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Mass spectrometry (MS) is becoming increasingly popular in the field of structural biology, with great implications for solving important biological questions. Two central techniques in structural MS are chemical cross-linking and covalent labeling. During the last 15 years, chemical cross-linking combined with MS and computational modeling has advanced from investigating three-dimensional structures of isolated proteins to deciphering protein interaction networks. As the chemical cross-linking/MS approach allows the capture of transient and weak interactions, it has the potential to become a routine technique for unraveling protein interaction networks in their natural cellular environment. More recently, covalent labeling with MS has begun to emerge as a reliable and complementary structural tool. The next frontier in this area of research is to develop new technologies enabling full characterization of dynamic biological assemblies under various physiological conditions. The knowledge obtained will significantly advance our understanding of cellular networks and molecular details underlying human pathologies. The 2019 Sanibel Conference will highlight both the latest technology development and emerging applications in structural MS using chemical cross-linking and covalent labeling technologies. In addition, bioinformatics tools for data analysis and structural modeling will be presented. The aim is to share ideas, harmonize protocols and software tools, and to facilitate interactions among different areas of work.