Simulates Protein ionization. More...

#include <OpenMS/SIMULATION/IonizationSimulation.h>

Inheritance diagram for IonizationSimulation:

Collaboration diagram for IonizationSimulation:

Public Types
enum	IonizationType { MALDI , ESI }
	possible ionization methods More...

Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...

Public Member Functions
	IonizationSimulation ()
	Default constructor. 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...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

virtual	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress () const
	Ends the progress display. More...

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Constructors and Destructors
IonizationType	ionization_type_
	ESI or MALDI ionization. More...

std::set< String >	basic_residues_

double	esi_probability_
	Probability for the binomial distribution of ESI charge states. More...

std::vector< double >	esi_impurity_probabilities_
	Discrete distribution of impure charge adducts like Na+, K+, Ca++ etc besides the usual H+. More...

Adduct::AdductsType	esi_adducts_
	Corresponding table to `esi_impurity_probabilities_` holding the actual element and its charge. More...

Size	max_adduct_charge_
	Maximal charge that any impure adduct from parameter list has. More...

std::vector< double >	maldi_probabilities_
	Preprocessed table of discrete distribution (MALDI charges) More...

SimTypes::SimCoordinateType	maximal_mz_measurement_limit_
	Maximum m/z detected by mass analyser. More...

SimTypes::SimCoordinateType	minimal_mz_measurement_limit_
	Minimum m/z detected by mass analyser. More...

SimTypes::MutableSimRandomNumberGeneratorPtr	rnd_gen_
	Random number generator. More...

	IonizationSimulation (SimTypes::MutableSimRandomNumberGeneratorPtr)

	IonizationSimulation (const IonizationSimulation &source)
	Copy constructor. More...

	~IonizationSimulation () override
	Destructor. More...

IonizationSimulation &	operator= (const IonizationSimulation &source)
	Assignment operator. More...

void	ionize (SimTypes::FeatureMapSim &features, ConsensusMap &charge_consensus, SimTypes::MSSimExperiment &experiment)
	Ionize all peptide features inside the Feature-Map. More...

void	ionizeEsi_ (SimTypes::FeatureMapSim &, ConsensusMap &charge_consensus)
	ionize using ESI More...

void	ionizeMaldi_ (SimTypes::FeatureMapSim &, ConsensusMap &charge_consensus)
	ionize using MALDI More...

bool	isFeatureValid_ (const Feature &feature) const
	check if feature is within mz bounds of detector More...

void	setFeatureProperties_ (Feature &f, const double &adduct_mass, const String &adduct_formula, const SimTypes::SimChargeType charge, const SimTypes::SimIntensityType new_intensity, const Size parent_index)
	set meta values, mz etc after adducts are ready More...

void	setDefaultParams_ ()
	set defaults More...

void	updateMembers_ () override
	Synchronize members with param class. More...

UInt	countIonizedResidues_ (const AASequence &) const
	counts all basic residues inside the amino acid sequence to give an upper bound on the maximal charge during ESI ionization More...

Additional Inherited Members
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 inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...

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...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

Simulates Protein ionization.

Supports ESI and MALDI. The abundance values are distributed among the charge states based on a binomial distribution for the ESI and based on discrete distribution for MALDI. In ESI mode, this class also supports different adduct types in addition to H+ (e.g. NH4+, K+) which can be specified by the user and influence the mass and induce more charge variation.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
ionization_type	string	ESI	MALDI, ESI	Type of Ionization (MALDI or ESI)
esi:ionized_residues	string list	[Arg, Lys, His]	Ala, Cys, Asp, Glu, Phe, Gly, His, Ile, Lys, Leu, Met, Asn, Pro, Gln, Arg, Sec, Ser, Thr, Val, Trp, Tyr	List of residues (as three letter code) that will be considered during ES ionization. The N-term is always assumed to carry a charge. This parameter will be ignored during MALDI ionization
esi:charge_impurity	string list	[H+:1]		List of charged ions that contribute to charge with weight of occurrence (their sum is scaled to 1 internally), e.g. ['H:1'] or ['H:0.7' 'Na:0.3'], ['H:4' 'Na:1'] (which internally translates to ['H:0.8' 'Na:0.2'])
esi:max_impurity_set_size	int	3		Maximal @#combinations of charge impurities allowed (each generating one feature) per charge state. E.g. assuming charge=3 and this parameter is 2, then we could choose to allow '3H+, 2H+Na+' features (given a certain 'charge_impurity' constraints), but no '3H+, 2H+Na+, 3Na+'
esi:ionization_probability	float	0.8		Probability for the binomial distribution of the ESI charge states
maldi:ionization_probabilities	float list	[0.9, 0.1, 0.0]		List of probabilities for different charge states (starting at charge=1, 2, ...) during MALDI ionization (the list must sum up to 1.0)
mz:lower_measurement_limit	float	200.0	min: 0.0	Lower m/z detector limit
mz:upper_measurement_limit	float	1200.0	min: 0.0	Upper m/z detector limit

Note:

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

Member Enumeration Documentation

◆ IonizationType

enum IonizationType

possible ionization methods

Enumerator
MALDI
ESI

Constructor & Destructor Documentation

◆ IonizationSimulation() [1/3]

IonizationSimulation ( )

Default constructor.

◆ IonizationSimulation() [2/3]

IonizationSimulation ( SimTypes::MutableSimRandomNumberGeneratorPtr )

explicit

◆ IonizationSimulation() [3/3]

IonizationSimulation ( const IonizationSimulation & source )

Copy constructor.

◆ ~IonizationSimulation()

~IonizationSimulation ( )

override

Destructor.

Member Function Documentation

◆ countIonizedResidues_()

UInt countIonizedResidues_ ( const AASequence & ) const

private

counts all basic residues inside the amino acid sequence to give an upper bound on the maximal charge during ESI ionization

The N-term contributes +1 always. All other ionizable residues (according to param "esi:ionized_residues") in the sequence are summed up.

◆ ionize()

void ionize	(	SimTypes::FeatureMapSim &	features,
		ConsensusMap &	charge_consensus,
		SimTypes::MSSimExperiment &	experiment
	)

Ionize all peptide features inside the Feature-Map.

Depending on the parameters the passed peptide features are ionized by MALDI or by ESI.

Parameters

features	FeatureMap which will be ionized
charge_consensus	ConsensusMap which groups children(=charge variants) of input-features
experiment	SimTypes::MSSimExperiment map which contains the simulated experiment

◆ ionizeEsi_()

void ionizeEsi_	(	SimTypes::FeatureMapSim &	,
		ConsensusMap &	charge_consensus
	)

private

ionize using ESI

◆ ionizeMaldi_()

void ionizeMaldi_	(	SimTypes::FeatureMapSim &	,
		ConsensusMap &	charge_consensus
	)

private

ionize using MALDI

◆ isFeatureValid_()

bool isFeatureValid_ ( const Feature & feature ) const

inlineprivate

check if feature is within mz bounds of detector

◆ operator=()

IonizationSimulation& operator= ( const IonizationSimulation & source )

Assignment operator.

◆ setDefaultParams_()

void setDefaultParams_ ( )

private

set defaults

◆ setFeatureProperties_()

void setFeatureProperties_	(	Feature &	f,
		const double &	adduct_mass,
		const String &	adduct_formula,
		const SimTypes::SimChargeType	charge,
		const SimTypes::SimIntensityType	new_intensity,
		const Size	parent_index
	)

private

set meta values, mz etc after adducts are ready

◆ updateMembers_()

void updateMembers_ ( )

overrideprivatevirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ basic_residues_

std::set<String> basic_residues_

private

◆ esi_adducts_

Adduct::AdductsType esi_adducts_

private

Corresponding table to esi_impurity_probabilities_ holding the actual element and its charge.

◆ esi_impurity_probabilities_

std::vector<double> esi_impurity_probabilities_

private

Discrete distribution of impure charge adducts like Na+, K+, Ca++ etc besides the usual H+.

◆ esi_probability_

double esi_probability_

private

Probability for the binomial distribution of ESI charge states.

◆ ionization_type_

IonizationType ionization_type_

private

ESI or MALDI ionization.

◆ maldi_probabilities_

std::vector<double> maldi_probabilities_

private

Preprocessed table of discrete distribution (MALDI charges)

◆ max_adduct_charge_

Size max_adduct_charge_

private

Maximal charge that any impure adduct from parameter list has.

◆ maximal_mz_measurement_limit_

SimTypes::SimCoordinateType maximal_mz_measurement_limit_

private

Maximum m/z detected by mass analyser.

◆ minimal_mz_measurement_limit_

SimTypes::SimCoordinateType minimal_mz_measurement_limit_

private

Minimum m/z detected by mass analyser.

◆ rnd_gen_

SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen_

protected

Random number generator.

Public Types

Public Member Functions

Constructors and Destructors

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ IonizationType

Constructor & Destructor Documentation

◆ IonizationSimulation() [1/3]

◆ IonizationSimulation() [2/3]

◆ IonizationSimulation() [3/3]

◆ ~IonizationSimulation()

Member Function Documentation

◆ countIonizedResidues_()

◆ ionize()

◆ ionizeEsi_()

◆ ionizeMaldi_()

◆ isFeatureValid_()

◆ operator=()

◆ setDefaultParams_()

◆ setFeatureProperties_()

◆ updateMembers_()

Member Data Documentation

◆ basic_residues_

◆ esi_adducts_

◆ esi_impurity_probabilities_

◆ esi_probability_

◆ ionization_type_

◆ maldi_probabilities_

◆ max_adduct_charge_

◆ maximal_mz_measurement_limit_

◆ minimal_mz_measurement_limit_

◆ rnd_gen_