Matrix-assisted laser desorption ionization (MALDI) mass spectrometry relies on the formation of intact molecular ions in order to achieve a high-accuracy molecular weight determination. Problems arising from metastable fragmentation strongly affect MALDI results in reflectron instruments due to the mass separation of the fragment ions with the reflectron. In this paper, it is shown that the extent of metastable fragmentation for proteins is strongly related to the matrix compound used. Among the matrix compounds tested, 3-hydroxypicolinic acid proved to be a highly superior matrix for MALDI analysis of proteins and it even allowed for desorption of intact glycoproteins containing labile functional groups, e.g., sialic acids, in a reflectron analyzer, whereas 4-hydroxy-α-cyanocinnamic acid induced strong metastable fragmentation even for standard proteins such as apomyoglobin