title: Analyzing trapped protein complexes by Virotrap and SFINX.
abstract: The analysis of protein interaction networks is one of the key challenges in the study of biology. It connects genotypes to phenotypes, and disruption of such networks is associated with many pathologies. Virtually all the approaches to the study of protein complexes require cell lysis, a dramatic step that obliterates cellular integrity and profoundly affects protein interactions. This protocol starts with Virotrap, a novel approach that avoids the need for cell homogenization by fusing the protein of interest to the HIV-1 Gag protein, trapping protein complexes in virus-like particles. By using the straightforward filtering index (SFINX), which is a powerful and intuitive online tool (http://sfinx.ugent.be) that enables contaminant removal from candidate lists resulting from mass-spectrometry-based analysis, we provide a complete workflow for researchers interested in mammalian protein complexes. Given direct access to mass spectrometers, researchers can process up to 24 samples in 7 d.
authors.affiliation: VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.|Department of Biochemistry, Ghent University, Ghent, Belgium.
authors.forename: Kevin
authors.initials: K
authors.lastname: Titeca
authors.affiliation: VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.|Department of Biochemistry, Ghent University, Ghent, Belgium.
authors.forename: Emmy
authors.initials: E
authors.lastname: Van Quickelberghe
authors.affiliation: VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.|Department of Biochemistry, Ghent University, Ghent, Belgium.
authors.forename: Noortje
authors.initials: N
authors.lastname: Samyn
authors.affiliation: VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.|Department of Biochemistry, Ghent University, Ghent, Belgium.
authors.forename: Delphine
authors.initials: D
authors.lastname: De Sutter
authors.affiliation: VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.|Department of Biochemistry, Ghent University, Ghent, Belgium.
authors.forename: Annick
authors.initials: A
authors.lastname: Verhee
authors.affiliation: VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.|Department of Biochemistry, Ghent University, Ghent, Belgium.
authors.forename: Kris
authors.initials: K
authors.lastname: Gevaert
authors.affiliation: VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.|Department of Biochemistry, Ghent University, Ghent, Belgium.
authors.forename: Jan
authors.initials: J
authors.lastname: Tavernier
authors.affiliation: VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.|Department of Biochemistry, Ghent University, Ghent, Belgium.
authors.forename: Sven
authors.initials: S
authors.lastname: Eyckerman
mesh_terms: D000818:Animals; D006801:Humans; D008322:Mammals; D013058:Mass Spectrometry / Q000379:methods; D011485:Protein Binding; D060066:Protein Interaction Maps; D055503:Protein Multimerization; D011506:Proteins / Q000302:isolation & purification* / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*
chemical_list: D011506:Proteins