Simulates Protein ionization. More...

#include <OpenMS/SIMULATION/IonizationSimulation.h>

Inheritance diagram for IonizationSimulation:

Public Types
enum	IonizationType { MALDI, ESI }
	possible ionization methods More...
Public Member Functions
IonizationSimulation &	operator= (const IonizationSimulation &source)
	Assignment operator.
void	ionize (FeatureMapSim &features, ConsensusMap &charge_consensus, MSSimExperiment &experiment)
	Ionize all peptide features inside the Feature-Map.
Constructors and Destructors

	IonizationSimulation (const SimRandomNumberGenerator &)
	IonizationSimulation (const IonizationSimulation &source)
	Copy constructor.
virtual	~IonizationSimulation ()
	Destructor.
Protected Attributes
SimRandomNumberGenerator const *	rnd_gen_
	Random number generator.
Private Member Functions
	IonizationSimulation ()
	Default constructor.
void	ionizeEsi_ (FeatureMapSim &, ConsensusMap &charge_consensus)
	ionize using ESI
void	ionizeMaldi_ (FeatureMapSim &, ConsensusMap &charge_consensus)
	ionize using MALDI
bool	isFeatureValid_ (const Feature &feature)
	check if feature is within mz bounds of detector
void	setFeatureProperties_ (Feature &f, const DoubleReal &adduct_mass, const String &adduct_formula, const SimChargeType charge, const SimIntensityType new_intensity, const Size parent_index)
	set meta values, mz etc after adducts are ready
void	setDefaultParams_ ()
	set defaults
void	updateMembers_ ()
	Synchronize members with param class.
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
Private Attributes
IonizationType	ionization_type_
	ESI or MALDI ionization.
std::set< String >	basic_residues_
DoubleReal	esi_probability_
	Probability for the binomial distribution of ESI charge states.
std::vector< double >	esi_impurity_probabilities_
	Discrete distribution of impure charge adducts like Na+, K+, Ca++ etc besides the usual H+.
Adduct::AdductsType	esi_adducts_
	Corresponding table to `esi_impurity_probabilities_` holding the actual element and its charge.
Size	max_adduct_charge_
	Maximal charge that any impure adduct from parameter list has.
std::vector< double >	maldi_probabilities_
	Preprocessed table of discrete distribution (MALDI charges).
SimCoordinateType	maximal_mz_measurement_limit_
	Maximum m/z detected by mass analyser.
SimCoordinateType	minimal_mz_measurement_limit_
	Minimum m/z detected by mass analyser.

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]		List of probabilities for the different charge states during MALDI ionization (the list must sum up to 1.0)
mz:lower_measurement_limit	float	200	min: 0	Lower m/z detector limit.
mz:upper_measurement_limit	float	2500	min: 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

enum IonizationType

possible ionization methods

Enumerator:

MALDI
ESI

Constructor & Destructor Documentation

IonizationSimulation ( const SimRandomNumberGenerator & )

IonizationSimulation ( const IonizationSimulation & source )

Copy constructor.

virtual ~IonizationSimulation ( ) [virtual]

Destructor.

IonizationSimulation ( ) [private]

Default constructor.

Member Function Documentation

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.

void ionize	(	FeatureMapSim &	features,
		ConsensusMap &	charge_consensus,
		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 childs(=charge variants) of input-features
	experiment	MSSimExperiment map which contains the simulated experiment

void ionizeEsi_	(	FeatureMapSim &	,
		ConsensusMap &	charge_consensus
	)			`[private]`

ionize using ESI

void ionizeMaldi_	(	FeatureMapSim &	,
		ConsensusMap &	charge_consensus
	)			`[private]`

ionize using MALDI

bool isFeatureValid_ ( const Feature & feature ) [inline, private]

check if feature is within mz bounds of detector

IonizationSimulation& operator= ( const IonizationSimulation & source )

Assignment operator.

void setDefaultParams_ ( ) [private]

set defaults

void setFeatureProperties_	(	Feature &	f,
		const DoubleReal &	adduct_mass,
		const String &	adduct_formula,
		const SimChargeType	charge,
		const SimIntensityType	new_intensity,
		const Size	parent_index
	)			`[private]`