Speed improvements of peptide-spectrum matching using Single-Instruction Multiple-Data instructions

• Published in: Proteomics (Weinheim) Vol. 11; no. 19; pp. 3779 - 3785
• Main Authors: Zhang, Jian, McQuillan, Ian, Wu, Fang-Xiang
• Format: Journal Article
• Language: English
• Published: Weinheim WILEY-VCH Verlag 01.10.2011; WILEY‐VCH Verlag; Wiley-VCH; Wiley Subscription Services, Inc
• Subjects: Algorithms; Analytical, structural and metabolic biochemistry; Bioinformatics; Biological and medical sciences; Data processing; Databases, Protein; Fundamental and applied biological sciences. Psychology; Mass spectra; Memory; Microprocessors; Miscellaneous; Parallel computing; Peptides; Peptides - chemistry; Proteins; proteomics; Single-Instruction Multiple-Data; Streaming; Tandem Mass Spectrometry - economics; Tandem Mass Spectrometry - methods; Time Factors; Parallel computing; Single-Instruction Multiple-Data; Peptides; Bioinformatics; MS; Proteomics
• ISSN: 1615-9853; 1615-9861; 1615-9861
• DOI: 10.1002/pmic.201100182

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 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 18‐fold speedup over the previous version of Real‐Time Peptide–Spectrum Matching algorithm [F. X. Wu et al., Rapid Commun. Mass Sepctrom. 2006, 20, 1199–1208]. Therefore, the developed algorithm can be employed to develop real‐time control methods for MS/MS.