Use of ammonium halides as co-matrices for matrix-assisted laser desorption/ionization studies of oligonucleotides

Four ammonium salts, NH4F, NH4Cl, NH4Br and NH4I were tested as co-matrices for the matrix-assisted laser desorption/ionization (MALDI) analysis of a number of DNA homopolymers, including phosphorylated d(T)8, d(A)4, d(C)4 and non-phosphorylated d(G)4, using 2-amino-5-nitropyridine (ANP) matrix. In the present study, all the ammonium halides displayed significant enhancement effects on the signal intensities of the intact molecular ions of the DNA homopolymers. Among the halides used, NH4F was found to exhibit the greatest enhancement effects. By comparison with results obtained using the corresponding isomorphous potassium halides as co-matrices, it is postulated that both the cationic and anionic portions of the co-matrix molecule play important roles in the desorption/ionization of the oligonucleotides under typical MALDI conditions. It was also demonstrated that the ANP matrix exhibits a strong inhibitory effect on the formation of alkali-metal adducts in oligonucleotide analysis.