High resolution characterization of DNA fragment ions produced by ultraviolet matrix-assisted laser desorption/ionization using linear and reflecting time-of-flight mass spectrometry

  • Joern Krause
  • Mark Scalf
  • Lloyd M. Smith


A mechanism for the gas phase fragmentation of DNA during the matrix-assisted laser desorption/ionization process has been proposed by ourselves and others, in which the initiating event is nucleobase protonation, followed by base loss and backbone cleavage. The proposed mechanism predicts the structures, and hence the masses, of the fragmentation products; however in earlier studies the mass resolution was insufficient to confirm the identities of these ions. In the present study a high resolution mass spectrometer equipped with a reflectron and delayed extraction capability was employed to determine the exact masses of the fragmentation products obtained from a number of short model oligonucleotide analytes. The fragment ions observed were found to have masses consistent with those predicted in the proposed mechanism. An additional species is observed in the mass spectra which was unresolved from other ions in previous studies; this species is hypothesized to correspond to the addition of water at the site of base loss from the DNA.


MALDI Metastable Fragmentation Fragmentation Product Base Loss Acceleration Potential 
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Copyright information

© American Society for Mass Spectrometry 1999

Authors and Affiliations

  1. 1.Department of ChemistryUniversity of WisconsinMadisonUSA

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