From Peptidome to PRIDE: public proteomics data migration at a large scale

Area of Science:

• Bioinformatics
• Proteomics
• Data Management

Background:

• The PRIDE database at the European Bioinformatics Institute (EBI) is a key repository for high-throughput mass spectrometry (MS)-based proteomics data.
• The National Center for Biotechnology Information (NCBI) developed Peptidome as a complementary resource, but it ceased operations in April 2011 due to funding issues.

Purpose of the Study:

• To prevent the loss of valuable proteomics data following the discontinuation of the Peptidome database.
• To ensure the continued accessibility and usability of Peptidome's data for the scientific community by migrating it to the PRIDE database.

Main Methods:

• A collaborative data migration effort was undertaken between the PRIDE and Peptidome teams.
• Low terabyte-scale data from Peptidome were systematically exported and integrated into the PRIDE database.

Main Results:

• Successful migration of extensive proteomics data from Peptidome to PRIDE.
• Data are now publicly available under PRIDE experiment accessions 17 900-18 271.
• The migrated dataset includes approximately 53 million mass spectra, 10 million peptide identifications, 650,000 protein identifications, and 1.1 million protein modifications across 28 species.

Conclusions:

• The joint data migration successfully preserved and enhanced access to a significant volume of proteomics data.
• The integration of Peptidome data into PRIDE strengthens its position as a comprehensive resource for MS-based proteomics research.
• Continued data sharing and repository collaboration are crucial for advancing the field of proteomics.