FPGA Supercomputing Solution for Peptide Mass Fingerprinting

D. Coca, I. Bogdan, and R. Beynon (UK)


Proteomics, Peptide Mass Fingerprinting, Reconfigurable Computers, Field Programmable Gate Arrays


This paper presents a complete high-performance reconfigurable computing solution for real-time Peptide Mass Fingerprinting. The system, which implements both stages of computation associated with this protein identification technique - the processing of the raw mass spectrum and the database search - in FPGA hardware, can deliver the complete search results in less than a quarter of a second. This represents an almost 2000 fold speed up compared with an equivalent software implementation in C, running on a single 3GHz Xeon workstation.

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