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

Fossati, Andrea; Li, Chen; Uliana, Federico; Wendt, Fabian; Frommelt, Fabian; Sykacek, Peter; Heusel, Moritz; Hallal, Mahmoud; Bludau, Isabell; Capraz, Tümay; Xue, Peng; Song, Jiangning; Wollscheid, Bernd; Purcell, Anthony W; Gstaiger, Matthias; Aebersold, Ruedi (2021). PCprophet: a framework for protein complex prediction and differential analysis using proteomic data. Nature methods, 18(5), pp. 520-527. Nature Publishing Group 10.1038/s41592-021-01107-5

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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.

Item Type:

Journal Article (Original Article)


04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR) > Unit Childrens Hospital > Forschungsgruppe Hämatologie (Erwachsene)
04 Faculty of Medicine > Department of Haematology, Oncology, Infectious Diseases, Laboratory Medicine and Hospital Pharmacy (DOLS) > Clinic of Haematology and Central Haematological Laboratory

UniBE Contributor:

Hallal, Mahmoud Malek


600 Technology > 610 Medicine & health




Nature Publishing Group




Pierrette Durand Lüthi

Date Deposited:

27 Apr 2021 15:24

Last Modified:

10 May 2021 01:34

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