Response to the Comments on "Determining Allele-Specific Protein Expression (ASPE) Using a Novel Quantitative Concatamer Proteomics Method".,Journal of Proteome Research

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Response to the Comments on "Determining Allele-Specific Protein Expression (ASPE) Using a Novel Quantitative Concatamer Proteomics Method".
Journal of Proteome Research ( IF 3.8 ) Pub Date : 2019-01-09 , DOI: 10.1021/acs.jproteome.8b00940
Jian Shi ₁ , Xinwen Wang ₁ , Huaijun Zhu _{1,

2} , Hui Jiang , Danxin Wang ₃ , Alexey Nesvizhskii , Hao-Jie Zhu ₁

Affiliation

Russell and colleagues deserve credit for being the first to use a QconCAT standard to simultaneously quantify both the wild-type and mutant peptides of a protein (i.e., CYP2B6) ( J. Proteome Res. 2013, 12 (12), 5934-5942. DOI: 10.1021/pr400279u). However, the rationale of their study was entirely different from ours ( J. Proteome Res. 2018, 17 (10), 3606-3612. DOI: 10.1021/acs.jproteome.8b00620). Their study focused on the quantification of individual drug-metabolizing enzymes and transporters, whereas ours developed a targeted proteomics method to determine the allele-specific protein expression (ASPE) of a gene and advocated the use of the ASPE imbalance as the phenotype for identifying cis-regulatory genetic variants of the gene. More importantly, the digestion enzyme trypsin interacts with three to four amino acid residues around scissile bonds, and certain residues, such as negatively charged amino acids, can significantly affect the digestion efficiency. The QconCAT standard reported in our study differs from conventional QconCAT standards such as that used by Russell et al. in that at least 15 native flanking amino acids were included to ensure accurate measurement of ASPE ratios.

中文翻译：

对有关“使用新型定量辅酶蛋白质组学方法确定等位基因特异性蛋白表达（ASPE）”评论的回应。

Russell及其同事因率先使用QconCAT标准同时量化蛋白质的野生型和突变型肽（即CYP2B6）而受到赞誉（J.Proteome Res.2013，12（12），5934-5942。 DOI：10.1021 / pr400279u）。但是，他们研究的理由与我们的研究完全不同（J.Proteome Res.2018，17（10），3606-3612.DOI：10.1021 / acs.jproteome.8b00620）。他们的研究集中于单个药物代谢酶和转运蛋白的定量，而我们的研究开发了一种靶向蛋白质组学方法来确定基因的等位基因特异性蛋白表达（ASPE），并提倡使用ASPE不平衡作为鉴定顺式的表型。基因的调控遗传变异。更重要的是，消化酶胰蛋白酶与易碎键周围的3至4个氨基酸残基相互作用，某些残基（例如带负电荷的氨基酸）会显着影响消化效率。我们研究中报告的QconCAT标准不同于常规的QconCAT标准，例如Russell等人使用的标准。因为至少包含15个天然侧翼氨基酸，以确保准确测量ASPE比率。

更新日期：2019-02-07

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