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Updated: Jun 8, 2025

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling
Published on: April 1, 2017
Protocol for mapping differential protein-protein interaction networks using affinity purification-mass spectrometry
Prashant Kaushal1, Manisha R Ummadi2, Gwendolyn M Jang2
1Department 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.
Abstract:
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.
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