Pyteomics documentation v3.4.2

Charge and pI

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Charge and pI

Electrochemical properties of polypeptides can be assessed via the pyteomics.electrochem module. For now, it allows to calculate:

The pyteomics.electrochem module is based on the Henderson-Hasselbalch equation.

Examples

Both functions in the module accept input in the form of a modX sequence, a parsed sequence or a dict with amino acid composition.

>>> from pyteomics import electrochem
>>> electrochem.charge('PEPTIDE', 7)
-2.9980189709606284
>>> from pyteomics import parser
>>> parsed_seq = parser.parse('PEPTIDE', show_unmodified_termini=True)
>>> electrochem.charge(parsed_seq, 7)
-2.9980189709606284
>>> aa_composition = parser.amino_acid_composition('PEPTIDE', show_unmodified_termini=True)
>>> electrochem.charge(aa_composition, 7)
-2.9980189709606284
>>> electrochem.pI('PEPTIDE')
2.87451171875
>>> electrochem.pI('PEPTIDE', precision_pI=0.0001)
2.876354217529297

(Source code, png, hires.png, pdf)

_images/charge_vs_ph.png

Customization

The pKas of individual amino acids are stored in dicts in the following format: {modX label : (pKa, charge)}. The module contains several datasets published in scientific journals: pyteomics.electrochem.pK_lehninger (used by default), pyteomics.electrochem.pK_sillero, pyteomics.electrochem.pK_dawson, pyteomics.electrochem.pK_rodwell.

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