A proton distribution model to calculate the proton distribution over charged peptides. More...

#include <OpenMS/ANALYSIS/ID/ProtonDistributionModel.h>

Inheritance diagram for ProtonDistributionModel:

Collaboration diagram for ProtonDistributionModel:

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

	ProtonDistributionModel (const ProtonDistributionModel &model)
	copy constructor More...

	~ProtonDistributionModel () override
	destructor More...

ProtonDistributionModel &	operator= (const ProtonDistributionModel &pdm)
	assignment operator 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...

Enumerations
enum	FragmentationType { ChargeDirected = 0, ChargeRemote, SideChain }
	the type of fragmentation More...

std::vector< double >	sc_charge_

std::vector< double >	bb_charge_

std::vector< double >	sc_charge_full_

std::vector< double >	bb_charge_full_

std::vector< double >	sc_charge_ion_n_term_

std::vector< double >	bb_charge_ion_n_term_

std::vector< double >	sc_charge_ion_c_term_

std::vector< double >	bb_charge_ion_c_term_

double	E_

double	E_c_term_

double	E_n_term_

void	getProtonDistribution (std::vector< double > &bb_charges, std::vector< double > &sc_charges, const AASequence &peptide, Int charge, Residue::ResidueType res_type=Residue::YIon)
	calculates a proton distribution of the given charged peptide More...

void	getChargeStateIntensities (const AASequence &peptide, const AASequence &n_term_ion, const AASequence &c_term_ion, Int charge, Residue::ResidueType n_term_type, std::vector< double > &n_term_intensities, std::vector< double > &c_term_intensities, FragmentationType type)
	calculates the charge state intensities of different charge states of the same ion More...

void	setPeptideProtonDistribution (const std::vector< double > &bb_charge, const std::vector< double > &sc_charge)
	sets the proton distributions of the whole peptide, they are needed for the getChargeStateIntensities_ method and need to be recalculated each time if not given More...

void	calculateProtonDistribution_ (const AASequence &peptide, Int charge, Residue::ResidueType res_type=Residue::YIon, bool fixed_proton=false, Size cleavage_site=0, bool use_most_basic_site=false)

void	calculateProtonDistributionCharge1_ (const AASequence &peptide, Residue::ResidueType res_type)

void	calculateProtonDistributionCharge2_ (const AASequence &peptide, Residue::ResidueType res_type, bool fixed_proton, Size cleavage_site, bool use_most_basic_site)

void	calculateProtonDistributionGreater2_ (const AASequence &peptide, Int charge, Residue::ResidueType res_type)

void	calculateProtonDistributionIonPair_ (const AASequence &peptide, Residue::ResidueType type, Size cleavage_site)

void	calcChargeStateIntensities_ (const AASequence &peptide, const AASequence &n_term_ion, const AASequence &c_term_ion, Int charge, Residue::ResidueType n_term_type, std::vector< double > &n_term_intensities, std::vector< double > &c_term_intensities, FragmentationType type)

void	calcChargeStateIntensities_ (const AASequence &peptide, const AASequence &n_term_ion, const AASequence &c_term_ion, Int charge, Residue::ResidueType n_term_type, double &n_term1, double &c_term1, double &n_term2, double &c_term2, FragmentationType type)

void	getLeftAndRightGBValues_ (const AASequence &peptide, double &left_gb, double &right_gb, Size position)

Additional Inherited Members
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 inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. 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...

Detailed Description

A proton distribution model to calculate the proton distribution over charged peptides.

The model uses proton affinity values of backbone nitrogens and sidechains to calculate the proton distribution of charged peptide among these sites. The possible sites are the peptide bonds between the amino acids, the side chains and the C-terminus and N-terminus. The calculation is done calculating a Boltzmann distribution of the sites.

Details and the proton affinities can be found in Z. Zhang, Prediction of Low-Energy Collision-Induced Dissociation Spectra of Peptides, Anal. Chem., 76 (14), 3908 - 3922, 2004

A proton distribution can be calculated using the getProtonDistribution method. The backbone probabilities are reported in the first parameter (index 0 for the N-terminus, index 1 for the first peptide bond...), the site chain probabilities are reported in the second parameter (index 0, for the first amino acid...). The peptide and the number of protons as well as type of peptide (can be Reside::YIon for peptides and y-ions and any other ion type).

Charge state intensities of differently charged equal (e.g. y7+ and y7++) ions can be calculated using the getChargeStateIntensities function.

Parameters of this class are:

Name	Type	Default	Description
gb_bb_l_NH2	float	916.840000000000032	Gas-phase basicity value of N-terminus
gb_bb_r_COOH	float	-95.819999999999993	Gas-phase basicity value of C-terminus
gb_bb_r_b-ion	float	36.460000000000001	Gas-phase basicity value of b-ion C-terminus
gb_bb_r_a-ion	float	46.850000000000001	Gas-phase basicity value of a-ion C-terminus
sigma	float	0.5	Width of the gaussian which distributes the mobile protons over the charge states, only for z > 3.
temperature	float	500.0	Temperature term

Note:

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

Member Enumeration Documentation

◆ FragmentationType

enum FragmentationType

the type of fragmentation

Enumerator
ChargeDirected
ChargeRemote
SideChain

Constructor & Destructor Documentation

◆ ProtonDistributionModel() [1/2]

ProtonDistributionModel ( )

default constructor

Constructor and destructors

◆ ProtonDistributionModel() [2/2]

ProtonDistributionModel ( const ProtonDistributionModel & model )

copy constructor

◆ ~ProtonDistributionModel()

~ProtonDistributionModel ( )

override

destructor

Member Function Documentation

◆ calcChargeStateIntensities_() [1/2]

void calcChargeStateIntensities_	(	const AASequence &	peptide,
		const AASequence &	n_term_ion,
		const AASequence &	c_term_ion,
		Int	charge,
		Residue::ResidueType	n_term_type,
		double &	n_term1,
		double &	c_term1,
		double &	n_term2,
		double &	c_term2,
		FragmentationType	type
	)

protected

◆ calcChargeStateIntensities_() [2/2]

void calcChargeStateIntensities_	(	const AASequence &	peptide,
		const AASequence &	n_term_ion,
		const AASequence &	c_term_ion,
		Int	charge,
		Residue::ResidueType	n_term_type,
		std::vector< double > &	n_term_intensities,
		std::vector< double > &	c_term_intensities,
		FragmentationType	type
	)

protected

◆ calculateProtonDistribution_()

void calculateProtonDistribution_	(	const AASequence &	peptide,
		Int	charge,
		Residue::ResidueType	res_type = `Residue::YIon`,
		bool	fixed_proton = `false`,
		Size	cleavage_site = `0`,
		bool	use_most_basic_site = `false`
	)

protected

◆ calculateProtonDistributionCharge1_()

void calculateProtonDistributionCharge1_	(	const AASequence &	peptide,
		Residue::ResidueType	res_type
	)

protected

◆ calculateProtonDistributionCharge2_()

void calculateProtonDistributionCharge2_	(	const AASequence &	peptide,
		Residue::ResidueType	res_type,
		bool	fixed_proton,
		Size	cleavage_site,
		bool	use_most_basic_site
	)

protected

◆ calculateProtonDistributionGreater2_()

void calculateProtonDistributionGreater2_	(	const AASequence &	peptide,
		Int	charge,
		Residue::ResidueType	res_type
	)

protected

◆ calculateProtonDistributionIonPair_()

void calculateProtonDistributionIonPair_	(	const AASequence &	peptide,
		Residue::ResidueType	type,
		Size	cleavage_site
	)

protected

◆ getChargeStateIntensities()

void getChargeStateIntensities	(	const AASequence &	peptide,
		const AASequence &	n_term_ion,
		const AASequence &	c_term_ion,
		Int	charge,
		Residue::ResidueType	n_term_type,
		std::vector< double > &	n_term_intensities,
		std::vector< double > &	c_term_intensities,
		FragmentationType	type
	)

calculates the charge state intensities of different charge states of the same ion

Parameters

peptide	the peptide
n_term_ion	the prefix ion sequence
c_term_ion	the suffix ion sequence
charge	the charge
n_term_type	the ion type of the N-terminal ion; valid values are Residue::AIon, Residue::BIon
n_term_intensities	the probability of seeing a charged prefix ions (first index corresponds to ion of charge 1)
c_term_intensities	the probability of seeing a charged suffix ions (first index corresponds to ion of charge 2)
type	the type of fragmentation (charge-directed, charge-remote of side chain)

◆ getLeftAndRightGBValues_()

void getLeftAndRightGBValues_	(	const AASequence &	peptide,
		double &	left_gb,
		double &	right_gb,
		Size	position
	)

protected

◆ getProtonDistribution()

void getProtonDistribution	(	std::vector< double > &	bb_charges,
		std::vector< double > &	sc_charges,
		const AASequence &	peptide,
		Int	charge,
		Residue::ResidueType	res_type = `Residue::YIon`
	)

calculates a proton distribution of the given charged peptide

Parameters

bb_charges	the calculated probabilities of the backbone sites (including N-terminus and C-terminus)
sc_charges	the calculated probabilities of the side chain sites
peptide	the peptide
charge	the charge
res_type	the type of the ion given in peptide. Peptides are handled as y-ions, i.e. Residue::YIon

◆ operator=()

ProtonDistributionModel& operator= ( const ProtonDistributionModel & pdm )

assignment operator

◆ setPeptideProtonDistribution()

void setPeptideProtonDistribution	(	const std::vector< double > &	bb_charge,
		const std::vector< double > &	sc_charge
	)

sets the proton distributions of the whole peptide, they are needed for the getChargeStateIntensities_ method and need to be recalculated each time if not given

Member Data Documentation

◆ bb_charge_

std::vector<double> bb_charge_

protected

◆ bb_charge_full_

std::vector<double> bb_charge_full_

protected

◆ bb_charge_ion_c_term_

std::vector<double> bb_charge_ion_c_term_

protected

◆ bb_charge_ion_n_term_

std::vector<double> bb_charge_ion_n_term_

protected

◆ E_

double E_

protected

◆ E_c_term_

double E_c_term_

protected

◆ E_n_term_

double E_n_term_

protected

◆ sc_charge_

std::vector<double> sc_charge_

protected

◆ sc_charge_full_

std::vector<double> sc_charge_full_

protected

◆ sc_charge_ion_c_term_

std::vector<double> sc_charge_ion_c_term_

protected

◆ sc_charge_ion_n_term_

std::vector<double> sc_charge_ion_n_term_

protected

Public Member Functions

Enumerations

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ FragmentationType

Constructor & Destructor Documentation

◆ ProtonDistributionModel() [1/2]

◆ ProtonDistributionModel() [2/2]

◆ ~ProtonDistributionModel()

Member Function Documentation

◆ calcChargeStateIntensities_() [1/2]

◆ calcChargeStateIntensities_() [2/2]

◆ calculateProtonDistribution_()

◆ calculateProtonDistributionCharge1_()

◆ calculateProtonDistributionCharge2_()

◆ calculateProtonDistributionGreater2_()

◆ calculateProtonDistributionIonPair_()

◆ getChargeStateIntensities()

◆ getLeftAndRightGBValues_()

◆ getProtonDistribution()

◆ operator=()

◆ setPeptideProtonDistribution()

Member Data Documentation

◆ bb_charge_

◆ bb_charge_full_

◆ bb_charge_ion_c_term_

◆ bb_charge_ion_n_term_

◆ E_

◆ E_c_term_

◆ E_n_term_

◆ sc_charge_

◆ sc_charge_full_

◆ sc_charge_ion_c_term_

◆ sc_charge_ion_n_term_