To investigate proteome-wide differences associated with Alzheimer’s disease (AD) and TDP-43 pathology, we selected three groups of cases: those with predominantly TDP-43 neuropathological changes (referred to as LATE-NC, or simply LATE), those with only Aβ plaque and tau tangle neuropathological changes (ADNC, or simply AD), and those with both AD and TDP-43 neuropathology (ADNC+LATE-NC or simply AD+LATE). Here, MAPT is linked to Alzheimer disease.