Ppx: Programmatic Access to Proteomics Data Repositories.

ABSTRACT: The volume of proteomics and mass spectrometry data available in public repositories continues to grow at a rapid pace as more researchers embrace open science practices. Open access to the data behind scientific discoveries has become critical to validate published findings and develop new computational tools. Here, we present ppx, a Python package that provides easy, programmatic access to the data stored in ProteomeXchange repositories, such as PRIDE and MassIVE. The ppx package can be used as either a command line tool or a Python package to retrieve the files and metadata associated with a project when provided its identifier. To demonstrate how ppx enhances reproducible research, we used ppx within a Snakemake workflow to reanalyze a published data set with the open modification sear

SUBMITTER: Fondrie WE 

PROVIDER: S-EPMC8457024 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature