Beyond the Reference: Discovering Novel Proteins with ProteoAnnotator

ProteoAnnotator enables researchers to move beyond static reference annotations by uncovering novel proteins that are not represented in the initial genome models. By integrating high-quality mass spectrometry data with genomic coordinates, the tool identifies peptides that map to unannotated regions or alternative splice junctions, providing direct experimental evidence for new protein-coding sequences. This approach strengthens genome annotation by revealing previously overlooked open reading frames, refining exon boundaries, and validating protein isoforms with translational support. As a result, ProteoAnnotator not only confirms the accuracy of existing gene models but also expands our understanding of the proteome, ensuring that biological databases remain dynamic, evidence-driven, and reflective of real cellular activity.