TAR DNA binding protein of 43 kDa (TDP-43) forms aggregates in neurodegenerative diseases, particularly certain forms of frontotemporal dementia and amyotrophic lateral sclerosis. Pathological modifications of TDP-43 include proteolytic fragmentation, phosphorylation, and ubiquitinylation. In this study, we systematically mapped TDP-42 ubiquitination as well as acetylation sites.