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Tube-Gel: A Fast and Effective Sample Preparation Method for High-Throughput Quantitative Proteomics

  • Leslie Muller
  • Luc Fornecker
  • Sarah Cianferani
  • Christine CarapitoEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1959)

Abstract

Sample preparation is a key step in proteomics workflows. Tube-gel (TG) is a fast and repeatable sample preparation method that consists in the instantaneous trapping of the sample in a polyacrylamide gel matrix. It takes advantage of in-gel sample preparations by allowing the use of high concentrations of sodium-dodecyl sulfate but avoids the time-consuming step of electrophoresis. Therefore, TG limits the sample handling and is thus particularly suitable for high-throughput quantitative proteomics when large sample numbers have to be processed, as it is often the case in biomarker research and clinical proteomics projects.

Key words

Tube-gel Sample preparation High-throughput Detergent-compatibility Quantitative proteomics 

Notes

Acknowledgments

This work was supported by the French Proteomic Infrastructure (ProFI; ANR-10-INBS-08-03).

References

  1. 1.
    Lu X, Zhu H (2005) Tube-gel digestion: a novel proteomic approach for high throughput analysis of membrane proteins. Mol Cell Proteomics 4(12):1948–1958. https://doi.org/10.1074/mcp.M500138-MCP200CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    An M, Dai J, Wang Q et al (2010) Efficient and clean charge derivatization of peptides for analysis by mass spectrometry. Rapid Commun Mass Spectrom 24(13):1869–1874. https://doi.org/10.1002/rcm.4589CrossRefPubMedGoogle Scholar
  3. 3.
    Cao L, Clifton JG, Reutter W et al (2013) Mass spectrometry-based analysis of rat liver and hepatocellular carcinoma Morris hepatoma 7777 plasma membrane proteome. Anal Chem 85(17):8112–8120. https://doi.org/10.1021/ac400774gCrossRefPubMedGoogle Scholar
  4. 4.
    Cao R, He Q, Zhou J et al (2008) High-throughput analysis of rat liver plasma membrane proteome by a nonelectrophoretic in-gel tryptic digestion coupled with mass spectrometry identification. J Proteome Res 7(2):535–545. https://doi.org/10.1021/pr070411fCrossRefPubMedGoogle Scholar
  5. 5.
    Han CL, Chien CW, Chen WC et al (2008) A multiplexed quantitative strategy for membrane proteomics: opportunities for mining therapeutic targets for autosomal dominant polycystic kidney disease. Mol Cell Proteomics 7(10):1983–1997. https://doi.org/10.1074/mcp.M800068-MCP200CrossRefPubMedGoogle Scholar
  6. 6.
    Smolders K, Lombaert N, Valkenborg D et al (2015) An effective plasma membrane proteomics approach for small tissue samples. Sci Rep 5:10917. https://doi.org/10.1038/srep10917CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Yu H, Wakim B, Li M et al (2007) Quantifying raft proteins in neonatal mouse brain by ‘tube-gel’ protein digestion label-free shotgun proteomics. Proteome Sci 5:17. https://doi.org/10.1186/1477-5956-5-17CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Zhou J, Xiong J, Li J et al (2010) Gel absorption-based sample preparation for the analysis of membrane proteome by mass spectrometry. Anal Biochem 404(2):204–210. https://doi.org/10.1016/j.ab.2010.05.013CrossRefPubMedGoogle Scholar
  9. 9.
    Muller L, Fornecker L, Van Dorsselaer A et al (2016) Benchmarking sample preparation/digestion protocols reveals tube-gel being a fast and repeatable method for quantitative proteomics. Proteomics 16(23):2953–2961. https://doi.org/10.1002/pmic.201600288CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Leslie Muller
    • 1
  • Luc Fornecker
    • 1
  • Sarah Cianferani
    • 1
  • Christine Carapito
    • 1
    Email author
  1. 1.Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO)IPHC, UMR 7178, Université de Strasbourg, CNRSStrasbourgFrance

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