Simulate SILAC experiments. More...

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

Inheritance diagram for SILACLabeler:

Collaboration diagram for SILACLabeler:

Public Member Functions
	SILACLabeler ()
	default constructor More...

	~SILACLabeler () override
	destructor More...

void	preCheck (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 &key_prefix="")
	Writes all parameters to meta values. More...

Protected Member Functions
void	addModificationToPeptideHit_ (Feature &feature, const String &modification) const

Feature	mergeFeatures_ (Feature &labeled_channel_feature, const String &unmodified_sequence, Map< String, Feature > &unlabeled_features_index, Int index_channel_id, Int labeled_channel_id) const

Feature	mergeAllChannelFeatures_ (Feature &heavy_channel_feature, const String &unmodified_feature_sequence, Map< String, Feature > &light_channel_feature_index, Map< String, Feature > &medium_channel_feature_index) const

bool	canModificationBeApplied_ (const String &modification_id, const String &aa) const

void	applyLabelToProteinHit_ (SimTypes::FeatureMapSim &protein_hit, const String &arginine_label, const String &lysine_label) const

void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...

String	getUnmodifiedSequence_ (const Feature &feature, const String &arginine_label, const String &lysine_label) const

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
String	medium_channel_lysine_label_

String	medium_channel_arginine_label_

String	heavy_channel_lysine_label_

String	heavy_channel_arginine_label_

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...

Static Private Attributes
static const int	LIGHT_FEATURE_MAPID_
	Map ID for the light/unlabeled channel. More...

static const int	MEDIUM_FEATURE_MAPID_
	Map ID for the medium labeled channel. More...

static const int	HEAVY_FEATURE_MAPID_
	Map ID for the heavy labeled channel. More...

Detailed Description

Simulate SILAC experiments.

Add modified features to MS1 scans.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
fixed_rtshift	float	1.0e-04	min: 0.0	Fixed retention time shift between labeled peptides. If set to 0.0 only the retention times computed by the RT model step are used.
medium_channel:modification_lysine	string	UniMod:481		Modification of Lysine in the medium SILAC channel
medium_channel:modification_arginine	string	UniMod:188		Modification of Arginine in the medium SILAC channel
heavy_channel:modification_lysine	string	UniMod:259		Modification of Lysine in the heavy SILAC channel. If left empty, two channelSILAC is assumed.
heavy_channel:modification_arginine	string	UniMod:267		Modification of Arginine in the heavy SILAC channel. If left empty, two-channel SILAC is assumed.

Note:

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

Constructor & Destructor Documentation

◆ SILACLabeler()

SILACLabeler ( )

default constructor

◆ ~SILACLabeler()

~SILACLabeler ( )

override

destructor

Member Function Documentation

◆ addModificationToPeptideHit_()

void addModificationToPeptideHit_	(	Feature &	feature,
		const String &	modification
	)		const

protected

◆ applyLabelToProteinHit_()

void applyLabelToProteinHit_	(	SimTypes::FeatureMapSim &	protein_hit,
		const String &	arginine_label,
		const String &	lysine_label
	)		const

protected

◆ canModificationBeApplied_()

bool canModificationBeApplied_	(	const String &	modification_id,
		const String &	aa
	)		const

protected

◆ create()

static BaseLabeler* create ( )

inlinestatic

create new object (needed by Factory)

Referenced by BaseLabeler::registerChildren().

◆ getProductName()

static const String getProductName ( )

inlinestatic

name of the model (needed by Factory)

Referenced by BaseLabeler::registerChildren().

◆ getUnmodifiedSequence_()

String getUnmodifiedSequence_	(	const Feature &	feature,
		const String &	arginine_label,
		const String &	lysine_label
	)		const

protected

◆ mergeAllChannelFeatures_()

Feature mergeAllChannelFeatures_	(	Feature &	heavy_channel_feature,
		const String &	unmodified_feature_sequence,
		Map< String, Feature > &	light_channel_feature_index,
		Map< String, Feature > &	medium_channel_feature_index
	)		const

protected

◆ mergeFeatures_()

Feature mergeFeatures_	(	Feature &	labeled_channel_feature,
		const String &	unmodified_sequence,
		Map< String, Feature > &	unlabeled_features_index,
		Int	index_channel_id,
		Int	labeled_channel_id
	)		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

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ heavy_channel_arginine_label_

String heavy_channel_arginine_label_

protected

◆ heavy_channel_lysine_label_

String heavy_channel_lysine_label_

protected

◆ HEAVY_FEATURE_MAPID_

const int HEAVY_FEATURE_MAPID_

staticprivate

Map ID for the heavy labeled channel.

◆ LIGHT_FEATURE_MAPID_

const int LIGHT_FEATURE_MAPID_

staticprivate

Map ID for the light/unlabeled channel.

◆ medium_channel_arginine_label_

String medium_channel_arginine_label_

protected

◆ medium_channel_lysine_label_

String medium_channel_lysine_label_

protected

◆ MEDIUM_FEATURE_MAPID_

const int MEDIUM_FEATURE_MAPID_

staticprivate

Map ID for the medium labeled channel.

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Static Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SILACLabeler()

◆ ~SILACLabeler()

Member Function Documentation

◆ addModificationToPeptideHit_()

◆ applyLabelToProteinHit_()

◆ canModificationBeApplied_()

◆ create()

◆ getProductName()

◆ getUnmodifiedSequence_()

◆ mergeAllChannelFeatures_()

◆ mergeFeatures_()

◆ postDetectabilityHook()

◆ postDigestHook()

◆ postIonizationHook()

◆ postRawMSHook()

◆ postRawTandemMSHook()

◆ postRTHook()

◆ preCheck()

◆ setUpHook()

◆ updateMembers_()

Member Data Documentation

◆ heavy_channel_arginine_label_

◆ heavy_channel_lysine_label_

◆ HEAVY_FEATURE_MAPID_

◆ LIGHT_FEATURE_MAPID_

◆ medium_channel_arginine_label_

◆ medium_channel_lysine_label_

◆ MEDIUM_FEATURE_MAPID_