Department of Applied Chemistry, College of Applied Science , Kyung Hee University , Yongin 17104 , Korea.
Center for RNA Research , Institute for Basic Science (IBS) , Seoul 08826 , Korea.
J Proteome Res. 2019 Mar 1;18(3):1078-1087. doi: 10.1021/acs.jproteome.8b00775. Epub 2019 Jan 29.
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 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.
氘是定量蛋白质组学中常用的稳定同位素标记物，由于氘代肽相对于氢化物的保留时间偏移，可能会降低蛋白质组定量的准确性和精密度。我们引入了一种新型的三肽“二乙基化”，仅使用乙醛的 C 同量异位体，并证明在 HeLa 蛋白质组的单次和多维 LC-MS/MS 分析中，与传统的基于氘的二甲基化标记相比，我们的方法在蛋白质组定量中的准确性和精密度有显著提高。此外，在 Xenopus laevis 早期胚胎发生的时间分辨分析中，我们的三肽二乙基化在定量准确性或蛋白质鉴定数量方面优于等压标记方法，产生了两倍以上的差异表达蛋白。我们具有成本效益且高度准确的三肽二乙基化方法可应用于各种类型的定量蛋白质组学应用中，其中三种多重性就足够了。
