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Rapid Profiling of ...
Rapid Profiling of Protein Complex Reorganization in Perturbed Systems
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- Bludau, Isabell (author)
- ETH Zürich,Max Planck Institute of Biochemistry
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- Nicod, Charlotte (author)
- ETH Zürich
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- Martelli, Claudia (author)
- ETH Zürich
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- Xue, Peng (author)
- ETH Zürich
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- Heusel, Moritz (author)
- Lund University,Lunds universitet,Infektionsmedicin,Sektion III,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,Infection Medicine Proteomics,Forskargrupper vid Lunds universitet,epIgG,Infection Medicine (BMC),Section III,Department of Clinical Sciences, Lund,Faculty of Medicine,Lund University Research Groups,ETH Zürich
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- Fossati, Andrea (author)
- The J. David Gladstone Institutes,ETH Zürich,University of California, San Francisco
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- Uliana, Federico (author)
- ETH Zürich
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- Frommelt, Fabian (author)
- ETH Zürich
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- Aebersold, Ruedi (author)
- ETH Zürich
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- Collins, Ben C. (author)
- Queen's University Belfast
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(creator_code:org_t)
- 2023
- 2023
- English 17 s.
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In: Journal of Proteome Research. - 1535-3893. ; 22:5, s. 1520-1536
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http://dx.doi.org/10... (free)
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Abstract
Subject headings
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- Protein complexes constitute the primary functional modules of cellular activity. To respond to perturbations, complexes undergo changes in their abundance, subunit composition, or state of modification. Understanding the function of biological systems requires global strategies to capture this contextual state information. Methods based on cofractionation paired with mass spectrometry have demonstrated the capability for deep biological insight, but the scope of studies using this approach has been limited by the large measurement time per biological sample and challenges with data analysis. There has been little uptake of this strategy into the broader life science community despite its rich biological information content. We present a rapid integrated experimental and computational workflow to assess the reorganization of protein complexes across multiple cellular states. The workflow combines short gradient chromatography and DIA/SWATH mass spectrometry with a data analysis toolset to quantify changes in a complex organization. We applied the workflow to study the global protein complex rearrangements of THP-1 cells undergoing monocyte to macrophage differentiation and subsequent stimulation of macrophage cells with lipopolysaccharide. We observed substantial proteome reorganization on differentiation and less pronounced changes in macrophage stimulation. We establish our integrated differential pipeline for rapid and state-specific profiling of protein complex organization.
Subject headings
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
Keyword
- DIA/SWATH
- protein complex
- protein−protein interactions
- quantitative interaction proteomics
Publication and Content Type
- art (subject category)
- ref (subject category)
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- By the author/editor
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Bludau, Isabell
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Nicod, Charlotte
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Martelli, Claudi ...
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Xue, Peng
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Heusel, Moritz
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Fossati, Andrea
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show more...
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Uliana, Federico
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Frommelt, Fabian
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Aebersold, Ruedi
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Collins, Ben C.
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show less...
- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Bioinformatics a ...
- Articles in the publication
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Journal of Prote ...
- By the university
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Lund University