10 years of ProteomeXchange (PXC), an international consortium of proteome resources

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  • Database Integration Coordination Program
Nov 29, 2022

In light of the 10th anniversary of the establishment of the international framework for proteome databases, ProteomeXchange Consortium (PXC) , a paper summarizing the activities and achievements of PXC over the past 10 years was published in Nucleic Acid Research on November 12, 2022.

This paper summarizes the history of PXC since its inception, changes in the number of datasets registered in PXC, and PXC's efforts to promote open science.

PXC consists of six repository databases as of June 2022. PXC was founded in 2012 by PRIDE in Europe and PeptideAtlas in the US, followed by MassIVE (US), jPOST (Japan), iProX (China) and Panorama Public (US) as members. jPOST is developed by Professor Yasushi Ishihama of the Kyoto University Graduate School of Pharmaceutical Sciences, as a research and development project "Development of functional and interactive database for proteomics" of JST-NBDC Database Integration Coordination Program (DICP). jPOST is mentioned in the paper as playing an important role in PXC as one of the main repositories of PXC.

The number of datasets registered to PXC continues to increase year by year. The number of proteome datasets registered with PXC is 34,233 in June of 2022. Of these, 20,062 (58.6%) were registered in the last three years.

PXC promotes open science based on FAIR Principles. Since established, they have standardized the data formats submitted to the repository, standardized the method of registering reanalysis data, constructed a common portal "ProteomeCentral" that can search all resources published by each organization, and have developed standardized Universal Spectrum Identifier (USI) to specify the unique, specific spectrum information by URL. In addition, they have integrated peptide and protein sequence data from PX resources to protein knowledgebases such as UniProt KnowledgeBase (UniProtKB) and neXtProt, and have developed a data pipeline and file formats and guidelines for providing information on post-translational modifications such as phosphorylation to UniProtKB. These efforts have made proteomics data easier to access and integrate with other omics data, especially for life scientists who are not proteomics experts.

This paper also mentioned the original activities of jPOST. jPOST has developed a workflow to re-analyze the registered data with a unified procedure, and released datasets of human, mouse, E. coli, SARS-CoV-2, etc. from jPOSTdb. jPOST has also launched a data journal, Journal of Proteome Data and Methods (JPDM), and established a system to collect high-quality data with accurate metadata directly from data producers.

For details, please see the original paper and the announcement from jPOST.

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