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

Nyakas, Adrien ; Blum, Lorenz ; Stucki, Silvan ; Reymond, Jean-Louis ; Schürch, Stefan

In: Journal of The American Society for Mass Spectrometry, 2013, vol. 24, no. 2, p. 249-256

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    Titel
    • OMA and OPA—Software-Supported Mass Spectra Analysis of Native and Modified Nucleic Acids
    Autor
    • Nyakas, Adrien. Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
    • Blum, Lorenz. Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
    • Stucki, Silvan. Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
    • Reymond, Jean-Louis. Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
    • Schürch, Stefan. Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
    Dokumententyp
    • Postprint
    Sprache
    • Englisch
    Veröffentlicht in
    • Journal of The American Society for Mass Spectrometry, 2013, vol. 24, no. 2, p. 249-256. Springer-Verlag
    Andere elektronische Ausgabe
    OAI-PMH-ID
    • oai:doc.rero.ch:321655
    Summary
    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