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Related Experiment Videos

Analyzing trapped protein complexes by Virotrap and SFINX.

Kevin Titeca1,2, Emmy Van Quickelberghe1,2, Noortje Samyn1,2

  • 1VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.

Nature Protocols
|March 31, 2017
PubMed
Summary

This study introduces Virotrap, a novel method for analyzing protein complexes without cell lysis. It utilizes virus-like particles and the SFINX tool for efficient contaminant removal in mass spectrometry analysis.

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Area of Science:

  • Molecular Biology
  • Proteomics
  • Systems Biology

Background:

  • Protein interaction network analysis is crucial for understanding genotype-phenotype connections and disease mechanisms.
  • Conventional methods for studying protein complexes involve cell lysis, which disrupts native interactions.
  • A need exists for protocols that preserve protein complex integrity during analysis.

Purpose of the Study:

  • To present a novel protocol for analyzing mammalian protein complexes.
  • To overcome the limitations of cell lysis in protein interaction studies.
  • To provide a complete workflow for researchers using mass spectrometry.

Main Methods:

  • Utilizing Virotrap, a method fusing proteins of interest to HIV-1 Gag to trap complexes in virus-like particles, avoiding cell homogenization.

Related Experiment Videos

  • Employing the Straightforward Filtering Index (SFINX) online tool for contaminant removal from mass spectrometry data.
  • Implementing a workflow compatible with direct access to mass spectrometers for high-throughput sample processing.

    • Main Results:

    • The Virotrap approach successfully traps protein complexes within virus-like particles, preserving their native state.
    • SFINX effectively removes contaminants from mass spectrometry-derived candidate lists.
    • The complete workflow enables the analysis of up to 24 mammalian protein complex samples within 7 days.

    Conclusions:

    • Virotrap offers a non-disruptive alternative for studying protein complexes.
    • The integrated workflow, including SFINX, streamlines proteomic analysis of protein complexes.
    • This method facilitates a deeper understanding of protein interactions in mammalian systems.