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Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging

Nature Methods volume 8, pages 933–935 (2011)Cite this article

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Abstract

We describe a mass spectrometry method, QuantMode, which improves accuracy of isobaric tag–based quantification by alleviating the pervasive problem of precursor interference, simultaneous isolation and fragmentation of impurities, through gas-phase purification. QuantMode analysis of a yeast sample 'contaminated' with interfering human peptides showed substantially improved quantitative accuracy compared to a standard scan, with a small loss of spectral identifications. This technique enables large-scale, multiplexed quantitative proteomics using isobaric tagging.

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Figure 1: Analysis of the precursor purity model and quantitative accuracy model samples with either HCD MS/MS or QuantMode.
Figure 2: Overview of QuantMode.

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Acknowledgements

We thank A.J. Bureta for figure illustrations, A. Williams for proofreading, A. Ledvina and D. Bailey for assistance with instrument firmware code modifications, S. Hubler for theoretical calculations regarding yeast and human peptides, J. Brumbaugh and J. Thomson for culturing the human cells, and J. Syka, J. Schwartz, V. Zabrouskov, J. Griep-Raming and D. Nolting for helpful discussions. This work was supported by US National Institutes of Health grant R01 GM080148 to J.J.C. D.H.P. acknowledges support from an National Institutes of Health Genomic Sciences Training Program (5T32HG002760).

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Authors and Affiliations

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

    Craig D Wenger, M Violet Lee, Graeme C McAlister, Douglas H Phanstiel & Joshua J Coon

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

    M Violet Lee, Alexander S Hebert, Michael S Westphall & Joshua J Coon

  3. Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA

    Alexander S Hebert & Joshua J Coon

Authors
  1. Craig D Wenger
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  2. M Violet Lee
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  3. Alexander S Hebert
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  4. Graeme C McAlister
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  5. Douglas H Phanstiel
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  6. Michael S Westphall
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  7. Joshua J Coon
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Contributions

C.D.W. designed and performed research, and wrote the paper; M.V.L., A.S.H. and G.C.M. designed and performed research; D.H.P. designed research; M.S.W. and J.J.C. designed research and wrote the paper.

Corresponding author

Correspondence to Joshua J Coon.

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Competing interests

Two patent applications, in part related to this manuscript, are pending: US 13/086638 (C.D.W., D.H.P. and J.J.C. are the inventors) and US 61/471461 (J.J.C. and M.S.W. are the inventors).

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Supplementary Figures 1–9, Supplementary Table 1, Supplementary Note, Supplementary Protocol (PDF 1940 kb)

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Wenger, C., Lee, M., Hebert, A. et al. Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging. Nat Methods 8, 933–935 (2011). https://doi.org/10.1038/nmeth.1716

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