title: OMA and OPA--software-supported mass spectra analysis of native and modified nucleic acids.
abstract: 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.
authors.affiliation: Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada.
authors.forename: Adrien
authors.initials: A
authors.lastname: Nyakas
authors.forename: Lorenz C
authors.initials: LC
authors.lastname: Blum
authors.forename: Silvan R
authors.initials: SR
authors.lastname: Stucki
authors.forename: Jean-Louis
authors.initials: JL
authors.lastname: Reymond
authors.forename: Stefan
authors.initials: S
authors.lastname: Schürch
mesh_terms: D002945:Cisplatin / Q000737:chemistry; D019295:Computational Biology; D009696:Nucleic Acids / Q000737:chemistry*; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*; D014584:User-Computer Interface
chemical_list: D009696:Nucleic Acids; D002945:Cisplatin