STAR Protocols (Dec 2024)

Protocol for mapping differential protein-protein interaction networks using affinity purification-mass spectrometry

  • Prashant Kaushal,
  • Manisha R. Ummadi,
  • Gwendolyn M. Jang,
  • Yennifer Delgado,
  • Sara K. Makanani,
  • Kareem Alba,
  • Declan M. Winters,
  • Sophie F. Blanc,
  • Jiewei Xu,
  • Benjamin Polacco,
  • Yuan Zhou,
  • Erica Stevenson,
  • Manon Eckhardt,
  • Lorena Zuliani-Alvarez,
  • Robyn Kaake,
  • Danielle L. Swaney,
  • Nevan J. Krogan,
  • Mehdi Bouhaddou

Journal volume & issue
Vol. 5, no. 4
p. 103286

Abstract

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Summary: Proteins congregate into complexes to perform diverse cellular functions. Protein complexes are remodeled by protein-coding mutations or cellular signaling changes, driving phenotypic outcomes in health and disease. We present an affinity purification-mass spectrometry (AP-MS) proteomics protocol to express affinity-tagged “bait” proteins in mammalian cells, identify and quantify purified protein interactors, and visualize differential protein-protein interaction networks between pairwise conditions. Our protocol possesses general applicability to various cell types and biological areas.For complete details on the use and execution of this protocol, please refer to Bouhaddou et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

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