Despite the immense disease burden caused by influenza viruses, there remains a lack of long-lasting, efficacious vaccines. Current seasonal vaccines induce antibody-based immunity and yet the resolution of established influenza infection is mediated by cytotoxic CD8+ T cells directed to viral peptide/human leukocyte antigen (HLA) class I complexes expressed on the surface of infected cells. The repertoire of HLA-bound peptides presented to the immune system (i.e., the immunopeptidome) represents a rich source of potential vaccine targets. A significant obstacle in influenza T cell epitope discovery in humans, however, is the lack of in vitro models that faithfully mimic natural infection across major HLA allotypes. Although we have successfully used high resolution mass spectrometry to identify numerous influenza CD8+ T cell epitopes presented by “monoallelic” HLA-transfected (C1R) cell lines, it is not known how accurately these B-lymphoblastoid cells reflect antigen presentation during natural infection. To address this, we are performing paired proteomic and immunopeptidomic analysis of influenza-infected lung epithelial A549 and Calu-3 cell lines which more closely resemble the natural targets of infection. Translating our in vitro model from C1R cells to more biologically relevant lung epithelia will uncover cell-type specific differences in antigen processing and presentation that contribute to infection outcomes, and provide insight into the optimal mode of antigen presentation for individual viral epitopes.