The ProteomeXchange consortium at 10 years: 2023 update

Area of Science:

• Proteomics
• Bioinformatics
• Data Science

Background:

• Mass spectrometry (MS) is central to high-throughput proteomics.
• The ProteomeXchange (PX) consortium was established to standardize public MS proteomics data submission and dissemination.
• The PX consortium has been operational for 10 years, with significant workflow development.

Purpose of the Study:

• To report developments in the ProteomeXchange consortium since 2020.
• To showcase data submission statistics and trends.
• To highlight improvements in data management and re-use.

Main Methods:

• Review of ProteomeXchange (PX) consortium activities and data.
• Analysis of data submission statistics from PX member resources (PRIDE, PeptideAtlas, MassIVE, jPOST, iProX, Panorama Public).
• Assessment of Universal Spectrum Identifiers and metadata annotation improvements.

Main Results:

• ProteomeXchange has seen a continuous annual increase in dataset submissions.
• Over 34,233 datasets were submitted to PX resources by June 2022, with 58.6% submitted in the last three years.
• Improvements in Universal Spectrum Identifiers and metadata capture, alongside increased data re-use, have been achieved.

Conclusions:

• The ProteomeXchange consortium continues to grow, with substantial increases in data submission and re-use.
• Enhanced data standardization and metadata capture facilitate broader connections and re-use of proteomics data.
• Current practices for managing sensitive human clinical proteomics data are summarized.