PeptiMapper: Expert Proteogenomic Workflow for Accurate Eukaryotic Genome Annotation

Accurate annotation of eukaryotic genomes remains a critical challenge in genomics research, particularly given the complexity of alternative splicing, post-translational modifications, and uncharacterized open reading frames. PeptiMapper offers a specialized proteogenomics workflow designed to address these challenges by integrating high-resolution mass spectrometry data with genomic and transcriptomic information. By mapping experimentally derived peptides directly onto genomic sequences, PeptiMapper allows researchers to validate predicted gene models, discover novel protein-coding regions, and refine annotations with high confidence. This expert workflow is particularly valuable for non-model organisms and newly sequenced genomes, where conventional annotation pipelines often fall short. Ultimately, PeptiMapper empowers scientists to generate more accurate, functionally relevant genome annotations, advancing our understanding of eukaryotic biology and supporting downstream applications in functional genomics, proteomics, and biotechnology.