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Deuterium-Free, Three-Plexed Peptide Diethylation for Highly Accurate Quantitative Proteomics

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Authors
Jung, Jaehun; Jeong, Kyowon; Choi, Yeon; Kim, Sun Ah; Kim, Hyunjoon; Lee, Joon Won; Kim, V. Narry; Kim, Kwang Pyo; Kim, Jong-Seo
Issue Date
2019-03
Citation
Journal of Proteome Research, Vol.18 No.3, pp.1078-1087
Keywords
diethylationdimethylationquantitative accuracydeuterium effectisotopic labelingisobaric labeling
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 C-13 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.
ISSN
1535-3893
URI
https://hdl.handle.net/10371/171922
DOI
https://doi.org/10.1021/acs.jproteome.8b00775
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College of Natural Sciences (자연과학대학)Dept. of Biological Sciences (생명과학부)Journal Papers (저널논문_생명과학부)
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