PCprophet : a framework for protein complex prediction and differential analysis using proteomic data

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.

Li, ChenETH Zürich,Monash University (författare)
Uliana, FedericoETH Zürich (författare)
Wendt, FabianETH Zürich (författare)
Frommelt, FabianETH Zürich (författare)
Sykacek, PeterUniversity of Natural Resources and Life Sciences, Vienna (författare)
Heusel, MoritzLund 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(Swepub:lu)mo3350he (författare)
Hallal, MahmoudUniversity of Bern (författare)
Bludau, IsabellETH Zürich,Max Planck Institute of Biochemistry (författare)
Capraz, TümayEuropean Molecular Biology Laboratory Heidelberg (författare)
Xue, PengETH Zürich (författare)
Song, JiangningMonash University (författare)
Wollscheid, BerndSwiss Institute for Bioinformatics (SIB),ETH Zürich (författare)
Purcell, Anthony W.Monash University (författare)
Gstaiger, MatthiasETH Zürich (författare)
Aebersold, RuediUniversity of Zurich,ETH Zürich (författare)
The J. David Gladstone InstitutesETH Zürich (creator_code:org_t)

Ingår i:Nature Methods: Springer Science and Business Media LLC18:5, s. 520-5271548-70911548-7105

Av författaren/redakt...: Fossati, Andrea; Li, Chen; Uliana, Federico; Wendt, Fabian; Frommelt, Fabian; Sykacek, Peter; visa fler...; Heusel, Moritz; Hallal, Mahmoud; Bludau, Isabell; Capraz, Tümay; Xue, Peng; Song, Jiangning; Wollscheid, Bern ...; Purcell, Anthony ...; Gstaiger, Matthi ...; Aebersold, Ruedi; visa färre...

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