MS-Based Proteomics Approach in Mapping Protein-Protein Interaction

Proteins are functional biomolecules whose modifications and activities reflect the state of health and well-being. However, while several proteins function independently, most proteins do not function in isolation but interact with other proteins within proximity, either transiently or stably at the molecular level to exert their functions. Understanding these proteins, their complexes, and interactions is a key factor in understanding molecular mechanisms in several disease-related pathways, in diagnoses, prognoses, and in the development of effective therapeutic targets. Post-translational modifications (PTMs) are the key regulators of protein-protein interactions, controlling the strength and specificity of interactions by modifying protein shape, net charge, and interaction motifs. Previously, several techniques have been employed in studying proteins, their PTMs, and PPI profiling, including yeast 2-hybrid, affinity purification, co-immunoprecipitation, proximity labeling, and crosslinking. While these techniques have been successful in mapping out thousands of both stable and transient PPIs, developments aimed at high-throughput mapping of PPIs with increased sensitivity and specificity, primarily with weakly transient interactions, would be crucial. In recent times, mass spectrometry (MS)-based proteomics approaches in tandem with bioinformatics, AI-based computational models, and other emerging tools have become central in the investigation of protein complexes and PPIs, enabling large-scale identification of protein patterns with increased sensitivity and specificity. With the sensitivity and robustness of MS and the automation and optimization of proteomics workflows, this development opens the door for the verification and validation of identified PPIs, and the high-throughput determination of novel PPIs and protein complex functions, thereby unraveling undiscovered pathogenic mechanisms.