蛋白质基因组学代表了肾脏病学的变革性交叉点，它将基因组学、转录组学和蛋白质组学结合起来，揭示肾脏疾病的分子复杂性。这篇综述概括了蛋白质基因组学的方法论本质及其对慢性肾脏病（CKD）研究的深远影响。我们探索蛋白质组学流程，强调基因组、转录组和蛋白质组数据的综合分析及其在增强我们对肾脏病理学理解方面的关键作用。通过案例研究，我们展示了蛋白质基因组学在透明细胞肾细胞癌 (ccRCC) 和常染色体隐性多囊肾病 (ARPKD) 中的应用，强调其在个性化治疗策略和生物标志物发现方面的潜力。该综述还解决了蛋白质基因组分析中的挑战，包括数据集成的复杂性和生物信息学的局限性，并提出了推进该领域的解决方案。最终，这篇综述强调了蛋白质基因组学在肾脏病学中的前景，特别是在推进个性化医疗和提供新颖的治疗见解方面。

Proteogenomics represents a transformative intersection in nephrology, uniting genomics, transcriptomics, and proteomics to unravel the molecular intricacies of kidney diseases. This review encapsulates the methodological essence of proteogenomics and its profound implications in chronic kidney disease (CKD) research. We explore the proteogenomic pipeline, highlighting the integrated analysis of genomic, transcriptomic, and proteomic data and its pivotal role in enhancing our understanding of kidney pathologies. Through case studies, we showcase the application of proteogenomics in clear cell renal cell carcinoma (ccRCC) and Autosomal Recessive Polycystic Kidney Disease (ARPKD), emphasizing its potential in personalized treatment strategies and biomarker discovery. The review also addresses the challenges in proteogenomic analysis, including data integration complexities and bioinformatics limitations, and proposes solutions for advancing the field. Ultimately, this review underscores the prospective future of proteogenomics in nephrology, particularly in advancing personalized medicine and providing novel therapeutic insights.