Dissect Protein Interactions Using Mass Spectrometry

Protein–protein interactions (PPIs) orchestrate the intricate and complex cellular activities of fundamental biological processes such as cellular communication, energy metabolism, and signal pathway modulation. Understanding the dynamic interplay between proteins is pivotal for unraveling the complexities of biological systems and identifying druggable targets. Mass spectrometry (MS) has emerged as a powerful tool in deciphering PPI networks, offering high sensitivity, resolution, and efficiency for the identification and quantification of thousands of proteins. In recent years, emerging MS-based proteomics techniques and methods have provided novel perspectives in unbiasedly mapping PPIs system-wide from various biological samples. Here, we review the basic mechanisms, strongpoints, limitations, and applications in profiling PPIs of these MS approaches, including affinity purification coupled to mass spectrometry (AP-MS), proximity labeling, cross-linking mass spectrometry (XL-MS), co-fractionation coupled with mass spectrometry (CF-MS), thermal proximity co-aggregation (TPCA), and limited proteolysis–mass spectrometry (LiP–MS).