Current approaches for protein biomarker discovery typically rely on quantitative mass spectrometry methods to identify proteins with altered expression levels in disease states. Described here is the use of protein folding and stability changes to characterize and diagnose disease states. Changes in protein folding and stability can result from a number of different disease-related phenomena including mutations, modifications, and altered protein-ligand binding interactions. Therefore, protein folding and stability changes have the potential to be a general probe of protein dysfunction in disease states. Presented here are the results of our studies using two different energetics-based approaches to investigate the folding and stability changes of proteins in a series of different cell culture models of breast cancer as a new strategy for biomarker discovery.