ProteomeXchange

What kind of data does this resource provide?

The ProteomeXchange Consortium is a collaborative effort that provides a global, coordinated submission and dissemination of mass spectrometry-based proteomics data to multiple databases, enabling easy data sharing and access across six different proteomics repositories located across three continents. These are PRIDE (Europe), MassIVE, Panorama Public and PeptideAtlas/PASSEL (all USA), jPOST(Japan) and iProX (China).

Give me an example of the impact of this resource

Data from ProteomeXchange has been reused in hundreds of studies, contributing to the development of artificial intelligence approaches and to improvements in proteomics data analysis workflows, meta-analyses involving proteomes from many different organisms, genome annotation projects and other applications. Staff across the ProteomeXchange network have led the development of open standards under the umbrella of the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI), such as mzML and the Universal Spectrum Identifiers for mass spectrometry data. ProteomeXchange teams have also played a leading role in the development of open source software to handle and visualise the data standards, such as jmzML and the PRIDE Inspector tool.

Hundreds of human datasets submitted to ProteomeXchange resources have been consistently reanalysed to contribute to the efforts of the Human Proteome Project (HPP) of HUPO.? The HPP aims to characterise at least one protein species (or ‘proteoform’) coming from the 19,823 predicted protein-coding genes in the human genome, creating a map of the protein based molecular architecture of the human body and a resource to help elucidate biological and molecular function, as well as the advance of diagnosis and treatment of diseases. The project started in 2010, and in its latest iteration (2023), experimental evidence has been found for around 93% of all predicted human proteins.

Key Facts

• The ProteomeXchange Consortium was established in 2011.? It includes one? resource in Europe: PRIDE (at EMBL-EBI), three resources in the USA (PeptideAtlas/PASSEL at the Institute for Systems Biology in Seattle, MassIVE at the? University of California San Diego and Panorama Public at the University of?Washington) and two resources in Asia (jPOST which is run by various institutions in Japan and iProX at Beijing Center for Proteomics in China).
• The amount of data stored and managed by ProteomeXchange is vast,?encompassing petabytes of proteomics data.
• Data in ProteomeXchange are submitted from over 70 countries on all continents.
• Data from ProteomeXchange have been generated in thousands of studies,? contributing to advances in various fields such as oncology, neurology, model?organism studies, crop science and infectious diseases, among many.?

proteomexchange.org