A correlation is found between the fragment ion yield and the degree of branching for oligosaccharides analyzed by matrix assisted laser desorption ionization/Fourier transform mass spectrometry (MALDI/FTMS). The most branched oligosaccharides produced the least amount of fragment ion. Another relationship is found between the size of the alkali metal ion and the yields of fragment ions. The smallest alkali metal ion produced the greatest amount of fragment ions. The presence of the quasimolecular ion is dependent on both the size of the metal ion and the size of the sugar. A minimum number of saccharide residues are necessary to stabilize the complex and produce a quasimolecular ion. Molecular mechanics calculations were performed and structures obtained consistent with the observed experimental behavior. The site of coordination plays a dominant role in the yield and types of fragment ions observed.