Institute of Computing Technology, Chinese Academy IR
| Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications | |
| Yang, Hao1,2; Chi, Hao1; Zhou, Wen-Jing1,2; Zeng, Wen-Feng1,2; He, Kun1,2; Liu, Chao1; Sun, Rui-Xiang1; He, Si-Min1,2 | |
| 2017-02-01 | |
| 发表期刊 | JOURNAL OF PROTEOME RESEARCH (IF:3.95[JCR-2017],4.033[5-Year]) |
| 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 | |
| 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. |
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