The evolution of the MHC class I antigen processing pathway has provided the adaptive immune system with an elegant means to scrutinize and eliminate pathogen-infected cells through CD8⁺ T cell responses. Despite an in-depth understanding of the underlying mechanisms leading to MHC presentation, our knowledge of the factors that govern whether or not a peptide is immunogenic, and the magnitude of the primed response in the case of the latter, remain poorly defined. Here we have used quantitative mass spectrometry to directly analyze the breadth and depth of influenza virus-derived peptides presented by murine MHC class I complexes following infection. The absolute abundance of 21 virus peptides (expanding upon the pool of previously known epitopes) was determined following direct presentation and compared to that following cross-presentation. Strikingly, in addition to identifying 9 novel immunogenic CTL epitopes, we find that cross-presentation dramatically alters the hierarchy of peptide abundance, with neither direct nor cross-presentation directly correlating with the acute phase CTL immunodominance hierarchy. Modelling the contributions of multiple parameters, including relative CTL precursor frequency, protein abundance, directly presented epitope abundance, and cross-presented epitope abundance, was able to capture up to 79% of the complexity of the CTL immunodominance hierarchy. These data represent a substantial advance in our understanding of the factors driving CD8⁺ T cell responses and have important ramifications for the development of vaccines.