Updated project metadata. Bovine paratuberculosis is a serious chronic disease of the gastrointestinal tract caused by Mycobacterium avium subspecies paratuberculosis (MAP). The aim of this study was to detect proteomic changes in peripheral blood mononuclear cells (PBMC) from cows of the same herd with different MAP infection status after co-incubation with viable MAP in vitro using label-free LC-MS/MS. Our data contribute to a better understanding of the bovine immune response and mechanisms of susceptibility to MAP.