The imbalance of protein homeostasis (proteostasis) is thought to be a major driver of pathology in many neurodegenerative diseases that involve widespread protein aggregation. One hypothesis is that the aggregation-prone disease proteins redirect protein folding quality control resources away from normal housekeeping folding functions, which can lead to an accumulation of unfolded and misfolded proteins that subsequently aggregate. However, it is still unknown which proteins in the proteome are most vulnerable to aggregation under proteostasis stress. Here, we have carried out extensive proteomic studies to measure the changes of proteome solubility arising from endoplasmic reticulum (ER) stress and inhibition of key chaperone heat shock protein 90 (Hsp90). We discovered that ER stress led to aggregation of 38 proteins which were involved in ER-mediation protein quality control. By contrast, Hsp90 inhibition led to the aggregation of a distinct set of proteins, especially those predicted to reside in the nucleus. Many of these proteins have reported roles in forming liquid droplets or gels through phase separation, suggesting that Hsp90 plays a key role in regulating phase separation. An unexpected result was an increase in the solubility of subunits of mitochondrial respiratory chain complexes and the mitochondrial ribosome, which may arise from a previously undescribed role of Hsp90 in mediating the formation of these complexes.