Tryptic Peptides Bearing C-Terminal Dimethyllysine Need to Be Considered during the Analysis of Lysine Dimethylation in Proteomic Study

doi:10.1021/acs.jproteome.7b00373

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	Tryptic Peptides Bearing C-Terminal Dimethyllysine Need to Be Considered during the Analysis of Lysine Dimethylation in Proteomic Study
	Chen, Ming 1,2,3; Zhang, Min 1,2,3; Zhai, Linhui 1,3; Hu, Hao 1,3; Liu, Ping 1,3; Tan, Minjia1,2,3
刊名	JOURNAL OF PROTEOME RESEARCH
	2017-09
卷号	16 期号:9 页码:3460-3469
关键词	trypsin lysine dimethylation proteomics terminal amine isotopic labeling of substrates (TAILS) mass spectrometry analysis
ISSN号	1535-3893
DOI	10.1021/acs.jproteome.7b00373
文献子类	Article
英文摘要	Lysine methylation plays important roles in structural and functional regulation of chromatin. Although trypsin is the most widely used protease in mass spectrometry-based proteomic analysis for lysine methylation substrates, the proteolytic activity of trypsin on dimethylated lysine residues remains an arguable issue. In this study, we tested the ability of trypsin to cleave dimethylated lysine residues in synthetic peptides, purified albumin, and whole cell lysate, and found that the C-terminal of dimethylated lysine residue could be cleaved in a protein sequence dependent manner. Kinetic studies revealed that the optimal digestion time and enzyme-to-substrate ratio for the cleavage of dimethylated lysine by trypsin was around 16 h and 1:50, respectively. We further showed the tryptic C-terminal lysine-dimethylated (C-Kme2) peptides could contribute to a significant portion of substrate identification in the proteomic study, which utilizes the chemical dimethylation labeling approach. More than 120 tryptic C-Kme2 peptides (7% of total peptides identified) were identified in chemically lysine-dimethyl-labeled HeLa whole cell lysate by a single-shot nanoflow high performance liquid chromatography with tandem mass spectrometry (nano-HPLC-MS/MS) analysis. Moreover, in an assay for substrate identification of protease Glu-C using stable isotope dimethyl labeling approach, our data showed the tryptic C-Kme2 peptides accounted for more than 13% of total tryptic peptides. Additionally, our in vivo methylome profiling data revealed some C-Kme2 peptides, which is of importance to identification and quantification of biologically relevant protein and lysine-methylated site. Therefore, we reason that the tryptic peptides bearing C-terminal dimethylated lysine need to be considered in the mass spectrometric analysis of lysine dimethylation.
资助项目	National Basic Research Program of China (973 Program)[2014CBA02001] ; Natural Science Foundation of China[31670066] ; Youth Science and Technology Talents in Shanghai Sail Plan of China[16YF1414000] ; Youth Science and Technology Talents in Shanghai Sail Plan of China[17YF1423200] ; Chinese Academy of Sciences[XDA12020314] ; Chinese Academy of Sciences[2060499]
WOS关键词	POSTTRANSLATIONAL MODIFICATIONS ; MASS-SPECTROMETRY ; STEM-CELLS ; N-TERMINI ; PROTEINS ; IDENTIFICATION ; METHYLATION ; TRYPSIN ; METHYLTRANSFERASES ; QUANTIFICATION
WOS研究方向	Biochemistry & Molecular Biology
语种	英语
出版者	AMER CHEMICAL SOC
WOS记录号	WOS:000410003500031
内容类型	期刊论文
源URL	[http://119.78.100.183/handle/2S10ELR8/272505]
专题	化学蛋白质组学研究中心中科院受体结构与功能重点实验室新药研究国家重点实验室
通讯作者	Tan, Minjia
作者单位	1.Chinese Acad Sci, State Key Lab Drug Res, Shanghai Inst Mat Med, Shanghai 201203, Peoples R China; 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 3.Chinese Acad Sci, Chem Prote Ctr, Shanghai 201203, Peoples R China;
推荐引用方式 GB/T 7714	Chen, Ming,Zhang, Min,Zhai, Linhui,et al. Tryptic Peptides Bearing C-Terminal Dimethyllysine Need to Be Considered during the Analysis of Lysine Dimethylation in Proteomic Study[J]. JOURNAL OF PROTEOME RESEARCH,2017,16(9):3460-3469.
APA	Chen, Ming,Zhang, Min,Zhai, Linhui,Hu, Hao,Liu, Ping,&Tan, Minjia.(2017).Tryptic Peptides Bearing C-Terminal Dimethyllysine Need to Be Considered during the Analysis of Lysine Dimethylation in Proteomic Study.JOURNAL OF PROTEOME RESEARCH,16(9),3460-3469.
MLA	Chen, Ming,et al."Tryptic Peptides Bearing C-Terminal Dimethyllysine Need to Be Considered during the Analysis of Lysine Dimethylation in Proteomic Study".JOURNAL OF PROTEOME RESEARCH 16.9(2017):3460-3469.