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	Speeding up tandem mass spectrometry-based database searching by longest common prefix
	Zhou, Chen1,2,3; Chi, Hao1,2,3; Wang, Le-Heng1,2; Li, You1,2; Wu, Yan-Jie1,2,3; Fu, Yan1,2; Sun, Rui-Xiang1,2; He, Si-Min1,2
刊名	Bmc bioinformatics
	2010-11-25
卷号	11页码:11
ISSN号	1471-2105
DOI	10.1186/1471-2105-11-577
通讯作者	He, si-min(smhe@ict.ac.cn)
英文摘要	Background: tandem mass spectrometry-based database searching has become an important technology for peptide and protein identification. one of the key challenges in database searching is the remarkable increase in computational demand, brought about by the expansion of protein databases, semi-or non-specific enzymatic digestion, post-translational modifications and other factors. some software tools choose peptide indexing to accelerate processing. however, peptide indexing requires a large amount of time and space for construction, especially for the non-specific digestion. additionally, it is not flexible to use. results: we developed an algorithm based on the longest common prefix (ablcp) to efficiently organize a protein sequence database. the longest common prefix is a data structure that is always coupled to the suffix array. it eliminates redundant candidate peptides in databases and reduces the corresponding peptide-spectrum matching times, thereby decreasing the identification time. this algorithm is based on the property of the longest common prefix. even enzymatic digestion poses a challenge to this property, but some adjustments can be made to this algorithm to ensure that no candidate peptides are omitted. compared with peptide indexing, ablcp requires much less time and space for construction and is subject to fewer restrictions. conclusions: the ablcp algorithm can help to improve data analysis efficiency. a software tool implementing this algorithm is available at http://pfind.ict.ac.cn/pfind2dot5/index.htm
WOS关键词	PROTEIN IDENTIFICATION ; PEPTIDE IDENTIFICATION ; SPECTRA ; ALGORITHM ; PFIND
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
语种	英语
出版者	BIOMED CENTRAL LTD
WOS记录号	WOS:000285250800001
内容类型	期刊论文
URI标识	http://www.corc.org.cn/handle/1471x/2408973
专题	中国科学院大学
通讯作者	He, Si-Min
作者单位	1.Chinese Acad Sci, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China 2.Chinese Acad Sci, Inst Comp Technol, Beijing 100190, Peoples R China 3.Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Zhou, Chen,Chi, Hao,Wang, Le-Heng,et al. Speeding up tandem mass spectrometry-based database searching by longest common prefix[J]. Bmc bioinformatics,2010,11:11.
APA	Zhou, Chen.,Chi, Hao.,Wang, Le-Heng.,Li, You.,Wu, Yan-Jie.,...&He, Si-Min.(2010).Speeding up tandem mass spectrometry-based database searching by longest common prefix.Bmc bioinformatics,11,11.
MLA	Zhou, Chen,et al."Speeding up tandem mass spectrometry-based database searching by longest common prefix".Bmc bioinformatics 11(2010):11.

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