MALDI-MS is of crucial importance for detection and identification of relevant molecules involved in biological pathways allowing a better understanding of physiological processes advantageously related to diagnosis strategies. However, many relevant biomarkers remain undetectable due to several parameters including low molecular weight, weak abundance, MS ionization potential or localization in a complex environment. To overcome these limitations, labeling strategies were developed to target reactive organic moieties of biomolecules of interest. More recently, activity-based probes or antibodies were implemented to match the current need for in vivo biomolecule specific labeling. Furthermore, with the development of MALDI-MS imaging, matrix-free derivatization techniques are currently in the spotlight. MALDI-MS labeling requires the development of a panel of tags designed to target different functional groups promoting signal enhancement for many biomolecules. This review recapitulates recent derivatization methods and available labeling reagents while putting into perspective the importance of MALDI-MS labels in the biochemical research context.