OMA and OPA—Software-Supported Mass Spectra Analysis of Native and Modified Nucleic Acids

  • Adrien Nyakas
  • Lorenz C. Blum
  • Silvan R. Stucki
  • Jean-Louis Reymond
  • Stefan Schürch
Research Article


The platform-independent software package consisting of the oligonucleotide mass assembler (OMA) and the oligonucleotide peak analyzer (OPA) was created to support the analysis of oligonucleotide mass spectra. It calculates all theoretically possible fragments of a given input sequence and annotates it to an experimental spectrum, thus, saving a large amount of manual processing time. The software performs analysis of precursor and product ion spectra of oligonucleotides and their analogues comprising user-defined modifications of the backbone, the nucleobases, or the sugar moiety, as well as adducts with metal ions or drugs. The ability to expand the library of building blocks and to implement individual structural variations makes it extremely useful for supporting the analysis of therapeutically active compounds. The functionality of the software tool is demonstrated on the examples of a platinated double-stranded oligonucleotide and a modified RNA sequence. Experiments also reveal the unique dissociation behavior of platinated higher-order DNA structures.

Key words

DNA RNA Oligonucleotides Tandem mass spectrometry Software Fragmentation Double-stranded DNA Nucleic acids Cisplatin 



The authors gratefully acknowledge financial support of this work by the Swiss National Science Foundation (grant no. 200020_121843).

Supplementary material

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Copyright information

© American Society for Mass Spectrometry 2012

Authors and Affiliations

  • Adrien Nyakas
    • 2
  • Lorenz C. Blum
    • 3
  • Silvan R. Stucki
    • 1
  • Jean-Louis Reymond
    • 1
  • Stefan Schürch
    • 1
  1. 1.Department of Chemistry and BiochemistryUniversity of BernBernSwitzerland
  2. 2.Genome BC Proteomics CentreUniversity of VictoriaVictoriaCanada
  3. 3.Institute of Molecular Systems Biology, ETH ZurichZürichSwitzerland

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