FiCOPS: Hardware/Software Co-Design of FPGA Computational Framework for Mass Spectrometry-Based Peptide Database Search

Improving the speed and efficiency of database search algorithms that deduce peptides from mass spectrometry (MS) data has been an active area of research for more than three decades. The significance of the need for faster database search methods has rapidly increased due to the growing interest in studying non-model organisms, meta-proteomics, and proteogenomic data, which are notorious for their enormous search space. Poor scalability of serial algorithms with the growing size of the database and increasing parameters of post-translational modifications is a widely recognized problem. While high-performance computing techniques can be used on supercomputing machines, the need for real-time, on-the-instrument solutions necessitates the development of an efficient system-on-chip that optimizes design constraints such as cost, performance, and power of the system. To show case that such a system can work, we present an FPGA-based computational framework called FiCOPS to accelerate database search using a hardware/software co-design methodology. First, we theoretically analyze the database-search algorithm (closed-search) to reveal opportunities for parallelism and uncover computational bottlenecks. We then design an FPGA-based architectural template to exploit parallelism inherent in the search workload. We also formulate an analytical performance model for the architecture template to perform rapid design space exploration and find a near-optimal accelerator configuration. Finally, we implement our design on the Intel Stratix 10 FPGA platform and evaluate it using real-world datasets. Our experiments demonstrate that FiCOPS achieves 3.5 times speed-up over existing CPU solutions and 3 times and 5 times reduction in power consumption compared to existing CPU and GPU solutions.