The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein-Protein Interactions (PPIs).

Proteins function through coordinated interactions and dynamic post-translational modifications (PTMs) that regulate cellular processes. This chapter provides a comprehensive overview of experimental and computational methods for detecting protein-protein interactions (PPIs) and characterizing PTMs, with emphasis on mass spectrometry-based approaches. We discuss classical techniques, including yeast two-hybrid screening, co-immunoprecipitation, and biophysical methods, alongside emerging proximity labeling and imaging strategies. The chapter examines major PTM classes-phosphorylation, ubiquitination, palmitoylation, glycosylation, methylation, acetylation, and SUMOylation-highlighting enrichment strategies, detection workflows, and biological significance. Together, these methodologies enable systems-level mapping of interactomes and post-translational regulatory networks, which are essential for understanding cellular function and disease mechanisms.