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Usage

Peptide Construction

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

A ~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"))
)

~pepfrag.Peptide modifications are defined using a sequence of ~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 ~pepfrag.Peptide.fragment method.

The generated fragment ions can be customized using the ion_types argument to ~pepfrag.Peptide.fragment, which takes a dictionary mapping the desired ~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 ~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

~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.