FPGA Implementation of Database Search Engine for Protein Identification by Peptide Fragment Fingerprinting

I.A. Bogdán, D. Coca, and R. Beynon (UK)


Tandem mass spectrometry (MS/MS), FPGA,optimisation, real time MS/MS


The large volume of data generated by tandem mass spectrometric analyses of protein digests has led to a computational bottleneck as researchers struggle to identify and quantify proteins from complex peptide mixtures. To address this challenge, this paper presents a novel peptide fragment fingerprinting digital-hardware solution implemented on a FPGA system which achieves over 1000× speed gain over an equivalent software implementation running on a dual quad-core server. The proposed solution is highly scalable as the performance can be ramped-up linearly by deploying the design on multiple FPGA devices.

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