Applying a proteogenomic approach for improving genome annotation in Leishmania panamensis using high-resolution mass spectrometry data

Leishmania panamensis , a protozoan parasite of the Viannia subgenus, causes American tegumentary leishmaniasis (ATL) throughout Central and South America, with significant clinical manifestations ranging from cutaneous lesions to mucosal involvement. Despite the availability of a reference genome for L. panamensis MHOM/COL/81/L13 strain, comprising approximately 30.69 megabases across 35 chromosomes and approximately 8,000 predicted protein-coding genes, comprehensive proteogenomic analyses to refine these annotations have remained limited. This study employed a proteogenomic approach to enhance the genome annotation of L. panamensis MHOM/COL/81/L13 strain by integrating publicly available liquid chromatography-tandem mass spectrometry data with a custom six-frame translated genome database. Through systematic peptide mapping and validation, we identified 50 novel protein-coding genes previously absent from the reference annotation and corrected the annotations of 50 existing genes. The newly identified genes encode proteins containing functionally significant domains, including thioredoxin, glucosyltransferases, and myotubularin, which likely contribute to parasite metabolism, host-pathogen interactions, and intracellular survival mechanisms. These findings substantially refine the genomic resource available for L. panamensis research and provide potential targets for diagnostic and therapeutic development. This work parallels recent proteogenomic studies in related Viannia species such as L. braziliensis , demonstrating the broader applicability of peptide-supported genome reannotation strategies across kinetoplastid parasites. The refined annotation enables more accurate functional genomic studies and enhances our understanding of the molecular basis underlying L. panamensis pathogenicity and immune evasion strategies.