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

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

Inheritance diagram for ProtonDistributionModel:

Public Types
Enumerations

enum	FragmentationType { ChargeDirected = 0, ChargeRemote, SideChain }
	the type of fragmentation More...
Public Member Functions
ProtonDistributionModel &	operator= (const ProtonDistributionModel &pdm)
	assignment operator
void	getProtonDistribution (std::vector< DoubleReal > &bb_charges, std::vector< DoubleReal > &sc_charges, const AASequence &peptide, Int charge, Residue::ResidueType res_type=Residue::YIon)
	calculates a proton distribution of the given charged peptide
void	getChargeStateIntensities (const AASequence &peptide, const AASequence &n_term_ion, const AASequence &c_term_ion, Int charge, Residue::ResidueType n_term_type, std::vector< DoubleReal > &n_term_intensities, std::vector< DoubleReal > &c_term_intensities, FragmentationType type)
	calculates the charge state intensities of different charge states of the same ion
void	setPeptideProtonDistribution (const std::vector< DoubleReal > &bb_charge, const std::vector< DoubleReal > &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


	ProtonDistributionModel ()
	default constructor
	ProtonDistributionModel (const ProtonDistributionModel &model)
	copy constructor
virtual	~ProtonDistributionModel ()
	destructor
Protected Member Functions
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< DoubleReal > &n_term_intensities, std::vector< DoubleReal > &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, DoubleReal &n_term1, DoubleReal &c_term1, DoubleReal &n_term2, DoubleReal &c_term2, FragmentationType type)
void	getLeftAndRightGBValues_ (const AASequence &peptide, DoubleReal &left_gb, DoubleReal &right_gb, Size position)
Protected Attributes
std::vector< DoubleReal >	sc_charge_
std::vector< DoubleReal >	bb_charge_
std::vector< DoubleReal >	sc_charge_full_
std::vector< DoubleReal >	bb_charge_full_
std::vector< DoubleReal >	sc_charge_ion_n_term_
std::vector< DoubleReal >	bb_charge_ion_n_term_
std::vector< DoubleReal >	sc_charge_ion_c_term_
std::vector< DoubleReal >	bb_charge_ion_c_term_
DoubleReal	E_
DoubleReal	E_c_term_
DoubleReal	E_n_term_

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	916.84	Gas-phase basicity value of N-terminus
gb_bb_r_COOH	float	-95.82	Gas-phase basicity value of C-terminus
gb_bb_r_b-ion	float	36.46	Gas-phase basicity value of b-ion C-terminus
gb_bb_r_a-ion	float	46.85	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	Temperature term

Note:

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

Member Enumeration Documentation

enum FragmentationType

the type of fragmentation

Enumerator:

ChargeDirected
ChargeRemote
SideChain

Constructor & Destructor Documentation

ProtonDistributionModel ( )

default constructor

Constructor and destructors

ProtonDistributionModel ( const ProtonDistributionModel & model )

copy constructor

virtual ~ProtonDistributionModel ( ) [virtual]

destructor

Member Function Documentation

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

void calcChargeStateIntensities_	(	const AASequence &	peptide,
		const AASequence &	n_term_ion,
		const AASequence &	c_term_ion,
		Int	charge,
		Residue::ResidueType	n_term_type,
		DoubleReal &	n_term1,
		DoubleReal &	c_term1,
		DoubleReal &	n_term2,
		DoubleReal &	c_term2,
		FragmentationType	type
	)			`[protected]`

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]`

void calculateProtonDistributionCharge1_	(	const AASequence &	peptide,
		Residue::ResidueType	res_type
	)			`[protected]`

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

void calculateProtonDistributionGreater2_	(	const AASequence &	peptide,
		Int	charge,
		Residue::ResidueType	res_type
	)			`[protected]`

void calculateProtonDistributionIonPair_	(	const AASequence &	peptide,
		Residue::ResidueType	type,
		Size	cleavage_site
	)			`[protected]`

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

void getLeftAndRightGBValues_	(	const AASequence &	peptide,
		DoubleReal &	left_gb,
		DoubleReal &	right_gb,
		Size	position
	)			`[protected]`

void getProtonDistribution	(	std::vector< DoubleReal > &	bb_charges,
		std::vector< DoubleReal > &	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

ProtonDistributionModel& operator= ( const ProtonDistributionModel & pdm )

assignment operator

void setPeptideProtonDistribution	(	const std::vector< DoubleReal > &	bb_charge,
		const std::vector< DoubleReal > &	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