Abstract

teractions is essential for understanding biological pro-cesses. Chemical cross-linking combined with mass spectrometry is an attractive approach for studying pro-tein-protein interactions and protein structure, but to date its use has been limited largely by low yields of informative cross-links (because of inefficient cross-linking reactions) and by the difficulty of confidently identifying the sequences of cross-linked peptide pairs from their fragmentation spectra. Here we present an approach based on a new MS labile cross-linking rea-gent, BDRG (biotin-aspartate-Rink-glycine), which ad-dresses these issues. BDRG incorporates a biotin han-dle (for enrichment of cross-linked peptides prior to MS analysis), two pentafluorophenyl ester groups that react with peptide amines, and a labile Rink-based bond be-