Ubiquitin is a versatile post-translational modification which regulates protein fate and function. It is covalently attached onto lysine residues of protein targets, as a single moiety but also as polyubiquitin chains. Although much of our understanding of the ubiquitin system relates to ubiquitin chains assembled through one linkage only (i.e. homotypic chains), more complex signals have now been identified. Amongst these, mixed and branched ubiquitin chains have been detected in cells where they regulate key cellular processes such as the cell cycle and NF-κB Signaling. Determining the biochemical properties and specificity of deubiquitinating enzymes has been instrumental in deciphering the ubiquitin code. Through structure-function studies, we previously established that the OTU deubiquitinase TRABID preferentially cleaves K29 and K33-linked di-ubiquitin. We have now identified an E3 ubiquitin ligase as a TRABID substrate and our data also show that TRABID regulates the stability of this E3. To further explore the function and specificity of this DUB-E3 pair, we determined the biochemical activity of the E3 ligase using in vitro autoubiquitination assays, Ubiquitin Chain Restriction Analysis (UBICREST) and Ubiquitin-AQUA proteomics. This revealed that this E3 ligase preferentially assembles branched ubiquitin chains. I will also discuss new and unpublished data on the cellular function(s) of this E3 ubiquitin ligase as well as the potential roles for these novel and complex ubiquitin signals.