Fig 1. Structures and reaction mechanisms of the cross-linkers used in this study.

(A) Amine-reactive, isotope-labeled cross-linker BS²G-D₀/D₄. (B) MS/MS-cleavable amine-reactive urea-linker; cleavable bonds are indicated in red; the fragments created under MS/MS conditions are denoted as “Bu” and “BuUr” according to [15]. (C) Reaction mechanism of the zero-length cross-linker DMTMM, connecting carboxyl and amine groups in proteins.