IsoelectricPoint Class Reference

Utility class for computing the isoelectric point (pI) and net charge of peptides. More...

#include <OpenMS/CHEMISTRY/IsoelectricPoint.h>

Classes
struct	PkaValues
	Internal struct holding pKa values for a given scale. More...

Static Public Member Functions
static double	computeCharge (const AASequence &seq, double pH, ProteomicsPkaScale scale=ProteomicsPkaScale::LEHNINGER)
	Computes the net charge of an amino acid sequence at a given pH.
static double	computePI (const AASequence &seq, ProteomicsPkaScale scale=ProteomicsPkaScale::LEHNINGER, double tolerance=1e-4)
	Computes the isoelectric point (pI) of an amino acid sequence via bisection.

Static Private Member Functions
static const PkaValues &	getPkaValues_ (ProteomicsPkaScale scale)
	Returns the pKa values for the specified scale.
static double	chargeAcidic_ (double pH, double pKa)
	Charge contribution from an acidic group (COOH, side chains of D, E, C, Y)
static double	chargeBasic_ (double pH, double pKa)
	Charge contribution from a basic group (NH2, side chains of H, K, R)

Detailed Description

Utility class for computing the isoelectric point (pI) and net charge of peptides.

This class provides methods to compute:

• The net charge of an amino acid sequence at a given pH using the Henderson-Hasselbalch equation
• The isoelectric point (pI), i.e. the pH at which the net charge is zero, found via bisection

The calculation considers:

• The N-terminal amino group (pKa), unless the peptide has an N-terminal modification
• The C-terminal carboxyl group (pKa), unless the peptide has a C-terminal modification
• Ionizable side chains of D, E, C, U, Y, H, K, R

The default pK values follow the Lehninger scale (Nelson & Cox, Lehninger Principles of Biochemistry). Other supported scales (EMBOSS, Sillero, Bjellqvist) can be selected via the ProteomicsPkaScale enum.

The Bjellqvist scale uses N-terminal-residue-dependent pKa values for the N-terminus (one value per N-terminal residue identity) and residue-dependent C-terminal pKas for D and E.

Side-chain PTM-specific pKa shifts are currently not modeled; modified residues are evaluated using the parent residue one-letter code. Pyrrolysine (O) is not supported and raises Exception::InvalidValue. If the zero crossing lies outside the searched pH interval [0, 14], computePI() returns the closer boundary and logs a warning.

References:

• Nelson DL, Cox MM. Lehninger Principles of Biochemistry. 6th ed. (2013).
• Sillero A, Ribeiro JM. Isoelectric points of proteins... Anal Biochem. 1989;179:319-325.
• Bjellqvist B et al. Isoelectric focusing in immobilized pH gradients... Electrophoresis 1993;14:1023-1031.

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Class Documentation

OpenMS::IsoelectricPoint::PkaValues

struct OpenMS::IsoelectricPoint::PkaValues

Internal struct holding pKa values for a given scale.

Class Members
double	C	Cysteine side chain.
double	cterm	pKa of the C-terminal carboxyl group (default; overridden per residue when cterm_by_residue is non-empty)
unordered_map< char, double >	cterm_by_residue	Per-residue C-terminal pKa (Bjellqvist scale). Overrides cterm for the last residue when non-empty.
double	D	Aspartate side chain.
double	E	Glutamate side chain.
double	H	Histidine side chain.
double	K	Lysine side chain.
double	nterm	pKa of the N-terminal amino group (default; overridden per residue when nterm_by_residue is non-empty)
unordered_map< char, double >	nterm_by_residue	Per-residue N-terminal pKa (Bjellqvist scale). Overrides nterm for the first residue when non-empty.
double	R	Arginine side chain
double	Y	Tyrosine side chain.

Member Function Documentation

chargeAcidic_()

static double chargeAcidic_ ( double  pH, double  pKa  )

staticprivate

Charge contribution from an acidic group (COOH, side chains of D, E, C, Y)

chargeBasic_()

static double chargeBasic_ ( double  pH, double  pKa  )

staticprivate

Charge contribution from a basic group (NH2, side chains of H, K, R)

computeCharge()

static double computeCharge ( const AASequence &  seq, double  pH, ProteomicsPkaScale  scale = ProteomicsPkaScale::LEHNINGER  )

static

Computes the net charge of an amino acid sequence at a given pH.

Parameters

seq	The amino acid sequence
pH	The pH value at which to compute the charge
scale	The pKa scale to use (default: Lehninger)

Returns

The net charge of the peptide at the given pH

Exceptions

Exception::InvalidValue

if the sequence is empty

computePI()

static double computePI ( const AASequence &  seq, ProteomicsPkaScale  scale = ProteomicsPkaScale::LEHNINGER, double  tolerance = 1e-4  )

static

Computes the isoelectric point (pI) of an amino acid sequence via bisection.

Parameters

seq	The amino acid sequence
scale	The pKa scale to use (default: Lehninger)
tolerance	The convergence tolerance for the bisection (default: 1e-4)

Returns

The isoelectric point (pH where net charge ≈ 0)

Exceptions

Exception::InvalidValue

if the sequence is empty

getPkaValues_()

static const PkaValues & getPkaValues_ ( ProteomicsPkaScale  scale )

staticprivate

Returns the pKa values for the specified scale.