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arXiv · 2409.13361

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

Sumukh Pinge·Weihong Xu·Wout Bittremieux·Niema Moshiri·Sang-Woo Jun·Tajana Rosing
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Abstract

Mass spectrometry (MS) is essential for protein analysis but faces significant challenges with large datasets and complex post-translational modifications, resulting in 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.

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Sumukh Pinge, Weihong Xu, Wout Bittremieux, Niema Moshiri, Sang-Woo Jun, Tajana Rosing. 2024-09-20. RapidOMS: FPGA-based Open Modification Spectral Library Searching with HD Computing. https://arxiv.org/abs/2409.13361

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