Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics

doi:10.1074/mcp.TIR118.000918

	Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics
	Yang, Hao 1,2,3; Li, Yan-Chang 4,5,6,7; Zhao, Ming-Zhi 4,5,6,7; Wu, Fei-Lin 4,5,6,7; Wang, Xi 1,2,3; Xiao, Wei-Di 4,5,6,7; Wang, Yi-Hao 4,5,6,7; Zhang, Jun-Ling 4,5,6,7; Wang, Fu-Qiang 4,5,6,7; Xu, Feng 4,5,6,7; Zengt, Wen-Feng 1,2,3; Overall, Christopher M.9; He, Si-Min 1,2,3; Chi, Hao 1,2,3; Xu, Ping 4,5,6,7,8,10
	2019-04-01
发表期刊	MOLECULAR & CELLULAR PROTEOMICS
ISSN	1535-9476
卷号	18 期号:4 页码:773-785
摘要	De novo peptide sequencing for large-scale proteomics remains challenging because of the lack of full coverage of ion series in tandem mass spectra. We developed a mirror protease of trypsin, acetylated LysargiNase (Ac-LysargiNase), with superior activity and stability. The mirror spectrum pairs derived from the Ac-LysargiNase and trypsin treated samples can generate full b and y ion series, which provide mutual complementarity of each other, and allow us to develop a novel algorithm, pNovoM, for de novo sequencing. Using pNovoM to sequence peptides of purified proteins, the accuracy of the sequence was close to 100%. More importantly, from a large-scale yeast proteome sample digested with trypsin and Ac-LysargiNase individually, 48% of all tandem mass spectra formed mirror spectrum pairs, 97% of which contained full coverage of ion series, resulting in precision de novo sequencing of full-length peptides by pNovoM. This enabled pNovoM to successfully sequence 21,249 peptides from 3,753 proteins and interpreted 44-152% more spectra than pNovo+ and PEAKS at a 5% FDR at the spectrum level. Moreover, the mirror protease strategy had an obvious advantage in sequencing long peptides. We believe that the combination of mirror protease strategy and pNovoM will be an effective approach for precision de novo sequencing on both single proteins and proteome samples.
DOI	10.1074/mcp.TIR118.000918
收录类别	SCI
语种	英语
资助项目	National Key R&D Program of China[2016YFA0501300] ; National Key R&D Program of China[2017YFC0906600] ; National Key R&D Program of China[2017YFA0505002] ; National Key R&D Program of China[2015CB910700] ; National Natural Science Foundation of China[31870824] ; National Natural Science Foundation of China[91839302] ; National Natural Science Foundation of China[31670834] ; National Natural Science Foundation of China[31700723] ; Youth Innovation Promotion Association CAS[2014091] ; National Megaprojects for Key Infectious Diseases[2018ZX10302302001] ; National Natural Science Foundation of Beijing[5152008] ; Beijing Training Project for The Leading Talents in ST[Z161100004916024] ; Foundation of State Key Laboratory of Proteomics[SKLP-Y201501] ; Foundation of State Key Laboratory of Proteomics[SKLP-K201705] ; Innovation Foundation of Medicine[2017CXJJ19] ; Innovation Foundation of Medicine[BWS17J032] ; Innovation Foundation of Medicine[16CXZ027] ; Innovation Foundation of Medicine[BWS14J052] ; CAS Interdisciplinary Innovation Team[Y604061000]
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemical Research Methods
WOS记录号	WOS:000466934700012
出版者	AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC
引用统计	被引频次：27[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/2XEOYT63/4246
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; Chi, Hao; Xu, Ping
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 100190, Peoples R China 3.Chinese Acad Sci, Inst Comp Technol, Beijing 100190, Peoples R China 4.State Key Lab Prote, Beijing 102206, Peoples R China 5.Beijing Proteome Res Ctr, Beijing 102206, Peoples R China 6.Natl Ctr Prot Sci Beijing, Beijing 102206, Peoples R China 7.Beijing Beijing Inst Life, Beijing 102206, Peoples R China 8.Wuhan Univ, Minist Educ, Key Lab Combinatorial Biosynth & Drug Discovery, Sch Pharmaceut Sci, Wuhan 430071, Hubei, Peoples R China 9.Univ British Columbia, Ctr Blood Res, Vancouver, BC, Canada 10.Hebei Univ, Coll Life Sci, Baoding 071002, Peoples R China
推荐引用方式 GB/T 7714	Yang, Hao,Li, Yan-Chang,Zhao, Ming-Zhi,et al. Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics[J]. MOLECULAR & CELLULAR PROTEOMICS,2019,18(4):773-785.
APA	Yang, Hao.,Li, Yan-Chang.,Zhao, Ming-Zhi.,Wu, Fei-Lin.,Wang, Xi.,...&Xu, Ping.(2019).Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics.MOLECULAR & CELLULAR PROTEOMICS,18(4),773-785.
MLA	Yang, Hao,et al."Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics".MOLECULAR & CELLULAR PROTEOMICS 18.4(2019):773-785.