RapidOMS: FPGA-based Open Modification Spectral Library Searching with HD Computing

• Published in: Biomedical Circuits and Systems Conference pp. 1 - 5
• Main Authors: Pinge, Sumukh, Xu, Weihong, Bittremieux, Wout, Moshiri, Niema, Jun, Sang-Woo, Rosing, Tajana
• Format: Conference Proceeding
• Language: English
• Published: IEEE 24.10.2024
• Subjects: Central Processing Unit; Energy efficiency; Field programmable gate arrays; FPGAs; Hyperdimensional Computing; Libraries; Mass Spectrometry; Mass spectroscopy; Medical services; MS Library Searching; Parallel processing; Protein engineering; Proteins; Proteomics
• ISSN: 2766-4465
• DOI: 10.1109/BioCAS61083.2024.10798176

Mass spectrometry (MS) is essential for protein analysis but faces significant challenges with large datasets and complex post-translational modifications, resultingin difficulties in spectral identification. Open Modification Search (OMS) improves the analysis of these modifications. We present RapidOMS, a solution leveraging the Samsung SmartSSD, which integrates SSD and FPGA in a near-storage configuration to minimize data movement and enhance the efficiency of large-scale database searching. RapidOMS employs hyperdimensional computing (HDC), a brain-inspired, high-dimensional data processing approach, exploiting the parallel processing and low-latency capabilities of FPGAs, making it well-suited for MS. Utilizing the parallelism and efficiency of bitwise operations in HDC, RapidOMS delivers up to a 60x speedup over the state-of-the-art (SOTA) CPU tool ANN-Solo and is 2.72x faster than the GPU tool HyperOMS. Furthermore, RapidOMS achieves an 11x improvement in energy efficiency compared to conventional systems, providing scalable, energy-efficient solutions for large-scale proteomics applications and advancing the efficient processing of proteomic data.