Refining Rat Genome Annotation Through Integrated Proteogenomic Analysis

Advances in high-throughput sequencing and mass spectrometry have opened the door to integrative proteogenomic analyses, enabling researchers to refine genome annotations with unprecedented accuracy. In recent studies, combining transcriptomic and proteomic data within a unified proteogenomic workflow has proven particularly effective for the rat model. By aligning RNA-seq datasets with mass spectrometry-derived peptide evidence, researchers can identify novel protein-coding regions, validate predicted genes, and resolve previously ambiguous annotations. This integrated approach not only enhances the accuracy of the rat reference genome but also provides a richer resource for functional studies, drug development, and translational research. The synergy of transcriptomic and proteomic evidence ensures that every gene model is supported by both expression and protein-level validation, setting a new standard for comprehensive genome annotation in laboratory models.