Minimizing base loss and internal fragmentation in collisionally activated dissociation of multiply deprotonated RNA

  • Monika Taucher
  • Ulrike Rieder
  • Kathrin Breuker


In recent years, new classes of nonprotein-coding ribonucleic acids (ncRNAs) with important cellular functions have been discovered. Of particular interest for biomolecular research and pharmaceutical developments are small ncRNAs that are involved in gene regulation, such as small interfering RNAs (21–28 nt), pre-microRNAs (70–80 nt), or riboswitches (34–200 nt). De novo sequencing of RNA by top-down mass spectrometry has so far been limited to RNA consisting of up to ∼20 nt. We report here complete sequence coverage for 34 nt RNA (10.9 kDa), along with 30 out of 32 possible complementary ion pairs from collisionally activated dissociation (CAD) experiments. The key to minimizing undesired base loss and internal fragmentation is to minimize the internal energy of fragment ions from primary backbone cleavage. This can be achieved by collisional cooling of primary fragment ions and selection of precursor ions of relatively low negative net charge (about −0.2/nt).


Collisionally Activate Dissociation Backbone Cleavage Base Loss Collisional Cool Collisionally Activate Dissociation Spectrum 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Supplementary material

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Supplementary material, approximately 686 KB.


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Copyright information

© American Society for Mass Spectrometry 2010

Authors and Affiliations

  • Monika Taucher
    • 1
  • Ulrike Rieder
    • 1
  • Kathrin Breuker
    • 1
  1. 1.Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI)University of InnsbruckInnsbruckAustria

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