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Pnovo: de novo peptide sequencing and identification using hcd spectra

文献类型:期刊论文

作者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
出版日期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
DOI10.1021/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
WOS记录号WOS:000277353200060
出版者AMER CHEMICAL SOC
URI标识http://www.irgrid.ac.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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来源:中国科学院大学

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