PROCESS - Proteomics data Collection, Software and Standards to support open access and long term management of data

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The PROCESS project will provide the framework needed for sharing, public data deposition and re-analysis of proteomics experimental data, based around mass spectrometry (MS), developed in the context of the Proteomics Standards Initiative (PSI), in which the applicants take a lead role. The framework comprises the evolution and maintenance of standard data formats (mzML, mzIdentML, mzQuantML and mzTab), controlled vocabularies (PSI-MS and PSI-MOD) and software tools (PRIDE Inspector, PSI Validator, and Java programming interfaces to the standards). The standards will be developed to cope with evolution in proteomics technology, including the capability to handle ambiguity in protein modification sites and protein grouping, data independent acquisition in MS and top-down proteomics. We will also develop international standards for compression of proteomics data sets to ensure that software performance and database architectures can scale up to the outputs of the newest instruments.

The PRIDE database at the EBI is the primary public database for experimental proteomics data. It has recently initiated a (potentially huge) raw data archive service for the community, in which the PSI standards play a central role. The PROCESS outputs will ensure that the wider research community will have long-term access to experimental proteomics data for re-use across a range of purposes. New modules will be created in the PRIDE Inspector software for data visualisation and analysis, and the further development of the programming interfaces will help bioinformatics developers to build tools for re-analysis of data sets.

The direct beneficiaries include:

- Vendors of commercial software, including UK SME's Matrix Science and Nonlinear Dynamics, will benefit (see Pathways to Impact)
- Vendors of instruments will benefits, through increased compatibility of their raw data with a range of analysis software and easier deposition of data into PRIDE. Letters of support from Waters and AB Sciex demonstrate their commitment to PROCESS.
- Numerous pharmaceutical companies use mass spectrometry for analysis of proteins or metabolites. They will benefit through easier connectivity between software packages and more data in the public domain for re-analysis.
- Research councils and charities funding research will benefit through the potential for increased impact of the (proteomics) projects they fund, as public data deposition becomes straightforward and expected of all projects.

As proteomics is a key technology in the Life Sciences, there is the potential for considerable indirect benefits as PROCESS will help the field to become less fragmented and data analysis to become more straightforward. These benefits could be realised in any area of basic biology, biomedical or clinical science, for example leading to new drugs or biomarkers being discovered.

Staff employed will benefit:
- Exposure to numerous international collaborations, through the PSI (see letters of support)
- New collaborations with industry, particularly in relation to the shared development of software (see letters of support)