Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Perspective
  • Published:

Native mass spectrometry: a bridge between interactomics and structural biology

Nature Methods volume 5, pages 927–933 (2008)Cite this article

Abstract

Native mass spectrometry is an emerging technology that allows the topological investigation of intact protein complexes with high sensitivity and a theoretically unrestricted mass range. This unique tool provides complementary information to established technologies in structural biology, and also provides a link to high-throughput interactomics studies, which do not generate information on exact protein complex-composition, structure or dynamics. Here I review the current state of native mass spectrometry technology and discuss several important biological applications. I also describe current experimental challenges in native mass spectrometry, encouraging readers to contribute to solutions.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Denatured and native mass spectra of H. pylori urease.
Figure 2: Tandem mass spectrometry of the intact 517 kDa RNA Pol II complex.
Figure 3: The ins and outs of native mass spectrometry.
Figure 4: Native mass spectra of intact HBV viral capsids.

Similar content being viewed by others

References

  1. Alberts, B. The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92, 291–294 (1998).

    Article  CAS  Google Scholar 

  2. Stelzl, U. et al. A human protein-protein interaction network: a resource for annotating the proteome. Cell 122, 957–968 (2005).

    Article  CAS  Google Scholar 

  3. Kocher, T. & Superti-Furga, G. Mass spectrometry-based functional proteomics: from molecular machines to protein networks. Nat. Methods 4, 807–815 (2007).

    Article  Google Scholar 

  4. Gingras, A.C., Gstaiger, M., Raught, B. & Aebersold, R. Analysis of protein complexes using mass spectrometry. Nat. Rev. Mol. Cell Biol. 8, 645–654 (2007).

    Article  CAS  Google Scholar 

  5. Krogan, N.J. et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637–643 (2006).

    Article  CAS  Google Scholar 

  6. Gavin, A.C. et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631–636 (2006).

    Article  CAS  Google Scholar 

  7. Robinson, C.V., Sali, A. & Baumeister, W. The molecular sociology of the cell. Nature 450, 973–982 (2007).

    Article  CAS  Google Scholar 

  8. Sprangers, R., Velyvis, A. & Kay, L.E. Solution NMR of supramolecular complexes: providing new insights into function. Nat. Methods 4, 697–703 (2007).

    Article  CAS  Google Scholar 

  9. Loo, J.A. Studying noncovalent protein complexes by electrospray ionization mass spectrometry. Mass Spectrom. Rev. 16, 1–23 (1997).

    Article  CAS  Google Scholar 

  10. van den Heuvel, R.H. & Heck, A.J. Native protein mass spectrometry: from intact oligomers to functional machineries. Curr. Opin. Chem. Biol. 8, 519–526 (2004).

    Article  CAS  Google Scholar 

  11. Kaddis, C.S. & Loo, J.A. Native protein MS and ion mobility large flying proteins with ESI. Anal. Chem. 79, 1778–1784 (2007).

    Article  CAS  Google Scholar 

  12. Sharon, M. & Robinson, C.V. The role of mass spectrometry in structure elucidation of dynamic protein complexes. Annu. Rev. Biochem. 76, 167–193 (2007).

    Article  CAS  Google Scholar 

  13. Uetrecht, C. et al. High-resolution mass spectrometry of viral assemblies: molecular composition and stability of dimorphic hepatitis B virus capsids. Proc. Natl. Acad. Sci. USA 105, 9216–9220 (2008).

    Article  CAS  Google Scholar 

  14. Uetrecht, C. et al. Stability and shape of hepatitis B virus capsids in vacuo. Angew. Chem. Int. Ed. 47, 6247–6251 (2008).

    Article  CAS  Google Scholar 

  15. Heck, A.J. & Van Den Heuvel, R.H. Investigation of intact protein complexes by mass spectrometry. Mass Spectrom. Rev. 23, 368–389 (2004).

    Article  CAS  Google Scholar 

  16. Benesch, J.L., Ruotolo, B.T., Simmons, D.A. & Robinson, C.V. Protein complexes in the gas phase: technology for structural genomics and proteomics. Chem. Rev. 107, 3544–3567 (2007).

    Article  CAS  Google Scholar 

  17. Hernandez, H. & Robinson, C.V. Determining the stoichiometry and interactions of macromolecular assemblies from mass spectrometry. Nat. Protoc. 2, 715–726 (2007).

    Article  CAS  Google Scholar 

  18. van Duijn, E. et al. Tandem mass spectrometry of intact GroEL-substrate complexes reveals substrate-specific conformational changes in the trans ring. J. Am. Chem. Soc. 128, 4694–4702 (2006).

    Article  CAS  Google Scholar 

  19. van Duijn, E. et al. Monitoring macromolecular complexes involved in the chaperonin-assisted protein folding cycle by mass spectrometry. Nat. Methods 2, 371–376 (2005).

    Article  CAS  Google Scholar 

  20. Vaughan, C.K. et al. Structure of an Hsp90-Cdc37-Cdk4 complex. Mol. Cell 23, 697–707 (2006).

    Article  CAS  Google Scholar 

  21. Sharon, M., Taverner, T., Ambroggio, X.I., Deshaies, R.J. & Robinson, C.V. Structural organization of the 19S proteasome lid: insights from MS of intact complexes. PLoS Biol. 4, e267 (2006).

    Article  Google Scholar 

  22. Sharon, M. et al. 20S proteasomes have the potential to keep substrates in store for continual degradation. J. Biol. Chem. 281, 9569–9575 (2006).

    Article  CAS  Google Scholar 

  23. Sharon, M., Witt, S., Glasmacher, E., Baumeister, W. & Robinson, C.V. Mass spectrometry reveals the missing links in the assembly pathway of the bacterial 20 S proteasome. J. Biol. Chem. 282, 18448–18457 (2007).

    Article  CAS  Google Scholar 

  24. Synowsky, S.A., van den Heuvel, R.H., Mohammed, S., Pijnappel, P.W. & Heck, A.J. Probing genuine strong interactions and post-translational modifications in the heterogeneous yeast exosome protein complex. Mol. Cell. Proteomics 5, 1581–1592 (2006).

    Article  CAS  Google Scholar 

  25. Hernandez, H., Dziembowski, A., Taverner, T., Seraphin, B. & Robinson, C.V. Subunit architecture of multimeric complexes isolated directly from cells. EMBO Rep. 7, 605–610 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Taverner, T. et al. Subunit architecture of intact protein complexes from mass spectrometry and homology modeling. Acc. Chem. Res. 41, 617–627 (2008).

    Article  CAS  Google Scholar 

  27. Lorenzen, K., Vannini, A., Cramer, P. & Heck, A.J. Structural biology of RNA polymerase III: mass spectrometry elucidates subcomplex architecture. Structure 15, 1237–1245 (2007).

    Article  CAS  Google Scholar 

  28. Sprangers, R. & Kay, L.E. Quantitative dynamics and binding studies of the 20S proteasome by NMR. Nature 445, 618–622 (2007).

    Article  CAS  Google Scholar 

  29. Medalia, O. et al. Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography. Science 298, 1209–1213 (2002).

    Article  CAS  Google Scholar 

  30. Loo, J.A. et al. Electrospray ionization mass spectrometry and ion mobility analysis of the 20S proteasome complex. J. Am. Soc. Mass Spectrom. 16, 998–1008 (2005).

    Article  CAS  Google Scholar 

  31. Cramer, P., Bushnell, D.A. & Kornberg, R.D. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292, 1863–1876 (2001).

    Article  CAS  Google Scholar 

  32. Fernandez-Tornero, C. et al. Insights into transcription initiation and termination from the electron microscopy structure of yeast RNA polymerase III. Mol. Cell 25, 813–823 (2007).

    Article  CAS  Google Scholar 

  33. Rigaut, G. et al. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17, 1030–1032 (1999).

    Article  CAS  Google Scholar 

  34. Synowsky, S.A. & Heck, A.J. The yeast Ski complex is a hetero-tetramer. Protein Sci. 17, 119–125 (2007).

    Article  Google Scholar 

  35. Benesch, J.L., Aquilina, J.A., Ruotolo, B.T., Sobott, F. & Robinson, C.V. Tandem mass spectrometry reveals the quaternary organization of macromolecular assemblies. Chem. Biol. 13, 597–605 (2006).

    Article  CAS  Google Scholar 

  36. Lorenzen, K., Olia, A.S., Uetrecht, C., Cingolani, G. & Heck, A.J. Determination of stoichiometry and conformational changes in the first step of the P22 tail assembly. J. Mol. Biol. 379, 385–396 (2008).

    Article  CAS  Google Scholar 

  37. Demmers, J.A., Haverkamp, J., Heck, A.J., Koeppe, R.E. II & Killian, J.A. Electrospray ionization mass spectrometry as a tool to analyze hydrogen/deuterium exchange kinetics of transmembrane peptides in lipid bilayers. Proc. Natl. Acad. Sci. USA 97, 3189–3194 (2000).

    Article  CAS  Google Scholar 

  38. Doyle, D.A. et al. The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280, 69–77 (1998).

    Article  CAS  Google Scholar 

  39. Sharon, M., Ilag, L.L. & Robinson, C.V. Evidence for micellar structure in the gas phase. J. Am. Chem. Soc. 129, 8740–8746 (2007).

    Article  CAS  Google Scholar 

  40. Barrera, N.P., Di Bartolo, N., Booth, P.J. & Robinson, C.V. Micelles protect membrane complexes from solution to vacuum. Science 321, 243–246 (2008).

    Article  CAS  Google Scholar 

  41. Rinner, O. et al. Identification of cross-linked peptides from large sequence databases. Nat. Methods 5, 315–318 (2008).

    Article  CAS  Google Scholar 

  42. Sinz, A. Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions. Mass Spectrom. Rev. 25, 663–682 (2006).

    Article  CAS  Google Scholar 

  43. Aloy, P. et al. Structure-based assembly of protein complexes in yeast. Science 303, 2026–2029 (2004).

    Article  CAS  Google Scholar 

  44. Eckers, C., Laures, A.M., Giles, K., Major, H. & Pringle, S. Evaluating the utility of ion mobility separation in combination with high-pressure liquid chromatography/mass spectrometry to facilitate detection of trace impurities in formulated drug products. Rapid Commun. Mass Spectrom. 21, 1255–1263 (2007).

    Article  CAS  Google Scholar 

  45. Ruotolo, B.T. et al. Evidence for macromolecular protein rings in the absence of bulk water. Science 310, 1658–1661 (2005).

    Article  CAS  Google Scholar 

  46. Pinkse, M.W., Maier, C.S., Kim, J.I., Oh, B.H. & Heck, A.J. Macromolecular assembly of Helicobacter pylori urease investigated by mass spectrometry. J. Mass Spectrom. 38, 315–320 (2003).

    Article  CAS  Google Scholar 

  47. Sobott, F., Hernandez, H., McCammon, M.G., Tito, M.A. & Robinson, C.V. A tandem mass spectrometer for improved transmission and analysis of large macromolecular assemblies. Anal. Chem. 74, 1402–1407 (2002).

    Article  CAS  Google Scholar 

  48. van den Heuvel, R.H. et al. Improving the performance of a quadrupole time-of-flight instrument for macromolecular mass spectrometry. Anal. Chem. 78, 7473–7483 (2006).

    Article  CAS  Google Scholar 

  49. Shvartsburg, A.A., Mashkevich, S.V., Baker, E.S. & Smith, R.D. Optimization of algorithms for ion mobility calculations. J. Phys. Chem. 111, 2002–2010 (2007).

    Article  CAS  Google Scholar 

  50. Ruotolo, B.T. et al. Ion mobility-mass spectrometry reveals long-lived, unfolded intermediates in the dissociation of protein complexes. Angew. Chem. Int. Ed. 46, 8001–8004 (2007).

    Article  CAS  Google Scholar 

  51. Ruotolo, B.T., Benesch, J.L., Sandercock, A.M., Hyung, S.J. & Robinson, C.V. Ion mobility-mass spectrometry analysis of large protein complexes. Nat. Protoc. 3, 1139–1152 (2008).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

I thank all colleagues in native MS who have contributed in making this area of research come to maturity. I acknowledge all members of my group, most notably the native MS (former) members whose material and input I have used here; K. Lorenzen, H. Mazon, M. Pinkse, S. Synowsky, C. Uetrecht, R. van den Heuvel, E. van Duijn and C. Versluis. K. Lorenzen and C. Uetrecht helped construct the figures. Additionally, I thank all collaborators whose samples, support and expertise have been instrumental in our work.

Author information

Authors and Affiliations

  1. Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, Utrecht, 3584, CA, The Netherlands

    Albert J R Heck

Authors
  1. Albert J R Heck
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Albert J R Heck.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Heck, A. Native mass spectrometry: a bridge between interactomics and structural biology. Nat Methods 5, 927–933 (2008). https://doi.org/10.1038/nmeth.1265

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nmeth.1265

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing