Protein ubiquitination is an important post-translational modification that regulates almost every aspect of cellular function and many cell signaling pathways in eukaryotes. Alterations of protein ubiquitination have been linked to many diseases, such as cancer, neurodegenerative diseases, cardiovascular diseases, immunological disorders and inflammatory diseases. To understand the roles of protein ubiquitination in these diseases and in cell signaling pathways, it is necessary to identify ubiquitinated proteins and their modification sites. However, owing to the nature of protein ubiquitination, it is challenging to identify the exact modification sites under physiological conditions. Recently, ubiquitin-remnant profiling, an immunoprecipitation approach, which uses monoclonal antibodies specifically to enrich for peptides derived from the ubiquitinated portion of proteins and mass spectrometry for their identification, was developed to determine ubiquitination events from cell lysates. This approach has now been widely applied to profile protein ubiquitination in several cellular contexts. In this review, we discuss mass-spectrometry-based methods for the identification of protein ubiquitination sites, analyze their advantages and disadvantages, and discuss their application for proteomic analysis of ubiquitination.

蛋白质泛素化是一种重要的翻译后修饰，可调节真核生物中细胞功能的几乎所有方面和许多细胞信号通路。蛋白质泛素化的改变与许多疾病有关，例如癌症、神经退行性疾病、心血管疾病、免疫紊乱和炎症性疾病。要了解蛋白质泛素化在这些疾病和细胞信号通路中的作用，有必要确定泛素化蛋白质及其修饰位点。然而，由于蛋白质泛素化的性质，在生理条件下确定确切的修饰位点具有挑战性。最近，泛素残留分析，一种免疫沉淀方法，它使用单克隆抗体专门富集蛋白质泛素化部分衍生的肽，并使用质谱法进行鉴定，开发用于确定细胞裂解物的泛素化事件。这种方法现在已广泛应用于几种细胞环境中的蛋白质泛素化分析。在这篇综述中，我们讨论了基于质谱的蛋白质泛素化位点识别方法，分析了它们的优缺点，并讨论了它们在泛素化蛋白质组学分析中的应用。