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

TL;DR

RapidOMS is 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 and achieves an 11x improvement in energy efficiency compared to conventional systems.

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.

Figures (6)

• Figure 1: MS Data Analysis Pipeline
• Figure 2: SmartSSDs eliminates data transfers vs NAS Systems
• Figure 3: MS Preprocessing + HLS-Optimized Spectra Encoder
• Figure 4: RapidOMS FPGA-Accelerated Spectral Library Searching Flow on Samsung SmartSSD®
• Figure 5: Search Quality and Energy Efficiency