Skip to content

Latest commit

 

History

History
112 lines (83 loc) · 3.38 KB

usage.rst

File metadata and controls

112 lines (83 loc) · 3.38 KB
Raw

Usage

Peptide Construction

:mod:`~pepfrag` provides one key public class: :class:`~pepfrag.Peptide`. This class includes public methods for calculating the mass of the peptide, including any configured modifications (:class:`~pepfrag.ModSite` s), and the peptide fragment ions, with configurable neutral losses.

A :class:`~pepfrag.Peptide` can be constructed from its amino acid sequence, charge state and modifications, for example:

from pepfrag import ModSite, Peptide

peptide = Peptide(
    "ABCMPK",
    2,
    (ModSite(15.994915, 4, "Oxidation"), ModSite(304.20536, "nterm", "iTRAQ8plex"))
)

:class:`~pepfrag.Peptide` modifications are defined using a sequence of :class:`~pepfrag.ModSite` instances.

Additional keyword arguments are available, allowing the use of average masses instead of monoisotopic masses and introducing radical peptide fragment generation.

Fragment Generation

Fragment ions can be generated using the :func:`~pepfrag.Peptide.fragment` method.

The generated fragment ions can be customized using the ion_types argument to :func:`~pepfrag.Peptide.fragment`, which takes a dictionary mapping the desired :class:`~pepfrag.IonType` s to their planned neutral losses. The default is:

from pepfrag import IonType

DEFAULT_IONS = {
    IonType.precursor: ['H2O', 'NH3', 'CO2'],
    IonType.imm: [],
    IonType.b: ['H2O', 'NH3', 'CO'],
    IonType.y: ['NH3', 'H2O'],
    IonType.a: [],
    IonType.c: [],
    IonType.z: []
}

The generated ions can be changed by providing a custom ion_types dictionary when calling :func:`~pepfrag.Peptide.fragment`, for example:

from pepfrag import IonType, Peptide

peptide = Peptide('AMYK', 2, [])
peptide.fragment(ion_types={
    IonType.precursor: [],
    IonType.b: ['NH3'],
    IonType.y: ['H2O']
})

outputs the following fragment ions, including precursor ions, b ions with NH3 losses and y ions with H2O losses:

[
    (72.044390252029, 'b1[+]', 1),
    (55.01784115090901, '[b1-NH3][+]', 1),
    (147.11280416609898, 'y1[+]', 1),
    (129.10223948206897, '[y1-H2O][+]', 1),
    (203.084875340499, 'b2[+]', 2),
    (186.058326239379, '[b2-NH3][+]', 2),
    (310.17613269973896, 'y2[+]', 2),
    (292.16556801570897, '[y2-H2O][+]', 2),
    (366.14820387413897, 'b3[+]', 3),
    (349.121654773019, '[b3-NH3][+]', 3),
    (183.57774017050897, 'b3[2+]', 3),
    (175.06446561994898, '[b3-NH3][2+]', 3),
    (441.21661778820896, 'y3[+]', 3),
    (423.206053104179, '[y3-H2O][+]', 3),
    (221.11194712754397, 'y3[2+]', 3),
    (212.10666478552898, '[y3-H2O][2+]', 3),
    (512.253731573359, '[M+H][+]', 4),
    (256.63050402011896, '[M+H][2+]', 4)
]

Customizing Neutral Losses

:mod:`~pepfrag` includes a number of common neutral losses available using only their string names. These are: NH3, H2O, CO2 and CO.

Additional neutral losses can be specified using a tuple of (label, mass). For example:

from pepfrag import IonType

ion_types = {
    IonType.b: [('testLoss1', 17.04), 'NH3']
}

This would generate b ions, along with b-testLoss1 and b-NH3 fragment ions.