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PCprophet : a frame...
PCprophet : a framework for protein complex prediction and differential analysis using proteomic data
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- Fossati, Andrea (author)
- The J. David Gladstone Institutes,ETH Zürich
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- Li, Chen (author)
- ETH Zürich,Monash University
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- Uliana, Federico (author)
- ETH Zürich
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- Wendt, Fabian (author)
- ETH Zürich
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- Frommelt, Fabian (author)
- ETH Zürich
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- Sykacek, Peter (author)
- University of Natural Resources and Life Sciences, Vienna
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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,Infection Medicine (BMC),Section III,Department of Clinical Sciences, Lund,Faculty of Medicine,Lund University Research Groups,ETH Zürich
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- Hallal, Mahmoud (author)
- University of Bern
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- Bludau, Isabell (author)
- Max Planck Institute of Biochemistry,ETH Zürich
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- Capraz, Tümay (author)
- European Molecular Biology Laboratory Heidelberg
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- Xue, Peng (author)
- ETH Zürich
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- Song, Jiangning (author)
- Monash University
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- Wollscheid, Bernd (author)
- Swiss Institute for Bioinformatics (SIB),ETH Zürich
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- Purcell, Anthony W. (author)
- Monash University
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- Gstaiger, Matthias (author)
- ETH Zürich
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- Aebersold, Ruedi (author)
- ETH Zürich,University of Zurich
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The J David Gladstone Institutes ETH Zürich (creator_code:org_t)
- 2021-04-15
- 2021
- English 8 s.
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In: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 18:5, s. 520-527
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Abstract
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- Despite the availability of methods for analyzing protein complexes, systematic analysis of complexes under multiple conditions remains challenging. Approaches based on biochemical fractionation of intact, native complexes and correlation of protein profiles have shown promise. However, most approaches for interpreting cofractionation datasets to yield complex composition and rearrangements between samples depend considerably on protein–protein interaction inference. We introduce PCprophet, a toolkit built on size exclusion chromatography–sequential window acquisition of all theoretical mass spectrometry (SEC-SWATH-MS) data to predict protein complexes and characterize their changes across experimental conditions. We demonstrate improved performance of PCprophet over state-of-the-art approaches and introduce a Bayesian approach to analyze altered protein–protein interactions across conditions. We provide both command-line and graphical interfaces to support the application of PCprophet to any cofractionation MS dataset, independent of separation or quantitative liquid chromatography–MS workflow, for the detection and quantitative tracking of protein complexes and their physiological dynamics.
Subject headings
- NATURVETENSKAP -- Kemi -- Analytisk kemi (hsv//swe)
- NATURAL SCIENCES -- Chemical Sciences -- Analytical Chemistry (hsv//eng)
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- art (subject category)
- ref (subject category)
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- By the author/editor
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Fossati, Andrea
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Li, Chen
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Uliana, Federico
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Wendt, Fabian
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Frommelt, Fabian
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Sykacek, Peter
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show more...
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Heusel, Moritz
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Hallal, Mahmoud
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Bludau, Isabell
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Capraz, Tümay
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Xue, Peng
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Song, Jiangning
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Wollscheid, Bern ...
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Purcell, Anthony ...
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Gstaiger, Matthi ...
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Aebersold, Ruedi
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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 Chemical Science ...
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and Analytical Chemi ...
- Articles in the publication
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Nature Methods
- By the university
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Lund University