DRAM-based Acceleration of Open Modification Search for Mass Spectrometry-based Proteomics

Mass spectrometry, commonly used for protein identification, generates a massive number of spectra that need to be matched against a large database. In reality, most of them remain unidentified or mismatched due to unexpected post-translational modifications. Open modification search (OMS) has been proposed as a strategy to improve the identification rate by considering changes in spectra, but it expands the search space exponentially. In this work, we propose HyperOMS, an algorithm-hardware co-design for boosted OMS, to cope with the enlarged database and expanded search space. HyperOMS encodes spectral data into binary vectors and performs the efficient OMS in high-dimensional space. We accelerate the HyperOMS algorithm using a DRAM-based PIM accelerator, which combines processing-using-memory and near-memory processing technologies. In order to maximize the parallelization and efficiency of the accelerator, we optimize the data allocation and devise an approximation strategy for similarity computation. Experimental results show that the HyperOMS accelerator yields up to 3.8× speedup and 119W higher energy efficiency compared to running HyperOMS on GPU, and up to 99× speedup and 1984× higher energy efficiency over the state-of-the-art OMS tool, ANN-SoLo 1, while providing comparable search quality to competing tools.