Sulfoxide-diazirine (SODA) as a cleavable photoaffinity group to enable identification of photolabeled modification sites via LC-MS3

Photoaffinity labeling is a common approach in chemical proteomics for identification of small molecule probe tar-gets. However, the modification site on the target protein remains difficult to identify, because of the probe modifica-tion and potential fragmentation during tandem mass spectrometry. We here introduce MS-cleavable photoaffinity groups for a better identification of the modification site. These are based on diazirine photoreactive groups and sul-foxide as MS-labile linker. We have applied these in photoaffinity probes based on the peptide-like aspartic protease inhibitor pepstatin A, and we demonstrate that we can identify and map binding hotspots on structural models of a target protease.