The presentation of peptide epitopes by major histocompatibility complex (MHC) class I molecules is a critical process governing anti-viral CD8⁺ T cell-mediated immunity. Here we have used quantitative mass spectrometry to profile the presentation of 46 vaccinia virus-derived MHC-bound epitopes during infection of dendritic cells and fibroblasts, including a comparison between immortalized cell lines and ex vivo primary cells. Our data show that, in general, dendritic cells outperform in terms of absolute presentation capacity, with ex vivo fibroblasts the poorest presenters. However, several epitopes remained refractory to this fibroblast deficiency, highlighting the need for such wide-scale analyses. Conversely, despite such differential presentation across cell lines, the kinetic profile of each epitope remained markedly unchanged – subsequent analysis of vaccinia proteome kinetics strongly supports the notion that nascent protein synthesis drives MHC-peptide display, and that the similarities in infection kinetics across cell types is therefore providing a comparable rate of peptide supply.

In order to try to relate this dataset to the immunogenicity of each peptide, we measured in parallel the CD8⁺ T cell response from infected mice, with the panel of peptides eliciting a robust immunodominance hierarchy. However, despite thorough analysis, the data so far show a complete disconnect between abundance and kinetics and the ensuing T cell response. These results highlight the complexities of epitope presentation during virus infection and the multifaceted processes that drive immunogenicity.