Speed improvements of peptide-spectrum matching using SIMD instructions

Peptide-spectrum matching is one of the most time-consuming portion of the database search method for assignment of tandem mass spectra to peptides. In this study, we develop a parallel algorithm for peptide-spectrum matching using Single-Instruction Multiple-Data (SIMD) instructions. Unlike other parallel algorithms in peptide-spectrum matching, our algorithm parallelizes the computation of matches between a single spectrum and a given peptide sequence from the database. It also significantly reduces the number of comparison operations. Extra improvements are obtained by using SIMD instructions to avoid conditional branches and unnecessary memory access within the algorithm. The implementation of the developed algorithm is based on the Streaming SIMD Extensions (SSE) technology that is embedded in most Intel microprocessors. Similar technology also exists in other modern microprocessors. A simulation shows that the developed algorithm achieves an eighteen-fold speedup over the previous version of Real-Time Peptide-Spectrum Matching algorithm, RT-PSM (in Rapid Communication in Mass Spectrometry, 2006, 20: 1199-1208) [1]. Therefore, the developed algorithm can be employed to develop real-time control methods for tandem mass spectrometry.