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

By Eric W. Deutsch, A. Csordas, Zhi Sun, Andrew F. Jarnuczak, Yasset Pérez-Riverol, Tobias Ternent, D. Campbell, Manuel Bernal Llinares, Shujiro Okuda, S. Kawano and 7 more. Nucleic Acids Res., 2016

818 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/558af0e9fbca07c5508c4db29af1c32a7d2b796d

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Citations in the corpus

The PRIDE database and related tools and resources in 2019: improving support for quantification data (2018, methodology): “The PX Submission tool (3) (available at https://github.”
jPOSTrepo: an international standard data repository for proteomes (2016, background): “However, data transfer to current submission points of ProteomeXchange, such as PRIDE in Europe and MassIVE in the USA for MS/MS datasets and PASSEL in the USA for SRM datasets via the Internet from Asia/Oceania is usually very slow and highly troublesome.”
Expression Atlas: gene and protein expression across multiple studies and organisms (2017, methodology): “We are developing analysis and QC pipelines and the additional needed infrastructure for enabling the routine integration of high-quality data sets, now that the availability of proteomics data in the public domain has become the norm (30,31).”
The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics (2019, methodology): “Since its inception, the ProteomeXchange (PX) consortium of proteomics resources (1,2) (http://www.”
iProX: an integrated proteome resource (2018, background): “The ProteomeXchange (PX) consortium (1,2) coordinates a stable, distributed infrastructure for proteomics data sharing.”