Systems vaccinology and big data in the vaccine development chain

Raeven, René H. M.; van Riet, Elly; Meiring, Hugo D.; Metz, Bernard; Kersten, Gideon F. A.

A new class of MS-cleavable cross-linking reagents has a great potential in interactomics. [34] [35] [36] Like all other cross-linking reagents, these compounds stabilize transient protein-protein interactions by the formation of covalent bonds under physiological conditions. But they also allow for the unambiguous identification of the spatially distributed peptides of the interacting proteins, based on the presence of characteristic reporter ions in the mass spectra that are representative for intramolecular or intermolecular cross-links. Liu et al. showed a good correlation between protein three-dimensional-structure data obtained from chemical cross-linking MS (XL-MS) using MS-cleavable reagents and data from cryo-electron microscopy (cryo-EM) on purified protein assemblies. In addition, they also identified in HeLa cell lysates crosslinks from protein domains lacking X-ray or cryo-EM three-dimensional-structure data, 37 illustrating the great potential of this strategy in identifying protein-protein interactions. To detect protein-protein interactions by XL-MS, it is mandatory that the amino acids in the interaction area are reactive with the cross-linker.