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

Moritz Heusel, Max Frank, Mario Köhler, Sabine Amon, Fabian Frommelt, George Rosenberger, Isabell Bludau, Simran Aulakh, Monika I Linder, Yansheng Liu, Ben C Collins, Matthias Gstaiger, Ulrike Kutay, Ruedi Aebersold

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Abstract

Living systems integrate biochemical reactions that determine the functional state of each cell. Reactions are primarily mediated by proteins. In proteomic studies, these have been treated as independent entities, disregarding their higher-level organization into complexes that 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 to a 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 suggest a model of nuclear pore complex disassembly, which we validate 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.

Original languageEnglish
Pages (from-to)133-155.e6
Number of pages23
JournalCell systems
Volume10
Issue number2
DOIs
Publication statusPublished - 05 Feb 2020
Externally publishedYes

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Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.

Cite this

Heusel, M., Frank, M., Köhler, M., Amon, S., Frommelt, F., Rosenberger, G., Bludau, I., Aulakh, S., Linder, M. I., Liu, Y., Collins, B. C., Gstaiger, M., Kutay, U., & Aebersold, R. (2020). A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS. Cell systems, 10(2), 133-155.e6. https://doi.org/10.1016/j.cels.2020.01.001