Sulfoxide-diazirine (SODA) as a Cleavable Photoaffinity Group To Enable the Identification of Photolabeled Modification Sites via LC–MS3

Photoaffinity labeling is a common approach in chemical proteomics for the identification of small-molecule probe targets. However, the modification site on the target protein remains difficult to identify because of the probe modification 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 sulfoxide as the 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.