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. 1994 Jul 11;22(13):2460–2465. doi: 10.1093/nar/22.13.2460

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

E Nordhoff 1, F Kirpekar 1, M Karas 1, R Cramer 1, S Hahner 1, F Hillenkamp 1, K Kristiansen 1, P Roepstroff 1, A Lezius 1
PMCID: PMC308196  PMID: 8041606

Abstract

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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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Fitzgerald M. C., Parr G. R., Smith L. M. Basic matrices for the matrix-assisted laser desorption/ionization mass spectrometry of proteins and oligonucleotides. Anal Chem. 1993 Nov 15;65(22):3204–3211. doi: 10.1021/ac00070a007. [DOI] [PubMed] [Google Scholar]
  2. Grotjahn L., Frank R., Blöcker H. Ultrafast sequencing of oligodeoxyribonucleotides by FAB-mass spectrometry. Nucleic Acids Res. 1982 Aug 11;10(15):4671–4678. doi: 10.1093/nar/10.15.4671. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Huth-Fehre T., Gosine J. N., Wu K. J., Becker C. H. Matrix-assisted laser desorption mass spectrometry of oligodeoxythymidylic acids. Rapid Commun Mass Spectrom. 1992 Mar;6(3):209–213. doi: 10.1002/rcm.1290060312. [DOI] [PubMed] [Google Scholar]
  4. Keough T., Baker T. R., Dobson R. L., Lacey M. P., Riley T. A., Hasselfield J. A., Hesselberth P. E. Antisense DNA oligonucleotides. II: The use of matrix-assisted laser desorption/ionization mass spectrometry for the sequence verification of methylphosphonate oligodeoxyribonucleotides. Rapid Commun Mass Spectrom. 1993 Mar;7(3):195–200. doi: 10.1002/rcm.1290070306. [DOI] [PubMed] [Google Scholar]
  5. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  6. Nordhoff E., Cramer R., Karas M., Hillenkamp F., Kirpekar F., Kristiansen K., Roepstorff P. Ion stability of nucleic acids in infrared matrix-assisted laser desorption/ionization mass spectrometry. Nucleic Acids Res. 1993 Jul 25;21(15):3347–3357. doi: 10.1093/nar/21.15.3347. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Nordhoff E., Ingendoh A., Cramer R., Overberg A., Stahl B., Karas M., Hillenkamp F., Crain P. F. Matrix-assisted laser desorption/ionization mass spectrometry of nucleic acids with wavelengths in the ultraviolet and infrared. Rapid Commun Mass Spectrom. 1992 Dec;6(12):771–776. doi: 10.1002/rcm.1290061212. [DOI] [PubMed] [Google Scholar]
  8. Pieles U., Zürcher W., Schär M., Moser H. E. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry: a powerful tool for the mass and sequence analysis of natural and modified oligonucleotides. Nucleic Acids Res. 1993 Jul 11;21(14):3191–3196. doi: 10.1093/nar/21.14.3191. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Schieltz D. M., Chou C. W., Luo C. W., Thomas R. M., Williams P. Mass spectrometry of DNA mixtures by laser ablation from frozen aqueous solution. Rapid Commun Mass Spectrom. 1992 Oct;6(10):631–636. doi: 10.1002/rcm.1290061009. [DOI] [PubMed] [Google Scholar]
  11. Smith R. D., Loo J. A., Edmonds C. G., Barinaga C. J., Udseth H. R. New developments in biochemical mass spectrometry: electrospray ionization. Anal Chem. 1990 May 1;62(9):882–899. doi: 10.1021/ac00208a002. [DOI] [PubMed] [Google Scholar]
  12. Spengler B., Pan Y., Cotter R. J., Kan L. S. Molecular weight determination of underivatized oligodeoxyribonucleotides by positive-ion matrix-assisted ultraviolet laser-desorption mass spectrometry. Rapid Commun Mass Spectrom. 1990 Apr;4(4):99–102. doi: 10.1002/rcm.1290040402. [DOI] [PubMed] [Google Scholar]
  13. Stemmler E. A., Hettich R. L., Hurst G. B., Buchanan M. V. Matrix-assisted laser desorption/ionization Fourier-transform mass spectrometry of oligodeoxyribonucleotides. Rapid Commun Mass Spectrom. 1993 Sep;7(9):828–836. doi: 10.1002/rcm.1290070910. [DOI] [PubMed] [Google Scholar]
  14. Tang K., Allman S. L., Chen C. H. Matrix-assisted laser desorption ionization of oligonucleotides with various matrices. Rapid Commun Mass Spectrom. 1993 Oct;7(10):943–948. doi: 10.1002/rcm.1290071016. [DOI] [PubMed] [Google Scholar]
  15. Wu K. J., Steding A., Becker C. H. Matrix-assisted laser desorption time-of-flight mass spectrometry of oligonucleotides using 3-hydroxypicolinic acid as an ultraviolet-sensitive matrix. Rapid Commun Mass Spectrom. 1993 Feb;7(2):142–146. doi: 10.1002/rcm.1290070206. [DOI] [PubMed] [Google Scholar]

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