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.
Highlights
Mass spectrometry (MS)-based proteomics approaches are becoming increasingly prominent in the life sciences
We provide an update of the activities of the PX consortium and its individual resources since the previous update paper was published in Nucleic Acids Research (NAR)
We will follow closely developments in this area, like those led by ELIXIR
Summary
Mass spectrometry (MS)-based proteomics approaches are becoming increasingly prominent in the life sciences. The ProteomeXchange (PX) consortium of proteomics resources [1,2] Org) has aimed to standardize data submission and dissemination of public MS proteomics data worldwide. The implementation of the PX consortium formally started in 2012 and since it has become the de facto standard for sharing MS proteomics datasets in the public domain. Thanks to the perceived reliability of PX resources and in parallel, to the requirements of scientific journals and funding agencies, common practice has changed rapidly in the proteomics field and data sharing has become the norm. The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.
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