phosphopeptides

Phosphopeptides are peptides that contain a phosphorylated amino acid. The most common residues in eukaryotes are serine, threonine, and tyrosine, yielding phosphoserine, phosphothreonine, and phosphotyrosine. Phosphorylation is a reversible post-translational modification that modulates protein activity, interactions, and localization. Kinases add phosphate groups; phosphatases remove them, enabling rapid regulation of cellular signaling.

Phosphorylation occurs in many contexts, notably signaling pathways such as receptor tyrosine kinases, MAPK cascades, and PI3K/Akt. It can activate or inhibit enzymes, create docking sites for interaction domains, influence complex assembly, or direct subcellular targeting. In some organisms, other phosphorylated residues (e.g., histidine and aspartate) participate in signaling, but these are less common in eukaryotic proteomics due to their lability.

Detection and analysis rely on phosphoproteomics. Because phosphorylation is often substoichiometric, enrichment before mass spectrometry is standard. Techniques include MOAC and IMAC enrichment, followed by LC-MS/MS to identify phosphopeptides and localize sites. Data analysis uses specialized search algorithms and scoring; quantitative approaches include label-free methods and targeted workflows such as SRM or PRM.

Applications include mapping signaling networks, biomarker discovery, and monitoring drug responses. Synthetic phosphopeptides serve as standards for method validation. Challenges include low abundance, dynamic regulation, neutral loss during fragmentation, and confident site localization. Advances in instrumentation, enrichment chemistries, and bioinformatics continue to improve detection and interpretation of phosphopeptides.