| BAP1 | BRCA1-associated protein 1 |
| DUB | Deubiquitinase |
| HIF-1α | Hypoxia-inducible factor 1α |
| JAMM | JAB1/MPN/MOV34 |
| LFQ | Label-free quantification |
| MINDY | MIU-containing novel DUB |
| MJD | Machado–Josephin domain-containing proteases |
| MS | Mass spectrometry |
| NEDD8 | Neural Precursor Cell Expressed, Developmentally Down-Regulated 8 |
| OTU | Ovarian tumor proteases |
| SUMO | Small ubiquitin-like modifier |
| UCH | Ubiquitin C-terminal hydrolase |
| ULD | UCHL37-like domain |
| USP | Ubiquitin-specific proteases |
| ZUP1 | zinc finger-containing ubiquitin peptidase 1 |