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Description:

pepfrag 0.4.1

pepfrag

pepfrag is a library for generating possible dissociation fragment ions of peptides
in tandem mass spectrometry experiments.
Table of Contents

Installation
Usage
License

Installation
pepfrag can be installed from PyPI.
Compatibility
pepfrag is written using Python 3 and should be compatible with most
operating systems. The package has been tested on

Windows 10
MacOS 10.15
Ubuntu 18.04 LTS

Because pepfrag includes C/C++ extensions, installation requires the
presence of a C++ 11 compatible compiler on your machine.
Instructions

Install Python 3 (>= version 3.6).
Install the latest version of the pepfrag library using pip:

pip install pepfrag

Usage
Peptide Construction
pepfrag provides one key public class: Peptide. This class includes public methods
for computing the mono/average mass of the peptide, including any configured modifications
(ModSites), and the peptide fragment ions, with configurable neutral losses.
A Peptide can be constructed from its amino acid sequence, charge state and modifications,
for example:
from pepfrag import MassType, ModSite, Peptide

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

Peptide modifications are defined using a sequence of ModSite instances, which
are namedtuples defined by the mass of the modification (float), the site of the
modification (string for terminal modifications or 1-indexed integer otherwise) and
the name of the modification.
The Peptide constructor has two keyword parameters:

mass_type:

Description: The type of mass to calculate.
Type: MassType enumeration.
Default: MassType.mono.

radical:

Description: Flag indicating whether radical cation fragments should be
generated.
Type: bool.
Default: False.

Fragment Generation
Fragment ions can be generated using the fragment method; for efficiency when the
same Peptide instance is used repeatedly, the resulting fragments are cached on the
instance. This cache is invalidated if the instance attributes are changed.
The fragment method has two keyword parameters:

ion_types:

Description: The types of fragment ion species to generate. The default
setup would generate precursor, immonium, b, y, a, c and z ions.
Type: dictionary mapping IonType enumeration instances to possible
neutral loss species, represented as strings for the most common neutral losses
(i.e. those configured in pepfrag, namely 'H2O', 'NH3', 'CO2' and 'CO').
For additional losses, these can be input as tuples of
(name (str), mass (float)).
Default:

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: []
}

Example:

from pepfrag import IonType, Peptide

peptide = Peptide('APYSMLK', 2, [])

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

force:

Description: Flag indicating whether fragments should be forcibly regenerated,
i.e. bypassing the cached ions.
Type: bool.
Default: False.

License
pepfrag is released under the terms of the MIT license.