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A photocleavable surfactant for top-down proteomics

Nature Methods volume 16, pages 417–420 (2019)Cite this article

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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.

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

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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.

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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

Authors and Affiliations

  1. Department of Chemistry, University of Wisconsin–Madison, Madison, WI, USA

    Kyle A. Brown, Bifan Chen, Tania M. Guardado-Alvarez, Leekyoung Hwang, Song Jin & Ying Ge

  2. Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI, USA

    Ziqing Lin, Serife Ayaz-Guner & Ying Ge

  3. Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI, USA

    Ziqing Lin & Ying Ge

Authors
  1. Kyle A. Brown
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  8. Ying Ge
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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.

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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.

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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

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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

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