How to submit data to PRIDE via ProteomeXchange

As proteomics repositories sometimes focus on or employ different types of data, data sharing among the different repositories is troublesome if not impossible.  Using PRIDE as the central submission point for MS/MS data in the PX consortium enables one-time submission to all the ProteomeXchange repositories. Each submission needs to include the following data types:

  • Metadata - Data that add context to the submitted experiment, such as what species the sample came from, are required as part of your submission to PRIDE/PX because they enable users to search for your experiments on the basis of the metadata. 
  • Peptide/ protein identifications (processed results).


There are two pipelines for submitting to PX depending on the supporting information available for each submission:

In both cases, you need to use the ProteomeXchange submission tool to perform the submission.

Once you have submitted your data, they can be held privately, allowing reviewers and journal editors access if desired, or until you choose to release the data to the public.

Next we will explore both pipelines.