Ensuring Accurate Peptide-to-Gene Mapping: Quality Control in ProteoAnnotator

A major strength of ProteoAnnotator lies in its built-in quality control measures that safeguard the accuracy of peptide-to-gene mapping. In proteogenomics, a single peptide may match multiple genomic regions or protein isoforms, which can lead to misinterpretation if not handled carefully. ProteoAnnotator addresses this by applying rigorous statistical filters, verifying peptide uniqueness, and grouping identifications to ensure that only high-confidence evidence is used for annotation. These checks help distinguish genuine protein-coding events from spurious matches, providing a more reliable foundation for refining gene models or proposing novel annotations. By embedding these validation steps into its workflow, ProteoAnnotator not only automates analysis but also maintains the precision and reproducibility required for genome annotation projects.