Despite enormous instrumental mass spectrometric (MS) developments, providing sufficient advantages towards highly selective and sensitive analytical protocols, including those related to different ionization techniques, the presented paper aimed to study the ionization UV-MALDI-MS process and to describe the chemical aspects and essential role of the types of the matrixes. Organic salts appeared promising as matrixes for analysis of natural products (NPs), including the imaging techniques, versusthe co-crystals of neutral polyfunctional carboxylic acids. Seven model crystals of organic salts, and their matrix–analyte polycrystals, were comprehensively studied using the MALDI-MS and ESI-MS methods. The MS data were compared and supported by theoretical and experimental data, using quantum chemical methods, optical spectroscopy, and single crystal X-ray diffraction. The role of proton transfer (PT) effects in the desorption/ionization UV-MALDI processes was clarified.