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FPGA Coprocessing Solution for Real-Time Protein Identification Using Tandem Mass Spectrometry

DANIEL COCA, ISTVÁN BOGDÁN, and ROBERT J. BEYNON

7.1 INTRODUCTION

Since the first applications of mass spectrometry (MS) to the identification of organic compounds were reported in the 1950s [1], MS has emerged as the most sensitive and powerful tool for protein identification and quantification [2]. Advances in high-throughput, liquid chromatography–tandem mass spectrometry provide the technological means to measure protein expression on a proteome-wide scale. This should provide unprecedented insight into protein function [3], a more comprehensive characterization of gene expression. and will accelerate the discovery of disease-associated protein biomarkers [4].

While the majority of proteome-wide studies aim to characterize the protein expression at steady state, our ability to quantitatively characterize the dynamics of protein expression on a global scale is key to increasing our understanding of complex biological processes [5, 6]. Obtaining protein expression time series on this scale requires the generation and processing of huge data sets of tandem mass spectrometry (MS/MS), given that the analysis of a substantial proteome in a single experiment can generate hundreds of gigabytes of raw mass spectrometric data. Moreover, modern mass spectrometers have typical acquisition rates of 200 spectra per second, while the analysis of single spectra can take tens of seconds on a high-end ...

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