Advanced (Nano)material-Based Enrichment Strategies for Quantitative Phosphoproteomics Analysis by Mass Spectrometry

Phosphorylation is one of the most prevalent and dynamic post-translational modifications. It regulates aspects of cellular signaling, metabolism, and disease progression. Comprehensive characterization of phosphoproteins and their phosphorylation remain analytically challenging due to their low abundance, the dynamic nature of the phosphorylation, substoichiometric modification levels, and the complexity of biological matrices. However, recent advancements in enrichment strategies have substantially increased the depth and precision of phosphoproteomics analyses using mass spectrometry. Strategies such as immobilized metal ion affinity chromatography and metal oxide affinity chromatography refine the selective isolation of phosphorylated peptides from complex mixtures. Emerging materials, such as advanced metal nanoparticles, MXenes, and carbon-based nanostructures, are increasingly being used in phosphoproteomics enrichment due to their inherent features such as high surface areas, easily tunable surface chemistry, and strong structural stability, which provide enhanced enrichment efficiency and selectivity. Here, we outline strategies and innovations in phosphoprotein enrichment materials in quantitative proteomics MS platforms.