A global screen for assembly state changes of the mitotic proteome by SEC-SWATH-MS

Abstract

Living systems integrate biochemical reactions that determine the functional state of each cell. Reactions are primarily mediated by proteins that have in systematic studies been treated as independent entities, disregarding their higher level organization into complexes which affects their activity and/or function and is thus of great interest for biological research. Here, we describe the implementation of an integrated technique to quantify cell state-specific changes in the physical arrangement of protein complexes, concurrently for thousands of proteins and hundreds of complexes. Applying this technique for comparison of human cells in interphase and mitosis, we provide a systematic overview of mitotic proteome reorganization. The results recall key hallmarks of mitotic complex remodeling and discover new events, such as a new model of nuclear pore complex disassembly, validated by orthogonal methods. To support the interpretation of quantitative SEC-SWATH-MS datasets, we extend the software CCprofiler and provide an interactive exploration tool, SECexplorer-cc.\n\nHighlightsO_LIQuantification of proteome assembly state changes using SEC-SWATH-MS\nC_LIO_LISystems-wide analysis of assembly state changes in the mitotic proteome\nC_LIO_LIDiscovery and validation of a novel mitotic disassembly intermediate of the nuclear pore complex\nC_LIO_LIHigher sensitivity and information content compared to thermostability-based approaches for global measurement of proteome states\nC_LIO_LISECexplorer, an online platform to browse results and investigate proteins newly implicated in cell division\nC_LI