Deubiquitinating enzymes (Dubs) function to remove covalently attached ubiquitin from
proteins, thereby controlling substrate activity and/or abundance. For most Dubs,
their functions, targets, and regulation are poorly understood. To systematically
investigate Dub function, we initiated a global proteomic analysis of Dubs and their
associated protein complexes. This was accomplished through the development of a software
platform called CompPASS, which uses unbiased metrics to assign confidence measurements
to interactions from parallel nonreciprocal proteomic data sets. We identified 774
candidate interacting proteins associated with 75 Dubs. Using Gene Ontology, interactome
topology classification, subcellular localization, and functional studies, we link
Dubs to diverse processes, including protein turnover, transcription, RNA processing,
DNA damage, and endoplasmic reticulum-associated degradation. This work provides the
first glimpse into the Dub interaction landscape, places previously unstudied Dubs
within putative biological pathways, and identifies previously unknown interactions
and protein complexes involved in this increasingly important arm of the ubiquitin-proteasome
pathway.