Proteogenomics in human populations

In human population studies, proteogenomics integrates genomic and proteomic data to uncover how genetic variation shapes protein expression and function. A central focus of proteogenomics is the identification of protein quantitative trait loci (pQTL), which link genetic variants to protein abundance and offer critical insights into the molecular basis of disease. Recent years have seen pQTL studies scale rapidly, driven by advances in high-throughput proteomic platforms, the expansion of large biobank datasets and increasingly powerful cross-cohort meta-analyses, thereby greatly extending the depth, breadth and translational potential of proteogenomics. This Review highlights recent progress in proteogenomics with a focus on pQTL mapping and its downstream integration with complementary molecular data to provide insights into human disease. We also address current challenges and propose future directions to harness proteogenomics for the development of personalized therapies and improvement of health outcomes.