Cancers are caused by accumulated DNA mutations. This recognition of the central role of mutations in cancer and recent advances in next-generation sequencing, has initiated the massive screening of clinical samples and the identification of 1000s of cancer-associated gene mutations. However, proteomic analysis of the expressed mutation products lags far behind genomic (transcriptomic) analysis. With comprehensive global proteomics analysis, only a small percentage of single nucleotide variants detected by DNA and RNA sequencing have been observed as single amino acid variants due to current technical limitations. Proteomic analysis of mutations is important with the potential to advance cancer biomarker development and the discovery of new therapeutic targets for more effective disease treatment. Targeted proteomics using selected reaction monitoring (also known as multiple reaction monitoring) and parallel reaction monitoring, has emerged as a powerful tool with significant advantages over global proteomics for analysis of protein mutations in terms of detection sensitivity, quantitation accuracy and overall practicality (e.g., reliable identification and the scale of quantification). Herein we review recent advances in the targeted proteomics technology for enhancing detection sensitivity and multiplexing capability and highlight its broad biomedical applications for analysis of protein mutations in human bodily fluids, tissues, and cell lines. Furthermore, we review recent applications of top-down proteomics for analysis of protein mutations. Unlike the commonly used bottom-up proteomics which requires digestion of proteins into peptides, top-down proteomics directly analyzes intact proteins for more precise characterization of mutation isoforms. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale targeted detection and quantification of important protein mutations are discussed.

中文翻译：

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基于质谱的靶向蛋白质组学用于蛋白质突变分析

癌症是由累积的 DNA 突变引起的。对突变在癌症中的核心作用的认识以及下一代测序的最新进展，已经启动了对临床样本的大规模筛查并鉴定了数千个与癌症相关的基因突变。然而，表达突变产物的蛋白质组学分析远远落后于基因组（转录组学）分析。通过全面的全球蛋白质组学分析，由于目前的技术限制，只有一小部分通过 DNA 和 RNA 测序检测到的单核苷酸变异被观察为单氨基酸变异。突变的蛋白质组学分析非常重要，有可能促进癌症生物标志物的开发和发现更有效的疾病治疗的新治疗靶点。使用选择性反应监测（也称为多反应监测）和平行反应监测的靶向蛋白质组学已成为一种强大的工具，在检测灵敏度、定量准确性和整体实用性方面比全局蛋白质组学具有显着优势，可用于蛋白质突变分析（例如，可靠的鉴定和量化规模）。在此，我们回顾了靶向蛋白质组学技术在增强检测灵敏度和多重分析能力方面的最新进展，并重点介绍了其在分析人体体液、组织和细胞系中蛋白质突变方面的广泛生物医学应用。此外，我们回顾了自上而下蛋白质组学在蛋白质突变分析中的最新应用。与常用的自下而上的蛋白质组学不同，自下而上的蛋白质组学需要将蛋白质消化成肽，自上而下的蛋白质组学直接分析完整的蛋白质，以更精确地表征突变亚型。最后，讨论了在大规模靶向检测和重要蛋白质突变定量方面实现高灵敏度和高样品通量的潜力的一般观点。