceptions

Exception::InvalidParameter if 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

set to either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX

◆ y_labeling_efficiency_

double y_labeling_efficiency_

protected

efficiency of "Y" labeling

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ ChannelInfo

◆ ChannelMapType

◆ IsotopeMatrices

Constructor & Destructor Documentation

◆ ITRAQLabeler()

◆ ~ITRAQLabeler()

Member Function Documentation

◆ addModificationToPeptideHit_()

◆ create()

◆ getItraqIntensity_()

◆ getProductName()

◆ getRTProfileIntensity_()

◆ labelPeptide_()

◆ mergeFeatures_()

◆ postDetectabilityHook()

◆ postDigestHook()

◆ postIonizationHook()

◆ postRawMSHook()

◆ postRawTandemMSHook()

◆ postRTHook()

◆ preCheck()

◆ setUpHook()

◆ updateMembers_()

Member Data Documentation

◆ channel_map_

◆ isotope_corrections_

◆ itraq_type_

◆ y_labeling_efficiency_