The thermofluor effect depends upon the partitioning of a dye between the high-dielectric environment of water and the "oily", low-dielectric environment that occurs when a protein is melted. Since integral membrane proteins are often solubilized with detergents or other hydrophobic compounds that also tend to absorb the dye, some level of experimentation may have to be done to establish whether thermofluor will work in a given system.
An efficient strategy for high throughput screening of recombinant integral membrane protein expression and stability. Fan J, et. al. Protein Expr Purif. 2011 Feb 24. PMID: 21354311