Automating Proteogenomics: How ProteoAnnotator Aligns Mass Spectrometry Data with Genomic Sequences

ProteoAnnotator streamlines the complex task of linking mass spectrometry (MS) evidence to genomic sequences, a critical step in modern proteogenomics. Traditionally, researchers needed to manually compare peptide identifications with predicted gene models, a process that was both time-consuming and prone to inconsistency. ProteoAnnotator automates this workflow by mapping peptides back to their genomic loci, integrating multiple search engine outputs, and applying rigorous statistical scoring to ensure reliability. This automation not only accelerates data analysis but also improves the accuracy of gene model validation, enabling researchers to confirm protein translation, refine annotations, and discover novel coding regions with greater confidence. By bridging proteomic evidence with genomic context, ProteoAnnotator enhances reproducibility and makes proteogenomic insights more accessible to the broader life sciences community.