Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications
Yang, Hao1,2; Chi, Hao2; Zhou, Wen-Jing1,2; Zeng, Wen-Feng1,2; He, Kun1,2; Liu, Chao2; Sun, Rui-Xiang2; He, Si-Min1,2
刊名JOURNAL OF PROTEOME RESEARCH
2017-02-01
卷号16期号:2页码:645-654
关键词tandem mass spectrometry de novo peptide sequencing dynamic programming unexpected modifications
ISSN号1535-3893
DOI10.1021/acs.jproteome.6b00716
英文摘要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.
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
语种英语
出版者AMER CHEMICAL SOC
WOS记录号WOS:000393539600026
内容类型期刊论文
源URL[http://119.78.100.204/handle/2XEOYT63/7557]  
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.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
2.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, 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.
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