The PRIDE database and related tools and resources in 2019: improving support for quantification data

Area of Science:

• Biochemistry
• Bioinformatics
• Proteomics

Background:

• The PRoteomics IDEntifications (PRIDE) database is a major repository for mass spectrometry-based proteomics data.
• Public data sharing via PRIDE, a member of the ProteomeXchange (PX) consortium, has become standard practice.
• Data re-use in proteomics research has significantly increased.

Purpose of the Study:

• To summarize recent developments in PRIDE resources and tools since 2016.
• To detail architectural enhancements in PRIDE Archive for scalability and broader data type support.
• To highlight improvements in handling quantitative proteomics data and data dissemination.

Main Methods:

• Description of the new architecture for PRIDE Archive, including storage backend and APIs.
• Implementation of an improved data submission framework.
• Enhanced support for quantitative proteomics data using the mzTab format.

Main Results:

• PRIDE Archive has undergone significant architectural development to accommodate growing data volumes and types.
• New scalable storage, APIs, and web interfaces have been implemented.
• Improved support for quantitative proteomics data and dissemination to external resources like UniProt.

Conclusions:

• PRIDE Archive has been successfully upgraded to handle increased data submission and diverse data types.
• Enhanced infrastructure and features facilitate wider adoption and re-use of proteomics data.
• PRIDE continues to be a vital resource for the global proteomics community and related bioinformatics resources.