Cation adduction to oligonucleotides and nucleic acids during mass spectrometric analysis is a recurrent problem. We have found that the use of organic base solutions of high gas-phase proton affinity, as used previously in electrospray ionization mass spectrometry, can significantly reduce the cation adduction problem during matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. A comparison of the utility of adding imidazole or triethylamine as a co-matrix versus the standard addition of cation exchange resin beads was made. The co-matrices studied were found to be more effective than the cation exchange resin beads at reducing cation adducts from samples containing a high level of salt. The use of co-matrices also appears to improve the gas-phase stability of larger oligonucleotides. MALDI-time-of-flight analysis of a binary mixture of oligoribonucleotide 27-mers with a co-matrix exhibited less metastable decomposition than the same analysis using cation exchange resin beads. The use of co-matrices may be a viable strategy for the mass spectrometric characterization of larger oligonucleotides obtained from media containing a high salt content such as polymerase chain reaction products.
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Simmons et al. (1997) studied this question.