Provided herein is synthesis of a novel acidic acid residue targeting sulfoxide-containing MS-cleavable homobifunctional cross-linker. The novel mass spectrometry-cleavable cross-linking agents can be used in mass spectrometry to facilitate structural analysis of intra-protein interactions in proteins and inter-protein interactions in protein complexes. Also disclosed herein are data based on the novel MS-cleavable homobifunctional cross-linker that are complimentary to amine-reactive sulfoxide-containing MS-cleavable reagents.