The concept of protein cross-linking in combination with mass spectrometry holds great promise to derive structural information on protein conformation and protein-protein interactions. We recently presented a dissociative amine-reactive cross-linker (NHS-BuUrBu-NHS) that is shown herein to be universally applicable to protein structure analysis under matrix-assisted laser desorption/ionization tandem mass spectrometric (MALDI-MS/MS) conditions, based on the examples of the peptides substance P, luteinizing hormone releasing hormone (LHRH), and the 32-kDa ligand-binding domain of peroxisome proliferator-activated receptor alpha (PPARα). The characteristic fragment ion patterns and constant neutral losses of the cross-linker greatly simplify the identification of different cross-linked species from complex mixtures and drastically reduce the potential of identifying false-positive cross-links. Therefore, this cross-linker holds an enormous potential for deriving structural information of proteins and protein complexes in a highly automated fashion. Copyright © 2010 John Wiley & Sons, Ltd.