pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra

doi:10.1021/pr100182k

	pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra
	Chi, Hao 1,2; Sun, Rui-Xiang 1; Yang, Bing 3; Song, Chun-Qing 3; Wang, Le-Heng 1; Liu, Chao 1,2; Fu, Yan 1; Yuan, Zuo-Fei 1,2; Wang, Hai-Peng 1,2; He, Si-Min 1; Dong, Meng-Qiu 3
	2010-05-01
发表期刊	JOURNAL OF PROTEOME RESEARCH
ISSN	1535-3893
卷号	9 期号:5 页码:2713-2724
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.
关键词	tandem mass spectrometry HCD de novo sequencing pNovo
DOI	10.1021/pr100182k
收录类别	SCI
语种	英语
资助项目	National Key Basic Research & Development Program (973) of China[2010CB912701] ; National Key Basic Research & Development Program (973) of China[2002CB713807] ; National High Technology Research and Development Program (863) of China[2007AA027315] ; National High Technology Research and Development Program (863) of China[2008AA02Z309] ; CAS[KGGX1-YW-13] ; National Natural Science Foundation of China[30900262]
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemical Research Methods
WOS记录号	WOS:000277353200060
出版者	AMER CHEMICAL SOC
引用统计	被引频次：129[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/2XEOYT63/12092
专题	中国科学院计算技术研究所期刊论文_英文
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.