The fast atom bombardment (FAB)mass spectra of a series of dinucleotide analogs, compounds 1–8 with alkaline earth metal chlorides (CaCl2, MgCl2, SrCl2 and BaCl2) were studied in a thioglycerol matrix. The positive-ion FAB mass spectra of 1–8 with CaCl2 gave [M+Ca-H]+, [M+CaCl]+ and [M+Ca2Cl-2H]+ ions. The formulae of [M+Ca-H]+ and [M+Ca2Cl-2H]+ ions from 2 were confirmed with high-resolution measurements. Compounds 1–8 with alkaline earth metal ions also give metal chelated dimerized species [2M+Ca3Cl-4H]+, [2M+Ca2-3H]+ and [2M+Ca-H]+], a process which is independent of the size of the polyether chain. The negative-ion FAB spectra also produce bimetallic ions with all substrates studied. Experiments with D2O addition using CaCl2 with compounds 2 and 6 suggested the elimination of acidic protons (amide and/or amine) in the formation of [M+MetxCly-nH] ions in either positive or negative modes. The site of the metal chelation was the same in both positive-and negative-ion mass spectra. The collision-activated dissociation data suggest the covalent bonding of the metal to the nitrogen base and coordination with the polyether chain.