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

STAR Protoc

Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA. Electronic address:

Published: December 2024

* The text describes a specific proteomics method called affinity purification-mass spectrometry (AP-MS) to study protein interactions by tagging "bait" proteins in mammalian cells.
* This protocol allows researchers to identify, quantify, and visualize changes in protein-protein interaction networks under different conditions and is adaptable across various cell types and biological studies.

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..

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11567037	PMC
http://dx.doi.org/10.1016/j.xpro.2024.103286	DOI Listing

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