The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics

TLDR

The ProteomeXchange consortium has standardized mass spectrometry proteomics data submission and dissemination worldwide since 2012, expanding from four to six member resources including PRIDE, PeptideAtlas, MassIVE, jPOST, iProX, and Panorama Public. This paper reviews the main developments since the 2017 update, outlines future plans, and details the expanded submission guidelines now covering six members. The updated guidelines now require submissions to be deposited in one of the six consortium members, streamlining data sharing across the community. Current statistics show over 14,100 datasets submitted to PX since 2012, with more than 9,500 in the last three years, and a surge in data re‑use activities that support big‑data research and new resources.

Abstract

Abstract The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) has standardized data submission and dissemination of mass spectrometry proteomics data worldwide since 2012. In this paper, we describe the main developments since the previous update manuscript was published in Nucleic Acids Research in 2017. Since then, in addition to the four PX existing members at the time (PRIDE, PeptideAtlas including the PASSEL resource, MassIVE and jPOST), two new resources have joined PX: iProX (China) and Panorama Public (USA). We first describe the updated submission guidelines, now expanded to include six members. Next, with current data submission statistics, we demonstrate that the proteomics field is now actively embracing public open data policies. At the end of June 2019, more than 14 100 datasets had been submitted to PX resources since 2012, and from those, more than 9 500 in just the last three years. In parallel, an unprecedented increase of data re-use activities in the field, including ‘big data’ approaches, is enabling novel research and new data resources. At last, we also outline some of our future plans for the coming years.