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

1. Install Python 3 (>= version 3.6).
2. 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.