Updated project metadata. Post-translational modification of amino acids changes the properties of a protein and increases the functional diversity of the proteome. For example, protein ubiquitination influences almost all cellular processes and can remodel the proteome in a matter of minutes. However, mostly due to technical limitations, global profiling of the plant ubiquitinome and proteome-wide identification of specific ubiquitinated residues remains challenging. Here, we made use of the COFRADIC technology to map ubiquitination sites in Arabidopsis thaliana. Across two biological replicates, we identified a total of 3,009 ubiquitination sites in 1,607 proteins. Our data increases the number of reported ubiquitin conjugation sites in Arabidopsis by a factor of 10. It contains well-known ubiquitination targets, including cell cycle proteins and key transcriptional regulators of phytohormone signaling as well as yet unreported targets, such as the Glutaredoxin S17 for which we provide here evidence of proteasomal degradation Finally, we could detect N-terminal ubiquitin conjugation on 19 proteins, a less commonly described type of protein modification.