Proteome-wide thermal stability of proteins can be measured by the recently developed thermal proteome profiling technology (TPP). Initially the technology was used to identify protein targets of small molecules in living cells. In recent years we further developed TPP, substantially increasing its sensitivity and specificity, and applied it to study the eukaryotic cell cycle. We observed pervasive variation of protein thermal stability and solubility on par, but independent of abundance variation. Many cellular pathways and components varied in thermal stability but not in abundance, such as for example cell-cycle factors, polymerases, and chromatin remodelers. The observed changes in protein thermal stability reflect enzyme activity, DNA binding, and complex assembly and disassembly in situ. Furthermore, a large cohort of intrinsically disordered and mitotically phosphorylated proteins was either stabilized or solubilized in mitosis, suggesting a fundamental remodeling of the biophysical environment of the mitotic cell. Most recently, enabled by new technological developments, we have mapped out the effects of key cellular metabolites on proteome stability and solubility revealing unexpected new functions of well-known metabolites.