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High-performance hardware implementation of a parallel database search engine for real-time peptide mass fingerprinting

This paper presents the world's first FPGA co-processing solution for protein identification using mass spectrometry (MS). The database search engine described in this paper led to development of a prototype commercial system, funded by a Follow-on BBRSC grant (BB/F52809X/1; ~£99K) and a Proof of Concept HEIF2 (£10K) grant. Following publication, we were contacted by Kratos Analytical Ltd. (contact details available) to help with the implementation of a FPGA acceleration solution in their flagship instruments. The remarkable performance of the solution helped secured further BBSRC support (BB/F004893/1; £515K) to develop a FPGA-system for processing data generated by tandem mass spectrometers.