Interrogating the architecture of protein assemblies and protein interaction networks by cross-linking mass spectrometry

Proteins are involved in almost all processes of the living cell. They are organized through extensive networks of interaction, by tightly bound macromolecular assemblies or more transiently via signaling nodes. Therefore, revealing the architecture of protein complexes and protein interaction networks is crucial to understand their function. Towards this aim, cross-linking mass spectrometry (XL-MS), which allows the elucidation of structures and interactions of proteins at low-resolution, has emerged as a valuable technology. Especially in recent years, the substantial development of cross-linking approaches and MS-based technologies, has led to noteworthy advances in the analysis of purified/in vitro reconstituted very large (megaDa) protein assemblies and various endogenous protein complexes in cells. Here we review the advances of XL-MS technologies and highlight some of the most recent studies. They clearly indicate that current XL-MS methodologies are ideally positioned to bridge the gap between proteomic-based interactome studies and high-resolution structural biology-based technologies.