OMA and OPA—Software-Supported Mass Spectra Analysis of Native and Modified Nucleic Acids
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- 作者：Adrien Nyakas (2)
Lorenz C. Blum (3)
Silvan R. Stucki (1)
Jean-Louis Reymond (1)
Stefan Schürch (1) - 关键词：DNA ; RNA ; Oligonucleotides ; Tandem mass spectrometry ; Software ; Fragmentation ; Double ; stranded DNA ; Nucleic acids ; Cisplatin
- 刊名：Journal of The American Society for Mass Spectrometry
- 出版年：2013
- 出版时间：February 2013
- 年：2013
- 卷：24
- 期：2
- 页码：249-256
- 全文大小：712KB
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Lorenz C. Blum (3)
Silvan R. Stucki (1)
Jean-Louis Reymond (1)
Stefan Schürch (1)
2. Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
3. Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
1. Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
文摘
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.