Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs

doi:10.1186/1471-2105-15-121

	Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs
	Li,You 1; Chi,Hao 2,3; Xia,Leihao 1; Chu,Xiaowen 1
	2014-04-28
发表期刊	BMC Bioinformatics
ISSN	1471-2105
卷号	15 期号:1
摘要	AbstractBackgroundTandem mass spectrometry-based database searching is currently the main method for protein identification in shotgun proteomics. The explosive growth of protein and peptide databases, which is a result of genome translations, enzymatic digestions, and post-translational modifications (PTMs), is making computational efficiency in database searching a serious challenge. Profile analysis shows that most search engines spend 50%-90% of their total time on the scoring module, and that the spectrum dot product (SDP) based scoring module is the most widely used. As a general purpose and high performance parallel hardware, graphics processing units (GPUs) are promising platforms for speeding up database searches in the protein identification process.ResultsWe designed and implemented a parallel SDP-based scoring module on GPUs that exploits the efficient use of GPU registers, constant memory and shared memory. Compared with the CPU-based version, we achieved a 30 to 60 times speedup using a single GPU. We also implemented our algorithm on a GPU cluster and achieved an approximately favorable speedup.ConclusionsOur GPU-based SDP algorithm can significantly improve the speed of the scoring module in mass spectrometry-based protein identification. The algorithm can be easily implemented in many database search engines such as X!Tandem, SEQUEST, and pFind. A software tool implementing this algorithm is available at http://www.comp.hkbu.edu.hk/~youli/ProteinByGPU.html
DOI	10.1186/1471-2105-15-121
语种	英语
WOS记录号	BMC:10.1186/1471-2105-15-121
出版者	BioMed Central
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/4026
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Chu,Xiaowen
作者单位	1.Hong Kong Baptist University; Department of Computer Science 2.Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences 3.Graduate University of Chinese Academy of Sciences
推荐引用方式 GB/T 7714	Li,You,Chi,Hao,Xia,Leihao,et al. Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs[J]. BMC Bioinformatics,2014,15(1).
APA	Li,You,Chi,Hao,Xia,Leihao,&Chu,Xiaowen.(2014).Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs.BMC Bioinformatics,15(1).
MLA	Li,You,et al."Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs".BMC Bioinformatics 15.1(2014).