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Nucleic Acids Research, 1994, Vol. 22, No. 13 2460-2465
© 1994

MOLECULAR BIOLOGY

Comparison of IR- and UV-matrix-assisted laser desorption/ionization mass spectrometry of oligodeoxynucleotides

E. Nordhoff*, F. Kirpekar2, M. Karas, R. Cramer, S. Hahner, F. Hillenkamp, K. Kristiansen2, P. Roepstorff2 and A. Lezius1

Institute for Medical Physics and Biophysics, University of Münster Robert-Koch-Str. 31, 48149 Münster, Germany 1Institute for Biochemistry, University of Münster Wilhelm-Klemm-Str. 2, 48149 Münster, Germany 2Department of Molecular Biology, University of Odense Campusvej 55, 5230 Odense M., Denmark

* To whom correspondence should be addressed

Received May 6, 1994. Revised June 1, 1994. Accepted June 1, 1994.

UV-matrix assisted laser desorption/ionization mass spectrometry (UV-MALDI-MS) with 3-hydroxypicolinic acid as matrix and IR-MALDI-MS with succinic acid as matrix have proved their feasibility for highly accurate and sensitive mass determination of nucleic acids (DNA and RNA). In this work, a detailed comparison of these two MALDI-methods and between positive- and negative ion mass spectra for the analysis of oligodeoxynucleotides is undertaken. Mass spectra of DNA sequences with up to 40 nucleotides are shown. Both linear and reflectron time-of-flight mass analyzers were used within this study and are compared for their potential in the MALDI analysis of oligodeoxynucleotides. The role of molecule-ion fragmentation is also discussed.


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