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

By Eric W. Deutsch, N. Bandeira, Vagisha Sharma, Yasset Pérez-Riverol, Jeremy J. Carver, D. J. Kundu, D. García-Seisdedos, Andrew F. Jarnuczak, S. Hewapathirana, B. Pullman and 11 more. Nucleic Acids Res., 2019

653 citations recorded by the source corpus.

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.

Subfields: Information Systems and Management, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/8894d431a768a35dc7ca4d762ebdba4f407b978c

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Citations in the corpus

The ProteomeXchange consortium at 10 years: 2023 update (2022, background): “Since the previous PX update paper (3), 20 064 datasets have been submitted to PX resources, meaning that 58.”
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences (2021, methodology): “The PRIDE database was one of the founders of the PX consortium in 2011 (3,8).”
Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex (2022, methodology): “Mass spectrometry proteomics data was deposited in the MassIVE/ProteomeXchange database (113) under accession number PXD032818.”
UniProt: the universal protein knowledgebase in 2021 (2020, background): “UniProt additionally integrates and visualizes unique and non-unique peptides identified by mass spectrometry proteomic data deposited through the ProteomeXchange Consortium (31) (e.g. PeptideAtlas (32), MassIVE (33) and jPOST (34)) and other large-scale initiatives (CPTAC (35), ProteomicsDB (36), M”
Obesity shapes metabolism in the tumor microenvironment to suppress anti-tumor immunity (2020, methodology): “The accession number for the TMT-proteomics data reported in this paper is ProteomeXchange: PXD019495.”