Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry

doi:10.1093/bioinformatics/bth186

	Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry
	Fu, Y ; Yang, Q ; Sun, RX ; Li, DQ ; Zeng, R ; Ling, CX ; Gao, W
	2004-08-12
发表期刊	BIOINFORMATICS
ISSN	1367-4803
卷号	20 期号:12 页码:1948-1954
摘要	Motivation: The correlation among fragment ions in a tandem mass spectrum is crucial in reducing stochastic mismatches for peptide identification by database searching. Until now, an efficient scoring algorithm that considers the correlative information in a tunable and comprehensive manner has been lacking. Results: This paper provides a promising approach to utilizing the correlative information for improving the peptide identification accuracy. The kernel trick, rooted in the statistical learning theory, is exploited to address this issue with low computational effort. The common scoring method, the tandem mass spectral dot product (SDP), is extended to the kernel SDP (KSDP). Experiments on a dataset reported previously demonstrate the effectiveness of the KSDP. The implementation on consecutive fragments shows a decrease of 10% in the error rate compared with the SDP. Our software tool, pFind, using a simple scoring function based on the KSDP, outperforms two SDP-based software tools, SEQUEST and Sonar MS/MS, in terms of identification accuracy.
DOI	10.1093/bioinformatics/bth186
收录类别	SCI
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
WOS记录号	WOS:000223588300014
出版者	OXFORD UNIV PRESS
引用统计	被引频次：90[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/14001
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Fu, Y
作者单位	1.Chinese Acad Sci, Inst Comp Technol, Beijing 100080, Peoples R China 2.Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China 3.Hong Kong Univ Sci & Technol, Dept Comp Sci, Kowloon, Hong Kong, Peoples R China 4.Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Biochem & Cell Biol, Key Lab Proteom,Res Ctr Proteome Anal, Shanghai 200031, Peoples R China 5.Univ Western Ontario, Dept Comp Sci, London, ON N6A 5B7, Canada
推荐引用方式 GB/T 7714	Fu, Y,Yang, Q,Sun, RX,et al. Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry[J]. BIOINFORMATICS,2004,20(12):1948-1954.
APA	Fu, Y.,Yang, Q.,Sun, RX.,Li, DQ.,Zeng, R.,...&Gao, W.(2004).Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry.BIOINFORMATICS,20(12),1948-1954.
MLA	Fu, Y,et al."Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry".BIOINFORMATICS 20.12(2004):1948-1954.