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Jung J, Jeong K, Choi Y, Kim SA, Kim H, Lee JW, Kim VN, Kim KP, Kim JS. Deuterium-Free, Three-Plexed Peptide Diethylation for Highly Accurate Quantitative Proteomics. J Proteome Res 2019; 18:1078-1087. [PMID: 30638020 DOI: 10.1021/acs.jproteome.8b00775] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The deuterium, a frequently used stable isotope in isotopic labeling for quantitative proteomics, could deteriorate the accuracy and precision of proteome quantification owing to the retention time shift of deuterated peptides from the hydrogenated counterpart. We introduce a novel three-plexed peptide "diethylation" using only 13C isotopologues of acetaldehyde and demonstrate that the accuracy and precision of our method in proteome quantification are significantly superior to the conventional deuterium-based dimethylation labeling in both a single-shot and multidimensional LC-MS/MS analysis of the HeLa proteome. Furthermore, in time-resolved profiling of Xenopus laevis early embryogenesis, our 3-plexed diethylation outperformed isobaric labeling approaches in terms of the quantification accuracy or the number of protein identifications, generating more than two times more differentially expressed proteins. Our cost-effective and highly accurate 3-plexed diethylation method could contribute to various types of quantitative proteomics applications in which three of multiplexity would be sufficient.
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Affiliation(s)
- Jaehun Jung
- Department of Applied Chemistry, College of Applied Science , Kyung Hee University , Yongin 17104 , Korea
| | - Kyowon Jeong
- Center for RNA Research , Institute for Basic Science (IBS) , Seoul 08826 , Korea.,School of Biological Sciences , Seoul National University , Seoul 08826 , Korea
| | - Yeon Choi
- Center for RNA Research , Institute for Basic Science (IBS) , Seoul 08826 , Korea.,School of Biological Sciences , Seoul National University , Seoul 08826 , Korea
| | - Sun Ah Kim
- Center for RNA Research , Institute for Basic Science (IBS) , Seoul 08826 , Korea.,School of Biological Sciences , Seoul National University , Seoul 08826 , Korea
| | - Hyunjoon Kim
- Center for RNA Research , Institute for Basic Science (IBS) , Seoul 08826 , Korea.,School of Biological Sciences , Seoul National University , Seoul 08826 , Korea
| | - Joon Won Lee
- Department of Applied Chemistry, College of Applied Science , Kyung Hee University , Yongin 17104 , Korea
| | - V Narry Kim
- Center for RNA Research , Institute for Basic Science (IBS) , Seoul 08826 , Korea.,School of Biological Sciences , Seoul National University , Seoul 08826 , Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, College of Applied Science , Kyung Hee University , Yongin 17104 , Korea
| | - Jong-Seo Kim
- Center for RNA Research , Institute for Basic Science (IBS) , Seoul 08826 , Korea.,School of Biological Sciences , Seoul National University , Seoul 08826 , Korea
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