ppx: A Python interface to ProteomeXchange

https://github.com/wfondrie/ppx/workflows/tests/badge.svg?branch=master Documentation Status

ppx provides a simple means to access the ProteomeXchange [1] repository from Python. Using ProteomeXchange identifiers, the user can retrieve metadata associated with a project and download project files from the PRIDE Archive [2], MassIVE, and other partner repositories.

Our intent is that ppx would provide an efficient method to reuse proteomics data from ProteomeXchange, allowing easier access for those developing proteomics tools and analyses in Python.


ppx was developed and tested for Python 3.6+, and only requires packages that are distributed as part of the Python Standard Library. The release version of ppx can be installed with pip (or pip3):

pip install ppx


ppx is distributed under the MIT license.

For R Users

ppx was inspired by the rpx R package [3] written by Laurent Gatto. If you are an R user and want many of the same functionalities that ppx offers, check it out on Bioconductor. and GitHub.

[1]Vizcaino J.A. et al. ProteomeXchange: globally co-ordinated proteomics data submission and dissemination, Nature Biotechnology 2014, 32, 223 – 226, doi:10.1038/nbt.2839.
[2]Vizcaíno JA, et al. 2016 update of the PRIDE database and related tools. Nucleic Acids Res. 2016, 44(D1): D447-D456. doi:10.1093/nar/gkv1145.
[3]Gatto L. rpx: R Interface to the ProteomeXchange Repository. 2018, R package version 1.16.0, https://github.com/lgatto/rpx.