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Analyzing trapped protein complexes by Virotrap and SFINX

Kevin Titeca (UGent) , Emmy Van Quickelberghe (UGent) , Noortje Samyn (UGent) , Delphine De Sutter (UGent) , Annick Verhee (UGent) , Kris Gevaert (UGent) , Jan Tavernier (UGent) and Sven Eyckerman (UGent)
(2017) NATURE PROTOCOLS. 12(5). p.881-898
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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.
Keywords
MASS-SPECTROMETRY DATA, AFFINITY PURIFICATION, INTERACTION NETWORKS, BIOTIN LIGASE, CELLS, PROTEOMICS, PARTICLES, GAG, MS, MECHANISMS

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Chicago
Titeca, Kevin, Emmy Van Quickelberghe, Noortje Samyn, Delphine De Sutter, Annick Verhee, Kris Gevaert, Jan Tavernier, and Sven Eyckerman. 2017. “Analyzing Trapped Protein Complexes by Virotrap and SFINX.” Nature Protocols 12 (5): 881–898.
APA
Titeca, Kevin, Van Quickelberghe, E., Samyn, N., De Sutter, D., Verhee, A., Gevaert, K., Tavernier, J., et al. (2017). Analyzing trapped protein complexes by Virotrap and SFINX. NATURE PROTOCOLS, 12(5), 881–898.
Vancouver
1.
Titeca K, Van Quickelberghe E, Samyn N, De Sutter D, Verhee A, Gevaert K, et al. Analyzing trapped protein complexes by Virotrap and SFINX. NATURE PROTOCOLS. 2017;12(5):881–98.
MLA
Titeca, Kevin, Emmy Van Quickelberghe, Noortje Samyn, et al. “Analyzing Trapped Protein Complexes by Virotrap and SFINX.” NATURE PROTOCOLS 12.5 (2017): 881–898. Print.
@article{8516588,
  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.},
  author       = {Titeca, Kevin and Van Quickelberghe, Emmy and Samyn, Noortje and De Sutter, Delphine and Verhee, Annick and Gevaert, Kris and Tavernier, Jan and Eyckerman, Sven},
  issn         = {1754-2189},
  journal      = {NATURE PROTOCOLS},
  keyword      = {MASS-SPECTROMETRY DATA,AFFINITY PURIFICATION,INTERACTION NETWORKS,BIOTIN LIGASE,CELLS,PROTEOMICS,PARTICLES,GAG,MS,MECHANISMS},
  language     = {eng},
  number       = {5},
  pages        = {881--898},
  title        = {Analyzing trapped protein complexes by Virotrap and SFINX},
  url          = {http://dx.doi.org/10.1038/nprot.2017.014},
  volume       = {12},
  year         = {2017},
}

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