A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS

Living systems integrate biochemical reactions that determine the functional state ofeach cell. Reactions are primarily mediated by proteins that have in systematic studiesbeen treated as independent entities, disregarding their higher level organization intocomplexes which affects their activity and/or function and is thus of great interest forbiological research. Here, we describe the implementation of an integrated techniqueto quantify cell state-specific changes in the physical arrangement of proteincomplexes, concurrently for thousands of proteins and hundreds of complexes.Applying this technique for comparison of human cells in interphase and mitosis, weprovide a systematic overview of mitotic proteome reorganization. The results recallkey hallmarks of mitotic complex remodeling and discover new events, such as a newmodel of nuclear pore complex disassembly, validated by orthogonal methods. Tosupport the interpretation of quantitative SEC-SWATH-MS datasets, we extend thesoftware CCprofiler and provide an interactive exploration tool, SECexplorer-cc.