Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

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


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.

This is a preview of subscription content, log in to check access.

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6


  1. 1.

    Wang, Z., Wan, K.X., Ramanathan, R., Taylor, J.S., Gross, M.L.: Structure and fragmentation mechanisms of isomeric T-rich oligodeoxynucleotides: A comparison of four tandem mass spectrometric methods. J. Am. Soc. Mass Spectrom. 9(7), 683–691 (1998)

  2. 2.

    Schürch, S., Bernal-Mendez, E., Leumann, C.J.: Electrospray tandem mass spectrometry of mixed-sequence RNA/DNA oligonucleotides. J. Am. Soc. Mass Spectrom. 13(8), 936–945 (2002)

  3. 3.

    Tromp, J.M., Schürch, S.: Gas-phase dissociation of oligoribonucleotides and their analogs studied by electrospray ionization tandem mass spectrometry. J. Am. Soc. Mass Spectrom. 16, 1262–1268 (2005)

  4. 4.

    Andersen, T.E., Kirpekar, F., Haselmann, K.F.: RNA fragmentation in MALDI mass spectrometry studied by H/D-exchange: mechanisms of general applicability to nucleic acids. J. Am. Soc. Mass Spectrom. 17(10), 1353–1368 (2006)

  5. 5.

    Wu, J., McLuckey, S.A.: Gas-phase fragmentation of oligonucleotide ions. Mass Spectrom. Rev. 237, 197–241 (2004)

  6. 6.

    McLuckey, S.A., VanBerkel, G.J., Glish, G.L.: Tandem mass-spectrometry of small, multiply charged oligonucleotides. J. Am. Soc. Mass Spectrom. 3(1), 60–70 (1992)

  7. 7.

    Nyakas, A., Eymann, M., Schürch, S.: The influence of cisplatin on the gas-phase dissociation of oligonucleotides studied by electrospray ionization tandem mass spectrometry. J. Am. Soc. Mass Spectrom. 20(5), 792–804 (2009)

  8. 8.

    Nyakas, A., Stucki, S.R., Schürch, S.: Tandem Mass Spectrometry of modified and platinated oligoribonucleotides. J. Am. Soc. Mass Spectrom. 22(5), 875–887 (2011)

  9. 9.

    Ganem, B., Li, Y.T., Henion, J.D.: Detection of oligonucleotide duplex forms by ion-spray mass-spectrometry. Tetrahedron Lett. 34(9), 1445–1448 (1993)

  10. 10.

    Light-Wahl, K.J., Springer, D.L., Winger, B.E., Edmonds, C.G., Camp, D.G., Thrall, B.D., Smith, R.D.: Observation of a small oligonucleotide duplex by electrospray ionization mass-spectrometry. J. Am. Chem. Soc. 115(2), 803–804 (1993)

  11. 11.

    Aaserud, D.J., Kelleher, N.L., Little, D.P., McLafferty, F.W.: Accurate base composition of double-strand DNA by mass spectrometry. J. Am. Soc. Mass Spectrom. 7(12), 1266–1269 (1996)

  12. 12.

    Bayer, E., Bauer, T., Schmeer, K., Bleicher, K., Maler, M., Gaus, H.J.: Analysis of double-stranded oligonucleotides by electrospray mass-spectrometry. Anal. Chem. 66(22), 3858–3863 (1994)

  13. 13.

    Doktycz, M.J., Habibi-Goudarzi, S., McLuckey, S.A.: Accumulation and storage of ionized duplex DNA-molecules in a quadrupole ion-trap. Anal. Chem. 66(20), 3416–3422 (1994)

  14. 14.

    Wan, K.X., Gross, M.L., Shibue, T.: Gas-phase stability of double-stranded oligodeoxynucleotides and their noncovalent complexes with DNA-binding drugs as revealed by collisional activation in an ion trap. J. Am. Soc. Mass Spectrom. 11(5), 450–457 (2000)

  15. 15.

    Egger, A.E., Hartinger, C.G., Ben Hamidane, H., Tsybin, Y.O., Keppler, B.K., Dyson, P.J.: High resolution mass spectrometry for studying the interactions of cisplatin with oligonucleotides. Inorg. Chem. 47(22), 10626–10633 (2008)

  16. 16.

    Groessl, M., Tsybin, Y.O., Hartinger, C.G., Keppler, B.K., Dyson, P.J.: Ruthenium versus platinum: interactions of anticancer metallodrugs with duplex oligonucleotides characterised by electrospray ionisation mass spectrometry. J. Biol. Inorg. Chem. 15(5), 677–688 (2010)

  17. 17.

    Ni, J.S., Pomerantz, S.C., Rozenski, J., Zhang, Y.H., McCloskey, J.A.: Interpretation of oligonucleotide mass spectra for determination of sequence using electrospray ionization and tandem mass spectrometry. Anal. Chem. 68(13), 1989–1999 (1996)

  18. 18.

    Rozenski, J.: Mongo oligo mass calculator. Available at: URL http://library.med.utah.edu/masspec/mongo.htm. Accessed February 5, 2011

  19. 19.

    Oberacher, H., Wellenzohn, B., Huber, C.G.: Comparative sequencing of nucleic acids by liquid chromatography tandem mass spectrometry. Anal. Chem. 74(1), 211–218 (2002)

  20. 20.

    Rozenski, J., McCloskey, J.A.: SOS: A simple interactive program for ab initio oligonucleotide sequencing by mass spectrometry. J. Am. Soc. Mass Spectrom. 13(3), 200–203 (2002)

  21. 21.

    Yu, E.T., Hawkins, A., Kuntz, I.D., Ran, L.A., Rothfuss, A., Sale, K., Young, M.M., Yang, C.L., Pancerella, C.M., Fabris, D.: The collaboratory for MS3D: a new cyberinfrastructure for the structural elucidation of biological macromolecules and their assemblies using mass spectrometry-based approaches. J Proteome Res. 7(11), 4848–4857 (2008)

  22. 22.

    Kellersberger, K.A., Yu, E.T., Kruppa, G.H., Young, M.M., Fabris, D.: Top-down characterization of nucleic acids modified by structural probes using high-resolution tandem mass spectrometry and automated data interpretation. Anal. Chem. 76(9), 2438 (2004)

  23. 23.

    Kretschmer, M., Lavine, G., McArdle, J., Kuchimanchi, S., Murugaiah, V., Manoharan, M.: An automated algorithm for sequence confirmation of chemically modified oligonucleotides by tandem mass spectrometry. Anal. Biochem. 405(2), 213–223 (2010)

Download references


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

Author information

Correspondence to Stefan Schürch.

Additional information

Adrien Nyakas, Lorenz C. Blum and Silvan R. Stucki contributed equally to this project.

Electronic supplementary material

Below is the link to the electronic supplementary material.


(JPEG 403 kb)


(JPEG 61 kb)


(JPEG 44 kb)


(JPEG 134 kb)


(DOC 44 kb)

High resolution image (TIFF 3221 kb)

High resolution image (TIFF 1367 kb)

High resolution image (TIFF 800 kb)

High resolution image (TIFF 1411 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Nyakas, A., Blum, L.C., Stucki, S.R. et al. OMA and OPA—Software-Supported Mass Spectra Analysis of Native and Modified Nucleic Acids. J. Am. Soc. Mass Spectrom. 24, 249–256 (2013). https://doi.org/10.1007/s13361-012-0529-1

Download citation

Key words

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