Genomic analyses in cancer have been enormously impactful, leading to the identification of driver mutations and development of targeted therapies. But the functions of the vast majority of somatic mutations and copy number variants in tumours remain unknown, and the causes of resistance to targeted therapies and methods to overcome them are poorly defined. Recent improvements in mass spectrometry-based proteomics now enable direct examination of the consequences of genomic aberrations, providing deep and quantitative characterization of tumour tissues. Integration of proteins and their post-translational modifications with genomic, epigenomic and transcriptomic data constitutes the new field of proteogenomics, and is already leading to new biological and diagnostic knowledge with the potential to improve our understanding of malignant transformation and therapeutic outcomes. In this Review we describe recent developments in proteogenomics and key findings from the proteogenomic analysis of a wide range of cancers. Considerations relevant to the selection and use of samples for proteogenomics and the current technologies used to generate, analyse and integrate proteomic with genomic data are described. Applications of proteogenomics in translational studies and immuno-oncology are rapidly emerging, and the prospect for their full integration into therapeutic trials and clinical care seems bright.

癌症的基因组分析产生了巨大的影响，导致驱动突变的识别和靶向治疗的发展。但肿瘤中绝大多数体细胞突变和拷贝数变异的功能仍然未知，靶向治疗耐药的原因和克服它们的方法也不清楚。基于质谱的蛋白质组学的最新改进现在可以直接检查基因组畸变的后果，提供肿瘤组织的深入和定量表征。蛋白质及其翻译后修饰与基因组、表观基因组和转录组数据的整合构成了蛋白质组学的新领域，并且已经产生了新的生物学和诊断知识，有可能提高我们对恶性转化和治疗结果的理解。在这篇综述中，我们描述了蛋白质组学的最新发展以及对多种癌症进行蛋白质组学分析的主要发现。描述了与蛋白质组学样本的选择和使用相关的考虑因素，以及用于生成、分析和整合蛋白质组学与基因组数据的当前技术。蛋白质组学在转化研究和免疫肿瘤学中的应用正在迅速兴起，它们完全融入治疗试验和临床护理的前景似乎一片光明。在这篇综述中，我们描述了蛋白质组学的最新发展以及对多种癌症进行蛋白质组学分析的主要发现。描述了与蛋白质组学样本的选择和使用相关的考虑因素，以及用于生成、分析和整合蛋白质组学与基因组数据的当前技术。蛋白质组学在转化研究和免疫肿瘤学中的应用正在迅速兴起，它们完全融入治疗试验和临床护理的前景似乎一片光明。在这篇综述中，我们描述了蛋白质组学的最新发展以及对多种癌症进行蛋白质组学分析的主要发现。描述了与蛋白质组学样本的选择和使用相关的考虑因素，以及用于生成、分析和整合蛋白质组学与基因组数据的当前技术。蛋白质组学在转化研究和免疫肿瘤学中的应用正在迅速兴起，它们完全融入治疗试验和临床护理的前景似乎一片光明。