Protein-protein interactions (PPIs) are essential for the assembly of protein complexes, which are the active molecular modules for controlling various biological processes to maintain cell viability and homeostasis. Detailed analysis of PPIs at the systems-level will not only advance our understanding of cellular structures and functions as well as their associations with human pathologies, but also facilitate the exploration of novel interactionbased therapeutics. However, obtaining an

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... ic portrait of endogenous PPI networks has been a challenging task. In recent years, cross-linking mass spectrometry (XL-MS) has proven effective in global profiling of protein interaction networks. In comparison to other PPI methods, XL-MS is unique due to its capability of capturing native PPIs from cellular environments, and uncovering their identities and connectivity simultaneously without cell engineering. Despite its great potential, XL-MS analysis remains difficult in effective detection and identification of cross-linked peptides from complex samples. 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 peptides. Our MS-cleavable reagents have been successfully applied to define global PPIs and elucidate architectures of protein complexes in vitro and in vivo. Here, we will present new developments in sulfoxide-containing MS-cleavable reagents based XL-MS approaches to further advance XL-MS studies. The analytical platform described here can be directly adopted to study PPIs in any organisms and sample origins. This work is supported by NIH grants R01GM074830 and R01GM130144 to L.H.