Evaluation of Common Posttranslational Modification Enrichment Strategies for Proteomics Analysis

Posttranslational modifications (PTMs) play critical regulatory roles in cellular processes, and their dysregulation is implicated in numerous diseases and pathological conditions. Their importance to biological functions has spawned many efforts to accurately identify and quantify protein modifications using high-throughput methods, especially liquid chromatography tandem-mass spectrometry (LC-MS/MS). The typically low stoichiometry of PTMs in biological samples often necessitates enrichment strategies to achieve sufficient analytical sensitivity. However, the growing number and diversity of published enrichment methods have made it challenging to evaluate key methodological differences and their respective advantages. This review examines enrichment strategies for the major PTM classes: phosphorylation, acetylation, ubiquitination, SUMOylation, methylation, glycosylation, and ADP-ribosylation. Immunoaffinity-based, chromatographic, and chemical derivatization approaches are compared for each class in terms of their underlying principles and practical trade-offs. Based on published methods, the review considers enrichment specificity, coverage depth, sample input requirements, and workflow compatibility, with the aim of providing a consolidated reference to guide method selection and optimization for single- and multi-PTM profiling.