Chemical cross-linking and high resolution mass spectrometry (MS) have been integrated successfully to capture protein interactions and provide low resolution structural data for proteins that are refractive to analyses by NMR or crystallography. Despite the versatility of these combined techniques, the array of products that is generated from the cross-linking and proteolytic digestion of proteins is immense and generally requires the use of labeling strategies and/or data base search algorithms to distinguish actual cross-linked peptides from the many side products of cross-linking. Most strategies reported to date have focused on the analysis of small cross-linked protein complexes (< 60 kDa), because the number of potential forms of covalently modified peptides increases dramatically with the number of peptides generated from the digestion of such complexes. We report herein the development of a user-friendly search engine, CrossSearch, that provides the foundation for an overarching strategy to detect cross-linked peptides from the digests of large (= 170 kDa) cross-linked proteins, i.e. conjugates. Our strategy combines the use of low excess of cross-linker, data-base searching, and Fourier transform ion cyclotron resonance MS to experimentally minimize and theoretically cull the side products of cross-linking. Using this strategy, the ({alpha,beta,gamma,delta})₄ phosphorylase kinase model complex was cross-linked to form with high specificity a 170 kDa {beta,gamma} conjugate, in which we identified residues involved in the intra-molecular cross-linking of the 125 kDa subunit between its regulatory N-terminus and its C-terminus. This finding provides an explanation for previously published homo-dimeric two-hybrid interactions of the subunit and suggests a dynamic structural role for the regulatory N-terminus of that subunit. The results offer proof of concept for the CrossSearch strategy for analyzing conjugates and are the first to reveal a tertiary structural element of either homologous or regulatory subunit of phosphorylase kinase.