Protein-protein interactions (PPIs) play a key role in defining protein functions in biological systems. Perturbations of native PPIs can cause deleterious effects on cellular activities and lead to various human diseases. As PPI interfaces have become an attractive drug target, their detailed characterization is not only critical to unraveling molecular details underlying human pathologies, but also important for identifying potential targets for better therapeutics. In recent years, cross-linking mass spectrometry (XL-MS) have become a powerful structural tool for mapping PPIs and elucidating architectures of large protein complexes. In comparison to standard structural methods, XL-MS offers distinct advantages due to speed, accuracy, sensitivity and versatility, especially for the study of heterogeneous and dynamic protein complexes. Despite its great potential, XL-MS analysis remains challenging due to the difficulty in unambiguous identification of cross-linked peptides. To advance XL-MS studies, we have developed a series of sulfoxide-containing MS-cleavable cross-linkers to enable simplified and accurate identification of cross-linked peptides1,2. In addition, we have developed new sample preparation strategies to facilitate XL-MS analysis of protein complexes. Moreover, quantitative XL-MS methods have been established to define conformational changes. Here, we will present new developments in sulfoxide-containing MS-cleavable reagents based XL-MS approaches and their integration with structural modeling to uncover protein structural dynamics that is inaccessible to other structural tools. The analytical platform described here can be adopted to study other protein complexes. Ref 1. Kao, A. et, al. MCP, 2011; 2. Yu, C. et al, Anal. Chem. 2018.