ADP-ribosylation is a post-translational modification of proteins that comprises the transfer of the ADP-ribose moiety from NAD+ to specific amino acid residues on substrate proteins or to ADP-ribose itself. It is catalyzed by ADP-ribosyltransferases, a family of currently 22 human proteins that all possess an ADP-ribosyltransferase catalytic domain. ADP-ribosylation is a reversible modification that can be hydrolyzed by ADP-ribosylhydrolases. In order to define the functional role of cellular ADP-ribosylation and the functional contribution of distinct ARTD family members, it is necessary to identify all ADP-ribosylated proteins, as well as their modified residues in the context of different cellular conditions and stresses. Here, we summarize the most recent progress in defining the cellular ADP-ribosylome and the efforts to detect ADP-ribose acceptor sites by enzymatic reactions and mass-spectrometry.