FPGA supercomputing technology for high-throughput identification and quantitation in proteomics

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Proteomics is the study of the entire complement of a cell in a particular state. It is the proteins that 'act out' the information in the genome, and we cannot really understand cellular function without a detailed knowledge of the activity, dynamics and interplay between the 'actors'. .However, the science and technology of proteomics does not lend itself to the same highly multiplexed approaches that can be applied to nucleic acids, and strategies for protein identification and quantification are still highly serial, require complex and sometimes arcane data processing, and are slow. We have almost completed a proof-of-concept BBSRC e-science project that aimed to implement two common methods in proteomics: mass spectrum preprocessing and peptide mass fingerprint database searching, as a hardware implementation using reconfigurable computer chips known as field programmable gate arrays (FPGAs). A key feature of this computational platform is that the bioinformatics algorithms which are normally implemented as a software program were translated into optimized digital hardware processors that could process data significantly faster by running multiple analyses in parallel. The successful outcome of this project was a complete implementation that has achieved a phenomenal 2000-fold speed increase. We now wish to build on our previous success, capitalize upon the capabilities we have developed thus far, and deliver similar speed gains to the most commonly used method of proteome analysis, based on tandem mass spectrometry. At the same time, we will address an emergent and pressing need for faster and enhanced quantification to deliver new quantitative approaches and capabilities to proteomics researchers. Such tools are critical if proteomics is to deliver what we expect of it as a science.