The ProteomeXchange consortium in 2026: making proteomics data FAIR.

Area of Science:

• Proteomics
• Bioinformatics
• Data Science

Background:

• The ProteomeXchange consortium was founded to standardize open data practices in mass spectrometry (MS)-based proteomics.
• Six global databases (PRIDE, PeptideAtlas, MassIVE, jPOST, iProX, Panorama Public) form the consortium.

Purpose of the Study:

• To report on the key developments within ProteomeXchange over the past three years.
• To highlight advancements in data submission, standardization, and data reuse.

Main Methods:

• Analysis of data submission statistics from ProteomeXchange member databases.
• Review of improvements in supporting Proteomics Standards Initiative standards (e.g., Universal Spectrum Identifiers, SDRF-Proteomics).
• Assessment of data reuse trends and the application of machine learning in proteomics data analysis.

Main Results:

• Data submissions to ProteomeXchange have accelerated, with 47% of the total 64,330 datasets submitted in the last three years (by June 2025).
• Enhanced support for Proteomics Standards Initiative standards has been implemented.
• Increased data reuse is evident, including reanalyses and novel machine learning applications.

Conclusions:

• ProteomeXchange continues to grow, facilitating open data practices in MS-based proteomics.
• Future efforts will focus on resources for controlled-access human proteomics data and non-MS proteomics approaches.