Cells have extensive quality control machinery, known as the proteostasis network, which is responsible for regulating protein synthesis, folding and transport. This machinery is often severely imbalanced in neurodegenerative diseases, such as Alzheimer’s and Motor Neuron disease. The defining characteristic of these diseases is the widespread aggregation and deposition of vulnerable unfolded proteins. After decades of dedicated examination, the folding and stability characteristics of many individual proteins are well understood in vitro. However, understanding the process of protein folding and unfolding in the complex cellular milieu remains a grand challenge. A key limitation has been our capacity to quantitatively assess the folding status of individual proteins at the proteome-wide scale in a biological context. To overcome this challenge, we developed a fluorogenic thiol-binding dye (TPE-MI) that can capture a snapshot of the balance of unfolded protein relative to folded states [1]. This approach has been proven to offer single-protein folding information for endogenous proteins at a proteome-wide scale. Here, we demonstrate the use of this probe to investigate the cellular response to pharmacological proteostasis challenge. We found no en masse unfolding of the proteome, but rather evidence of large-scale proteome remodelling. Moreover, changes in individual proteins were often not conserved in response to different proteostasis modifiers. However, these proteins mapped onto a common set of proteostasis hubs reflecting the cell’s exquisite ability to fine-tune the stress response. This probe represents an invaluable tool empowering researchers to quantitatively probe proteome conformation across diverse disease states in a variety of model organisms.