Matrix influence on the formation of positively charged oligonucleotides in matrix-assisted laser desorption/ionization mass spectrometry

Chau Wen Chou, Peter Williams, Patrick A. Limbach

Research output: Contribution to journalArticlepeer-review

19 Scopus citations


The ionization efficiency of various ultraviolet matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) matrices was investigated. A site of fixed positive charge was generated on an oligonucleotide by addition of a quaternary ammonium. This quaternary ammonium-tagged oligonucleotide was then used as an internal standard to probe the relative ionization capabilities of 3-hydroxypicolinic acid (3-HPA), 2',4',6'-trihydroxyacetophenone (THAP) and 2,5-dihydroxybenzoic acid (DHBA) in positive-ion mode. MALDI-MS analysis of equimolar mixtures of the quaternary ammonium-tagged oligonucleotide and an unmodified polythymidylic acid, dT12, found that 3-HPA yielded more abundant protonated dT12 molecular ions than either THAP or DHBA. These results demonstrate that the low ion yields previously reported for polythymidylic acid are due to the matrix utilized and are not due to the low proton affinity of thymidine. Primary, secondary and tertiary amines were also incorporated into dT12 to examine the effect of these different amines on the protonation efficiency of the three matrices under investigation. Similar results were obtained, regardless of the amine-tag utilized, with protonation efficiency following the trend 3-HPA > THAP > DHBA. Consideration of the various factors that might influence the overall production of positively charged polythymidylic acid finds that it is the matrix:phosphodiester backbone interaction that might play the important role in determining the optimal MALDI-MS response. These results are a step towards understanding the matrix properties necessary for optimal production of oligonucleotide molecular ions in MALDI-MS. (C) 1999 Elsevier Science B.V.

Original languageEnglish (US)
Pages (from-to)15-27
Number of pages13
JournalInternational Journal of Mass Spectrometry
Issue number1
StatePublished - Oct 28 1999


  • Charge tags
  • Ionization efficiency
  • Polythymidylic acid
  • Proton affinity

ASJC Scopus subject areas

  • Instrumentation
  • Condensed Matter Physics
  • Spectroscopy
  • Physical and Theoretical Chemistry


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