A photocleavable surfactant for top-down proteomics

Abstract

We report the identification of a photocleavable anionic surfactant, 4-hexylphenylazosulfonate (Azo), which can be rapidly degraded by ultraviolet irradiation, for top-down proteomics. Azo can effectively solubilize proteins with performance comparable to that of sodium dodecyl sulfate (SDS) and is compatible with mass spectrometry. Azo-aided top-down proteomics enables the solubilization of membrane proteins for comprehensive characterization of post-translational modifications. Moreover, Azo is simple to synthesize and can be used as a general SDS replacement in SDS–polyacrylamide gel electrophoresis.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1: Synthesis and characterization of a photocleavable anionic surfactant, Azo.
Fig. 2: Photocleavable Azo-enabled top-down membrane proteomics.

Data availability

All data generated or analyzed during this study are presented in this article or in the provided supplementary materials. Raw gel, blot and mass spectra data are available as Supplementary Data, and source data for Fig. 1 and Supplementary Figs. 4, 9, 10 and 13 are available online. Proteomics data have been uploaded to the PRIDE repository via ProteomeXchange with identifier PXD010825.

References

  1. 1.

    Aebersold, R. et al. Nat. Chem. Biol. 14, 206–214 (2018).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  2. 2.

    Siuti, N. & Kelleher, N. L. Nat. Methods 4, 817–821 (2007).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  3. 3.

    Cai, W. X., Tucholski, T. M., Gregorich, Z. R. & Ge, Y. Expert Rev. Proteomics 13, 717–730 (2016).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  4. 4.

    Chen, B., Brown, K. A., Lin, Z. & Ge, Y. Anal. Chem. 90, 110–127 (2018).

    CAS  Article  PubMed  Google Scholar 

  5. 5.

    Barrera, N. P. & Robinson, C. V. Annu. Rev. Biochem 80, 247–271 (2011).

    CAS  Article  PubMed  Google Scholar 

  6. 6.

    Speers, A. E. & Wu, C. C. Chem. Rev. 107, 3687–3714 (2007).

    CAS  Article  PubMed  Google Scholar 

  7. 7.

    Loo, R. R., Dales, N. & Andrews, P. C. Protein Sci. 3, 1975–1983 (1994).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  8. 8.

    Wisniewski, J. R., Zougman, A., Nagaraj, N. & Mann, M. Nat. Methods 6, 359–362 (2009).

    CAS  Article  PubMed  Google Scholar 

  9. 9.

    Kachuk, C. & Doucette, A. A. J. Proteomics 175, 75–86 (2018).

    CAS  Article  PubMed  Google Scholar 

  10. 10.

    Chang, Y.-H. et al. J. Proteome Res. 14, 1587–1599 (2015).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  11. 11.

    Yu, Y. Q., Gilar, M., Lee, P. J., Bouvier, E. S. & Gebler, J. C. Anal. Chem. 75, 6023–6028 (2003).

    CAS  Article  PubMed  Google Scholar 

  12. 12.

    Chen, E. I., Cociorva, D., Norris, J. L. & Yates, J. R. J. Proteome Res. 6, 2529–2538 (2007).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  13. 13.

    Meng, F. et al. Anal. Chem. 74, 2923–2929 (2002).

    CAS  Article  PubMed  Google Scholar 

  14. 14.

    Bradley, M., Vincent, B., Warren, N., Eastoe, J. & Vesperinas, A. Langmuir 22, 101–105 (2006).

    CAS  Article  PubMed  Google Scholar 

  15. 15.

    Hwang, L., Guardado-Alvarez, T. M., Ayaz-Gunner, S., Ge, Y. & Jin, S. Langmuir 32, 3963–3969 (2016).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  16. 16.

    Kim, M. S. & Diamond, S. L. Bioorg. Med. Chem. Lett. 16, 4007–4010 (2006).

    CAS  Article  PubMed  Google Scholar 

  17. 17.

    Dunkin, I. R., Gittinger, A., Sherrington, D. C. & Whittaker, P. J. Chem. Soc. Perkin Trans. I 2, 1837–1842 (1996).

    Article  Google Scholar 

  18. 18.

    Laganowsky, A., Reading, E., Hopper, J. T. S. & Robinson, C. V. Nat. Protoc. 8, 639–651 (2013).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  19. 19.

    MacLennan, D. H. & Kranias, E. G. Nat. Rev. Mol. Cell Biol. 4, 566–577 (2003).

    CAS  Article  PubMed  Google Scholar 

  20. 20.

    He, J. et al. Proc. Natl Acad. Sci. USA 115, 2988–2993 (2018).

    CAS  Article  PubMed  Google Scholar 

  21. 21.

    Saveliev, S. V. et al. Anal. Chem. 85, 907–914 (2013).

    CAS  Article  PubMed  Google Scholar 

  22. 22.

    Lee, H. B. et al. J. Org. Chem. 69, 701–713 (2004).

    CAS  Article  PubMed  Google Scholar 

  23. 23.

    Saveliev, S., Simpson, D. & Wood, K. V. Cleavable surfactants. US patent 0095628 A1 (2009).

  24. 24.

    Mezger, T., Nuyken, O., Meindl, K. & Wokaun, A. Prog. Org. Coat. 29, 147–157 (1996).

    CAS  Article  Google Scholar 

  25. 25.

    Wientzek, M. & Katz, S. J. Mol. Cell. Cardiol. 23, 1149–1163 (1991).

    CAS  Article  PubMed  Google Scholar 

  26. 26.

    Peng, Y. et al. Mol. Cell. Proteomics 13, 2752–2764 (2014).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  27. 27.

    Kou, Q., Xun, L. & Liu, X. Bioinformatics 32, 3495–3497 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. 28.

    Apweiler, R. et al. Nucleic Acids Res. 32, D115–D119 (2004).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  29. 29.

    Cai, W. et al. Mol. Cell. Proteomics 15, 703–714 (2016).

    CAS  Article  PubMed  Google Scholar 

  30. 30.

    Fellers, R. T. et al. Proteomics 15, 1235–1238 (2015).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  31. 31.

    Ashburner, M. et al. Nature Genet. 25, 25–29 (2000).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  32. 32.

    Szklarczyk, D. et al. Nucleic Acids Res. 45, D362–D368 (2017).

    CAS  Article  PubMed  Google Scholar 

  33. 33.

    Cai, W. et al. Anal. Chem. 89, 5467–5475 (2017).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This research is supported by National Institutes of Health R01 GM117058 (to S.J. and Y.G.). Y.G. acknowledges R01 HL109810, R01 HL096971, R01 GM125085 and S10 OD018475. MaSDeS was a gift from S. Saveliev (Promega Corporation). We thank A. Chen, E. Chang and W. Tang for their assistance in the early stage of the project, S. Mitchell and T. Tucholski for the help with graphics, and T. Hacker for providing the swine hearts. We thank M. Willetts at Bruker for his assistance with DataAnalysis software. We also acknowledge A. Carr, E. Bayne and J. Melby for their help testing the Supplementary Protocol to ensure reproducible results.

Author information

Affiliations

Authors

Contributions

K.A.B. designed and performed experiments, analyzed the data and wrote the manuscript. B.C. designed and performed experiments, analyzed the data and wrote the manuscript. T.M.G.-A. designed and performed experiments, analyzed the data and wrote the manuscript. Z.L. performed experiments and analyzed the data. L.H. performed experiments and analyzed the data. S.A.-G. performed experiments and analyzed the data. S.J. designed the experiments, supervised the project and wrote the manuscript. Y.G. conceived the idea, designed the experiments, supervised the project and wrote the manuscript.

Corresponding author

Correspondence to Ying Ge.

Ethics declarations

Competing interests

The University of Wisconsin–Madison has filed a provisional patent application P180335US01, US serial number 62/682027 (7 June 2018) on the basis of this work. Y.G., S.J., K.B. and T.M.G.-A. are named as inventors on the provisional patent application.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Figs. 1–19, Supplementary Table 1 and Supplementary Notes 1–6

Reporting Summary

Supplementary Protocol

Supplementary Table 2

Detected proteoforms from LC–MS/MS run 1 (cardiac tissue)

Supplementary Table 3

Total detected proteoforms in 3 LC–MS/MS experiments: run 1 (cardiac tissue), run 2 (sarcoplasmic reticulum (SR) and mitochondria (Mit) enriched cardiac tissue), and run 3 (SR and Mit enriched cardiac tissue)

Supplementary Table 4

Proteoforms identified by TopPIC from cardiac tissue using Azo from all three LC–MS/MS runs in this study

Supplementary Table 5

Proteins identified by TopPIC from cardiac tissue using Azo from all three LC–MS/MS runs in this study

Supplementary Table 6

Subunits of the electron transport chain identified from cardiac tissue samples using Azo in this study

Supplementary Table 7

Integral membrane proteins identified from cardiac tissue samples using Azo in this study

Supplementary Table 8

ATP synthase subunits identified from cardiac tissue using Azo in this study

Supplementary Table 9

TopPIC proteoform identification: Azo protein extraction of human embryonic kidney (HEK) cell

Supplementary Table 10

TopPIC protein identification: Azo protein extraction of human embryonic kidney (HEK) cell

Supplementary Data

Full gels, blots and raw mass spectra

Source data

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Brown, K.A., Chen, B., Guardado-Alvarez, T.M. et al. A photocleavable surfactant for top-down proteomics. Nat Methods 16, 417–420 (2019). https://doi.org/10.1038/s41592-019-0391-1

Download citation

Further reading