Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications

doi:10.1021/acs.jproteome.6b00716

	Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications
	Yang, Hao 1,2; Chi, Hao 1; Zhou, Wen-Jing 1,2; Zeng, Wen-Feng 1,2; He, Kun 1,2; Liu, Chao 1; Sun, Rui-Xiang 1; He, Si-Min 1,2
	2017-02-01
发表期刊	JOURNAL OF PROTEOME RESEARCH
ISSN	1535-3893
卷号	16 期号:2 页码:645-654
摘要	De novo peptide sequencing has improved remarkably, but sequencing full-length peptides with unexpected modifications is still a challenging problem. Here we present an open de novo sequencing tool, Open-pNovo, for de novo sequencing of peptides with arbitrary types of modifications. Although the search space increases by 300 times, Open-pNovo is close to or even similar to 10-times faster than the other three proposed algorithms. Furthermore, considering top-1 candidates on three MS/MS data sets, Open-pNovo can recall over 90% of the results obtained by any one traditional algorithm and report 5-87% more peptides, including 14-250% more modified peptides. On a high-quality simulated data set, similar to 85% peptides with arbitrary modifications can be recalled by Open-pNovo, while hardly any results can be recalled by others. In summary, Open-pNovo is an excellent tool for open de novo sequencing and has great potential for discovering unexpected modifications in the real biological applications.
关键词	tandem mass spectrometry de novo peptide sequencing dynamic programming unexpected modifications
DOI	10.1021/acs.jproteome.6b00716
收录类别	SCI
语种	英语
资助项目	National Key Research and Development Program of China[2016YFA0501301] ; National High Technology Research and Development Program of China (863)[2014AA020902] ; National High Technology Research and Development Program of China (863)[2014AA020901] ; National Natural Science Foundation of China[31470805] ; Youth Innovation Promotion Association CAS[2014091]
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemical Research Methods
WOS记录号	WOS:000393539600026
出版者	AMER CHEMICAL SOC
引用统计	被引频次：24[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/2XEOYT63/7558
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Chi, Hao; He, Si-Min
作者单位	1.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Yang, Hao,Chi, Hao,Zhou, Wen-Jing,et al. Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications[J]. JOURNAL OF PROTEOME RESEARCH,2017,16(2):645-654.
APA	Yang, Hao.,Chi, Hao.,Zhou, Wen-Jing.,Zeng, Wen-Feng.,He, Kun.,...&He, Si-Min.(2017).Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications.JOURNAL OF PROTEOME RESEARCH,16(2),645-654.
MLA	Yang, Hao,et al."Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications".JOURNAL OF PROTEOME RESEARCH 16.2(2017):645-654.