The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition

Abstract

The ProteomeXchange (PX) Consortium of proteomics resources (http://www.proteomexchange.org) was formally started in 2011 to standardize data submission and dissemination of mass spectrometry proteomics data worldwide. We give an overview of the current consortium activities and describe the advances of the past few years. Augmenting the PX founding members (PRIDE and PeptideAtlas, including the PASSEL resource), two new members have joined the consortium: MassIVE and jPOST. ProteomeCentral remains as the common data access portal, providing the ability to search for data sets in all participating PX resources, now with enhanced data visualization components.We describe the updated submission guidelines, now expanded to include four members instead of two. As demonstrated by data submission statistics, PX is supporting a change in culture of the proteomics field: public data sharing is now an accepted standard, supported by requirements for journal submissions resulting in public data release becoming the norm. More than 4500 data sets have been submitted to the various PX resources since 2012. Human is the most represented species with approximately half of the data sets, followed by some of the main model organisms and a growing list of more than 900 diverse species. Data reprocessing activities are becoming more prominent, with both MassIVE and PeptideAtlas releasing the results of reprocessed data sets. Finally, we outline the upcoming advances for ProteomeXchange.

Differential Protein Expression Marks the Transition From Infection With Opisthorchis viverrini to Cholangiocarcinoma

“…The MS proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.prote omexchange.org) via the MassIVE partner repository (18) with the data set identifier PXD002818.…”

jPOSTrepo: an international standard data repository for proteomes

“…The repository is expected to have a dramatic increase in the number of deposits. Furthermore, the repository will contribute to improving the sustainability of the PX consortium by receiving some of the increasing data deposits in worldwide, which is currently performed by other PX repositories located only in Europe and the USA (11). Our repository, like other PX repositories, will contribute to proteome data sharing among worldwide researchers.…”

Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project

“…The scheme for the HPP Data Workflow was published last year 5 (see Supplementary Figure 1). ProteomeXchange 9, 10 had 3496 publicly released datasets, of which 1478 are from human samples, up from 900 a year ago (www.proteomecentral.proteomexchange.org) as of 2017-04-27. The 2016 HPP Metrics paper 5 presented substantial detail about the features of PeptideAtlas, GPMDB, and neXtProt, including PTMs, proteoforms defined by N and C termini, sequence variants, and splice isoforms.…”