Post-translational modifications controlling a large number of biological functions are key aspects of protein diversity. They have an important role controlling cellular processes and may be advantageously utilized. Qualitative and quantitative analyses of post-translational modifications are useful for biomarker research and an integral part of the characterization of protein biopharmaceuticals. Due to its sensitivity and widespread applicability, mass spectrometry has become the core technology of the analysis especially when combined with chromatographic and other separation techniques. The aim of this article is to present a general overview of mass spectrometry applications in the field of PTM mapping. We also present the analytical challenges of particular PTMs, primarily focusing on the most frequent modifications.