Updated publication reference for PubMed record(s): 30429547. Protein misfolding is linked to a wide variety of human disease. Protective cellular protein quality control (PQC) mechanisms evolved to selectively recognize misfolded proteins and limit their toxic effects. Using yeast as a model system, we previously discovered that the misfolded protein VHL interacts with various PQC machines on its way to being cleared by the ubiquitin-proteasome system. However, the clearance of nuclear and cytoplasmic VHL has difference PQC requirements. In this study, we performed SILAC-based AP-MS of nuclear (NLS) versus cytoplasmic (NES) VHL to identify, in an unbiased manner, the similarities and differences between nuclear and cytoplasmic PQC. We found that 4 molecular chaperones of the Hsp70 family, and multiple subunits of the proteasome, were significantly enriched with both nuclear and cytoplasmic VHL. By contrast, the chaperone Hsp90 and Sis1 were only associated with cytoplasmic VHL, whereas 6 of the 8 TRiC/chaperonin subunits were specifically enriched with nuclear VHL. Our study highlights unexpected differences between nuclear and cytoplasmic PQC, with important implications for our understanding of a wide range of protein misfolding diseases.