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

Heusel, Moritz LU ; Frank, Max ; Köhler, Mario ; Amon, Sabine ; Frommelt, Fabian ; Rosenberger, George ; Bludau, Isabell ; Aulakh, Simran ; Linder, Monika I. and Liu, Yansheng , et al. (2020) In Cell systems 10(2). p.6-155
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... (More)

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.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
cell cycle, monitoring state of proteome organization, protein complexes, size exclusion chromatography, SWATH-MS
in
Cell systems
volume
10
issue
2
pages
6 - 155
publisher
Cell Press
external identifiers
  • pmid:32027860
  • scopus:85079593296
ISSN
2405-4712
DOI
10.1016/j.cels.2020.01.001
language
English
LU publication?
yes
id
7b65f413-be1c-45e0-8e40-36e3c9356e58
date added to LUP
2020-03-04 09:01:54
date last changed
2020-09-23 08:07:13
@article{7b65f413-be1c-45e0-8e40-36e3c9356e58,
  abstract     = {<p>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.</p>},
  author       = {Heusel, Moritz and Frank, Max and Köhler, Mario and Amon, Sabine and Frommelt, Fabian and Rosenberger, George and Bludau, Isabell and Aulakh, Simran and Linder, Monika I. and Liu, Yansheng and Collins, Ben C. and Gstaiger, Matthias and Kutay, Ulrike and Aebersold, Ruedi},
  issn         = {2405-4712},
  language     = {eng},
  number       = {2},
  pages        = {6--155},
  publisher    = {Cell Press},
  series       = {Cell systems},
  title        = {A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS},
  url          = {http://dx.doi.org/10.1016/j.cels.2020.01.001},
  doi          = {10.1016/j.cels.2020.01.001},
  volume       = {10},
  year         = {2020},
}