Post-translational modification (PTM) refers to the chemical modification of proteins following translation, which can regulate protein activity, localization, folding, and interactions with other biomacromolecules (including proteins, nucleic acids, and lipids). Increasing evidence suggests that many critical biological processes and disease pathogenesis are not only associated with protein abundance but are more importantly regulated by various post-translational modifications. Consequently, protein modification omics—by enabling in-depth analysis of changes in PTM levels—plays a significant role in elucidating the mechanisms underlying life activities, identifying clinical disease markers, and discovering drug targets.