Methylation of proteins has considerable impacts on physiological processes including signal transduction, DNA damage repair, transcriptional regulation, gene activation, and inhibition of gene expression. However, the traditional proteomics-based approach suffers from limited identification rates of these critical methylation sites on endogenous peptides. In this work, a peptidomics-based workflow was established to discover and characterize the global methylome of endogenous peptides in human cells. The reliability of our strategy was validated by methyl-SILAC labeling, resulting in 83% true-positive identifications in the HeLa cell line. We applied this approach to seven human cell lines, and 700 methylated forms on 646 putative methylation sites were identified in total, with over 61% of the methylation sites being newly identified. This study provides a complementary strategy for a traditional proteomics-based approach that enables identification of missing methylation sites and creates a first methylome draft of endogenous peptides of human cell lines, offering a valuable resource for in-depth studies of biological functions of methylated endogenous peptides.

中文翻译：

---

人类细胞系内源性肽缺失甲基化位点的发现。

蛋白质的甲基化对生理过程有相当大的影响，包括信号转导、DNA 损伤修复、转录调控、基因激活和基因表达抑制。然而，传统的基于蛋白质组学的方法在内源性肽上的这些关键甲基化位点的识别率有限。在这项工作中，建立了基于肽组学的工作流程，以发现和表征人类细胞中内源性肽的全局甲基化组。我们的策略的可靠性通过甲基 SILAC 标记进行了验证，在 HeLa 细胞系中产生了 83% 的真阳性鉴定。我们将这种方法应用于 7 个人类细胞系，在 646 个假定的甲基化位点上总共鉴定了 700 个甲基化形式，其中超过 61% 的甲基化位点是新鉴定的。