Software assisted data analysis

Tandem mass spectrometric analysis can generate product ion spectra of tremendous complexity, as the number of possible fragments grows rapidly with increasing sequence length. The fact that structural modifications affect the dissociation pathways greatly increases the variety of analytically valuable fragment ions. In contrast to the processing of peptide product ion spectra, which nowadays is highly automated, there is a lack of tools assisting the interpretation of oligonucleotide data. Consequently, the software package OMA & OPA was created to support the interpretation of mass spectra of natural and modified oligonucleotides. A selection of common structural modifications has already been integrated in the software, but the user can add any modified building block or adduct to the library. The tool can rapidly calculate all theoretically possible fragment ions for a given input sequence and annotate them to an experimental spectrum, thus, saving a large amount of manual processing time. The OMA & OPA software is programmed in the platform-independent language Java and it therefore runs on all major operating systems.

How to cite

To cite any application in relation to the software or the original publication, please cite:

A. Nyakas, L. C. Blum, S. R. Stucki, J.-L. Reymond, S. Schürch. OMA and OPA - software-supported mass spectra analysis of native and modified nucleic acidsJ. Am. Soc. Mass Spectrom. 201324, 249-256. 10.1007/s13361-012-0529-1.

Terms & Conditions

This program was developed in the hope that it will be useful. However, the software is provided "as-is", without warranty of any kind. It was developed for research purposes only and in no event the authors shall be held liable for any damages or other consequences arising from the use of the software. You may download and use the software free of charge, but you are not allowed to modify or to redistribute it without the written permission of the authors. All data provided by the user for download will be treated confidential.


OMA & OPA software package


is found here.


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