Center, NCI launch open-source software for proteomics analysis

The Hutchinson Center and the National Cancer Institute have announced the first open release of a comprehensive, Web-based software platform called the Computational Proteomics Analysis System, or CPAS. The new software platform is intended as the first comprehensive, freely available resource for proteomics researchers. A paper describing the base system appears in the Jan. 1, print edition of the Journal of Proteome Research.

The software package was developed at the Center as part of an NCI-funded research consortium created to develop basic platforms for research into proteomics, the systematic study of proteins in biological materials. The Canary Fund, a nonprofit organization run by Center supporter Don Listwin, also helped fund the software development and dissemination.

The field of proteomics is central to the development of early detection blood tests — a key research initiative at the Center. Proteomics technology leverages the results from the completion of the human-genome sequence and generates vast amounts of complex data that require sophisticated processing before interpretation can begin.

Dr. Martin McIntosh, Public Health Sciences Division, is principal investigator of the consortium and leads the research group that developed CPAS. Dr. Amanda Paulovich, Clinical Research Division, is consortium co-principal investigator and leads its laboratory component. The team also includes Drs. Ruedi Aebersold, founding member of the Institute for Systems Biology in Seattle; Richard D. Smith, Batelle Fellow and chief scientist of the Biological Sciences Division and Environmental Molecular Sciences Laboratory at the Pacific Northwest National Laboratories in Richland, Wash.; and Leigh Anderson, chief executive officer at the Plasma Proteome Institute in Washington, D.C..

CPAS was specifically developed to facilitate cooperative proteomics and cancer research following the examples of the Human Genome Project and NCI's cancer Biomedical Informatics Grid (caBIG ™, which accelerate research by creating freely available resources for data sharing. CPAS not only helps analyze proteomics data but also provides researchers with the ability to share and communicate their data openly; open-source tools are provided for organizing, managing, and interpreting data generated by all kinds of biological experiments that may be required by cancer researchers. Web-based communications tools help with project-management activities and promote collaboration, even among geographically disparate research groups.

Substantial effort was given to making the CPAS platform usable for the wider research community and generally extensible as a platform for further development. The developers intend to support an open-source development model for CPAS based on other open-source projects such as Linux, which offers the code publicly and extends the project by a community effort.

Community development already has begun, and several nonprofit and for-profit institutes have joined the CPAS development, including early adopters at the University of Michigan, proteomics laboratories in Korea and Asia, and the private software companies Genologics and LabKey.

For more information about cancer-proteomics research, visit http://proteomics.fhcrc.org, http://cpas.fhcrc.org or http://proteomics.cancer.gov.