A peptide-centric local stability assay enables proteome-scale identification of the protein targets and binding regions of diverse ligands

Here, we found that ligand-induced protein local stability shifts can be sensitively detected on a proteome-wide scale by a limited proteolysis strategy using a large amount of trypsin to generate peptides directly from native proteins. This enabled the development of the “peptide-centric local stability assay” (PELSA), a modification-free approach that achieves unprecedented sensitivity in proteome-wide target identification and binding-region determination. We demonstrate the versatility of PELSA by investigating the interactions across various biological contexts.