Enabling Computational Proteomics by Public and Local Data Management Systems

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.

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Analyzing trapped protein complexes by Virotrap and SFINX

Titeca

Quickelberghe

Samyn

et al. 2017

Nat Protoc

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Enabling Computational Proteomics by Public and Local Data Management Systems

Cited by 1 publication

References 61 publications

Analyzing trapped protein complexes by Virotrap and SFINX

Analyzing trapped protein complexes by Virotrap and SFINX

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