Proteomics Standards Initiative

Overview of Project

The HUPO Proteomics Standards Initiative (PSI) defines community standards for data representation in proteomics to facilitate data comparison, exchange and verification.

PSI Governance

• Sandra Orchard, Chair
• Eric Deutsch, Co-chair
• Juan Antonio Vizcaino, Co-chair

The main organizational unit of the Proteomics Standards Initiative is the work group. Currently, there are the following work groups:

• Molecular Interactions (MI)
• Mass Spectrometry (MS)
• Proteomics Informatics (PI)
• Protein Modifications (MOD)
• Protein Separation (PS)

The standard deliverables of each work group are

• Minimum Information Specification: For the given domain, this specifies the minimum information required for the useful reporting of experimental results in this domain.
• Formal exchange format for experimental results in the domain. This will usually be an XML format, capable of representing at least the Minimum Information, and normally significant additional detail.
• Controlled vocabularies.
• Support for implementation of the standard in publicly available tools.

Collaborations with other Initiatives

The HUPO PSI has a subsidiary role supporting other HUPO projects and workgroups, aiming to ensure collaboration and consistency in the data management approaches taken by the HUPO proteomics initiatives. We contribute to data management and long-term data repository support for the HUPO Plasma Proteome (I), Brain and Liver Proteome Projects. Currently, major proteomics repositories represented in the PSI mass spectrometry work group (PRIDE, PeptideAtlas, Tranche) are defining the systematic data capture for the second phase of the Plasma Proteome Project, as well as for the proposed joint HUPO project. A first, large scale dataset for HUPO PPP II has been processed through the proposed pipeline. In the context of the EU ProteomeBinders project, an ongoing collaboration with the HUPO Antibody initiative had significant impact on the recently released “Community standard for the representation of protein affinity reagents (PSI-PAR)”.

A successful interaction with the HUPO publications committee (joint workshops) has resulted in strong connections to key proteomics journals, highly valuable for dissemination and implementation of PSI standards.