Making proteomics data accessible and reusable: current state of proteomics databases and repositories

Area of Science:

• Proteomics
• Bioinformatics
• Data Science

Background:

• Public deposition and storage of mass spectrometry-based proteomics data lag behind other data-intensive fields like genomics.
• This is due to the inherent complexity and diverse data types in proteomics experiments.
• Several public repositories have been developed to address this gap.

Purpose of the Study:

• To review major public repositories for mass spectrometry-based proteomics data.
• To discuss tools for data integration, mining, and reuse.
• To highlight challenges and pitfalls in proteomics data sharing.

Main Methods:

• Review of established and recently developed public proteomics databases.
• Description of the ProteomeXchange consortium for data integration.
• Discussion of data integration and mining tools.

Main Results:

• Identified key resources: GPMDB, PeptideAtlas, PRIDE, ProteomicsDB, MassIVE, Chorus, MaxQB, PASSEL, MOPED, and Human Proteinpedia.
• Highlighted the role of ProteomeXchange in coordinating data sharing.
• Acknowledged the existence of tools for data integration and analysis.

Conclusions:

• Despite progress, challenges remain in integrating and sharing proteomics data.
• Public repositories and consortia are crucial for advancing proteomics research.
• Further efforts are needed to overcome current pitfalls in data management.