Concept

This document provides detailed the first version of the guidelines for the submission of mass spectrometry derived proteomics data to the ProteomXchange consortium databases PRIDE, PeptideAtlas, and Tranche. It is expected that this document will be updated in the next months.

First the policy is summarized in this section; then in subsequent sections, definitions of terms, descriptions of the relevant resources, details on the submission path, and policies regarding data ownership and data privacy are provided. This policy has been adopted by the HUPO Plasma Proteome Project for the collection of its Phase II data; it is hoped that widespread adoption will follow.

Each submission shall consist of three major components: mass spectrometer output files, study metadata, and peptide/protein identifications (further details in section 4; definitions provided in section 2). All submissions will include all three components and will be made to the PRIDE repository using data sufficiency guidelines established by PRIDE as described below.

At the time when the submitted data are declared publicly available by the submitter, all mass spectrometer output files will be deposited in the Tranche repository. Hash keys required to download this information from Tranche and study metadata will be displayed in PRIDE and actively transmitted to PeptideAtlas and any other participating ProteomExchange repositories (see section 3 for information about the individual repositories) for further processing.

This insures that a simple one-time submission from a contributer is automatically distributed to all ProteomeXchange repositories with sufficient information.