Command Line Interface

Use this command line utility to download files from the PRIDE

and MassIVE proteomics repositories. The paths to the downloaded files are written to stdout.

usage: ppx [-h] [-l LOCAL] [-t TIMEOUT] [-f] [--version]
           identifier [files ...]

Positional Arguments


The ProteomeXchange, PRIDE, or MassIVE identifier for the project.


One or more files to download. If none are provided, all files associated with the project are downloaded. Unix-style glob wildcards can be used, but they will need to be enclosed in quotation marks so as not to match files in your current working directory.

Named Arguments

-l, --local

The local directory where data will be downloaded. The default is ~/.ppx/<identifier>. This can also be changed globally by setting the PPX_DATA_DIR environment variable to your desired location.

-t, --timeout

The maximum amount of time to wait for a server response.

-f, --force

Should ppx download files that are already present in the local data directory?

Default: False


Get the version of ppx.

More documentation and examples at: