PEPSeek-mediated identification of novel epitopes from viral and bacterial pathogens and the impact on host cell immunopeptidomes

Here, we develop PEPSeek, a web-server-based software to allow higher performance in the identification of pathogen-derived epitope candidates detected via mass spectrometry in MHC class I immunopeptidomes. We apply it to human and mouse cell lines infected with SARSCoV-2, Listeria monocytogenes, or Chlamydia trachomatis, thereby identifying a large number of novel antigens and epitopes that we prove to be recognized by CD8⁺ T cells. In infected cells, we identified antigenic peptide features that suggested how the processing and presentation of pathogenic antigens differ between pathogens. The quantitative tools of PEPSeek also helped to define how C. trachomatis infection cycle could impact the antigenic landscape of the host human cell system, likely reflecting metabolic changes that occurred in the infected cells.