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Protein post-translational modifications (PTMs) play a critical role in modulating cellular functions. PTMs also vary in response to different stimuli thereby tuning cellular mechanisms. Assessment of PTMs on a proteomic scale is a challenging task since they are sub-stoichiometric, transient and reversible. However, accurate qualitative and quantitative mapping of modification sites on proteins is of immense value because it may provide specific biomarkers and protein targets for various biological and physiological conditions. In recent years, a wide variety of proteomic approaches using gel electrophoresis, liquid chromatography and mass spectrometry has been developed to detect PTMs, and many exciting results produced by using sophisticated procedures integrating innovative separation and enrichment methods along with advanced mass spectrometric analyses have been published. This special issue aims to summarize recent progresses in PTM proteomics and posts further directions for the biomarker and target identification by proteomics.