| Pnovo: de novo peptide sequencing and identification using hcd spectra | |
| Chi, Hao1,2; Sun, Rui-Xiang1; Yang, Bing3; Song, Chun-Qing3; Wang, Le-Heng1; Liu, Chao1,2; Fu, Yan1; Yuan, Zuo-Fei1,2; Wang, Hai-Peng1,2; He, Si-Min1 | |
| 刊名 | Journal of proteome research
 |
| 2010-05-01 | |
| 卷号 | 9期号:5页码:2713-2724 |
| 关键词 | Tandem mass spectrometry Hcd De novo sequencing Pnovo |
| ISSN号 | 1535-3893 |
| DOI | 10.1021/pr100182k |
| 通讯作者 | He, si-min(smhe@ict.ac.cn) |
| 英文摘要 | De novo peptide sequencing has improved remarkably in the past decade as a result of better instruments and computational algorithms. however, de novo sequencing can correctly interpret only similar to 30% of high- and medium-quality spectra generated by collision-induced dissociation (cid), which is much less than database search. this is mainly due to incomplete fragmentation and overlap of different ion series in cid spectra. in this study, we show that higher-energy collisional dissociation (hcd) is of great help to de novo sequencing because it produces high mass accuracy tandem mass spectrometry (ms/ms) spectra without the low-mass cutoff associated with cid in ion trap instruments. besides, abundant internal and immonium ions in the hcd spectra can help differentiate similar peptide sequences. taking advantage of these characteristics, we developed an algorithm called pnovo for efficient de novo sequencing of peptides from hcd spectra. pnovo gave correct identifications to 80% or more of the hcd spectra identified by database search. the number of correct full-length peptides sequenced by pnovo is comparable with that obtained by database search. a distinct advantage of de novo sequencing is that deamidated peptides and peptides with amino acid mutations can be identified efficiently without extra cost in computation. in summary, implementation of the hcd characteristics makes pnovo an excellent tool for de novo peptide sequencing from hcd spectra. |
| WOS关键词 | TANDEM MASS-SPECTROMETRY ; COLLISION-INDUCED DISSOCIATION ; PROTEIN IDENTIFICATION ; AUTOMATED INTERPRETATION ; SOFTWARE AID ; SEARCH ; DATABASE ; ALGORITHM ; MODEL ; PERFORMANCE |
| WOS研究方向 | Biochemistry & Molecular Biology |
| WOS类目 | Biochemical Research Methods |
| 语种 | 英语 |
| 出版者 | AMER CHEMICAL SOC |
| WOS记录号 | WOS:000277353200060 |
| 内容类型 | 期刊论文 |
| URI标识 | http://www.corc.org.cn/handle/1471x/2406807 |
| 专题 | 中国科学院大学 |
| 通讯作者 | 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.Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China 3.Natl Inst Biol Sci, Beijing 102206, Peoples R China |
| 推荐引用方式 GB/T 7714 | Chi, Hao,Sun, Rui-Xiang,Yang, Bing,et al. Pnovo: de novo peptide sequencing and identification using hcd spectra[J]. Journal of proteome research,2010,9(5):2713-2724. |
| APA | Chi, Hao.,Sun, Rui-Xiang.,Yang, Bing.,Song, Chun-Qing.,Wang, Le-Heng.,...&Dong, Meng-Qiu.(2010).Pnovo: de novo peptide sequencing and identification using hcd spectra.Journal of proteome research,9(5),2713-2724. |
| MLA | Chi, Hao,et al."Pnovo: de novo peptide sequencing and identification using hcd spectra".Journal of proteome research 9.5(2010):2713-2724. |
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