SUMMARY: PepMapViz is a versatile R package that provides flexible peptide mapping and visualization capabilities. PepMapViz can import peptide data output from multiple popular mass spectrometry analysis tools, map peptides to their parent protein sequences, highlight protein domains and modifications, and enable comparative visualization across multiple experimental conditions. Beyond enabling visualization of MHC-presented peptide clusters in different antibody regions to predict potential immunogenicity of antibody-based therapies, PepMapViz can also aid in the visualization of cross-software mass spectrometry results at the peptide level for specific proteins, domain details in a linearized format, and post-translational modification coverage across different experimental conditions. AVAILABILITY AND IMPLEMENTATION: PepMapViz is freely available on GitHub at https://github.com/Genentech/PepMapViz and on CRAN. The package is implemented in R and includes documentation and example datasets.