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Multiplexed proteome analysis with neutron-encoded stable isotope labeling in cells and mice

Nature Protocols volume 13, pages 293306 (2018) | Download Citation

Abstract

We describe a protocol for multiplexed proteomic analysis using neutron-encoded (NeuCode) stable isotope labeling of amino acids in cells (SILAC) or mice (SILAM). This method currently enables simultaneous comparison of up to nine treatment and control proteomes. Another important advantage over traditional SILAC/SILAM is that shorter labeling times are required. Exploiting the small mass differences that correspond to subtle differences in the neutron-binding energies of different isotopes, the amino acids used in NeuCode SILAC/SILAM differ in mass by just a few milliDaltons. Isotopologs of lysine are introduced into cells or mammals, via the culture medium or diet, respectively, to metabolically label the proteome. Labeling time is 2 weeks for cultured cells and 3–4 weeks for mammals. The proteins are then extracted, relevant samples are combined, and these are enzymatically digested with lysyl endopeptidase (Lys-C). The resultant peptides are chromatographically separated and then mass analyzed. During mass spectrometry (MS) data acquisition, high-resolution MS1 spectra (≥240,000 resolving power at m/z = 400) reveal the embedded isotopic signatures, enabling relative quantification, while tandem mass spectra, collected at lower resolutions, provide peptide identities. Both types of spectra are processed using NeuCode-enabled MaxQuant software. In total, the approximate completion time for the protocol is 3–5 weeks.

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Acknowledgements

We are grateful to M. Rush for comments during the writing process. This work was supported by the National Institutes of Health (P41 GM108538). K.A.O. gratefully acknowledges the support from a US National Library of Medicine training grant (5T15LM007359).

Author information

Affiliations

  1. Genome Center, University of Wisconsin–Madison, Madison, Wisconsin, USA.

    • Katherine A Overmyer
    • , Alex S Hebert
    • , Michael S Westphall
    •  & Joshua J Coon
  2. Morgridge Institute for Research, Madison, Wisconsin, USA.

    • Katherine A Overmyer
    •  & Joshua J Coon
  3. Max Planck Institute of Biochemistry, Martinsried, Germany.

    • Stefka Tyanova
    •  & Jürgen Cox
  4. Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA.

    • Joshua J Coon
  5. Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA.

    • Joshua J Coon

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Contributions

S.T. and J.C. developed the MaxQuant analysis tool. K.A.O., A.S.H., and M.S.W. analyzed the data. K.A.O., A.S.H., J.C., and J.J.C. wrote the manuscript.

Competing interests

A.S.H. and J.J.C. are co-inventors on a patent application (US 13/660677) related in part to the material presented here. The other authors declare no competing financial interests.

Corresponding author

Correspondence to Joshua J Coon.

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DOI

https://doi.org/10.1038/nprot.2017.121

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