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Ning X, Li Q, Zi J, Mei Z, Liu J, Zhang Y, Bi M, Ren Y, Liu X, Lv C, Yao H, Sun J, Rao F, Li S, Liu S. New Set of Isobaric Labeling Reagents for Quantitative 16Plex Proteomics. Anal Chem 2023; 95:5788-5795. [PMID: 36958307 DOI: 10.1021/acs.analchem.3c00235] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Peptide labeling by isobaric tags is a powerful approach for the relative quantitative analysis of proteomes in multiple groups. There has been a revolution in the innovation of new isobaric reagents; however, great effort is being made to expand simultaneous labeling groups to identify more labeled peptides and reduce reporter ion signal suppression. We redesigned the original chemical structure of the deuterium isobaric amine-reactive tag developed in our laboratory. We optimized the synthetic pathway to create a new set of 16-plex isobaric tags (IBT-16plex). The novel reagent enabled almost complete labeling of peptides within 90 min, with all labeling reporter ions exhibiting comparable MS/MS signals. Compared to a typical 16plex reagent, TMTpro-16plex, the peptides and proteins identified by IBT-16plex in trypsinized HeLa cells were significantly increased by 14.8 and 8.6%, respectively. Moreover, differences in peptide abundance within 10-fold among multiple groups were barely suppressed in IBT-16plex, whereas the dynamic range in TMTpro-16plex-labeled groups was smaller. After quantitative examination of MCF7 cell proteins, IBT-16plex was confirmed as feasible and useful for evaluating protein responses of glucose-starved MCF7 cells to a glucose-rich medium.
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Affiliation(s)
- Xiaolian Ning
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Qidan Li
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Jin Zi
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Zhejiang, Hangzhou 310022, China
| | | | - Jie Liu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | | | - Mao Bi
- School of Life Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yan Ren
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Zhejiang, Hangzhou 310022, China
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xingang Liu
- Nanjing Apollomics Biotech Inc., Nanjing, Jiangsu 210033, China
| | - Chao Lv
- Nanjing Apollomics Biotech Inc., Nanjing, Jiangsu 210033, China
| | - Hequan Yao
- China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Jianguo Sun
- China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Feng Rao
- School of Life Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Shuwei Li
- Nanjing Apollomics Biotech Inc., Nanjing, Jiangsu 210033, China
- China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Siqi Liu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Zhejiang, Hangzhou 310022, China
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