RapidOMS: FPGA-based Open Modification Spectral Library Searching with HD Computing
<|reference_start|>RapidOMS: FPGA-based Open Modification Spectral Library Searching with HD Computing: 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.<|reference_end|>
@article{pinge2024rapidoms:,
    title={RapidOMS: FPGA-based Open Modification Spectral Library Searching with
  HD Computing},
    author={Sumukh Pinge, Weihong Xu, Wout Bittremieux, Niema Moshiri, Sang-Woo
  Jun, and Tajana Rosing},
    journal={arXiv preprint arXiv:2409.13361},
    year={2024},
    archivePrefix={arXiv},
    eprint={2409.13361},
    primaryClass={cs.DC cs.AR}
}