Determination of proteome-wide thermal stability by the recently developed thermal proteome profiling technology (TPP) can be used to identify drug targets in living cells. This is achieved by combining the cellular thermal shift assay with multiplexed quantitative mass spectrometry. We have recently further developed this technology and substantially increased the sensitivity of detection of thermal stability changes and applied it to study the eukaryotic cell cycle. We observed pervasive variation of protein thermal stability and also of solubility with most changes occurring in mitosis and G1. A number of cellular pathways and components varied in thermal stability but not in abundance, such as cell-cycle factors, polymerases, and chromatin remodelers. We could show that changes in thermal stability reflect enzyme activity, DNA binding, and complex formation in situ. A large cohort of intrinsically disordered and mitotically phosphorylated proteins was stabilized and solubilized in mitosis, suggesting a fundamental remodeling of the biophysical environment of the mitotic cell. Thus protein thermal stability provides complementary information on the state of biological systems. In our latest work we have studied the effects of adenosine triphosphate, ATP, and have revealed novel effects of this metabolite on protein thermal stability and solubility.