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

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. Access through your institution Buy or subscribe This is a preview of subscription content, access via your institution ACCESS OPTIONS Access through your

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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). AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * 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 * Genome Center of Wisconsin, University of Wisconsin–Madison, Madison, Wisconsin, USA M Violet Lee, Alexander S

Hebert, Michael S Westphall & Joshua J Coon * Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA Alexander S Hebert & Joshua J Coon

Authors * Craig D Wenger View author publications You can also search for this author inPubMed Google Scholar * M Violet Lee View author publications You can also search for this author

inPubMed Google Scholar * Alexander S Hebert View author publications You can also search for this author inPubMed Google Scholar * Graeme C McAlister View author publications You can also

search for this author inPubMed Google Scholar * Douglas H Phanstiel View author publications You can also search for this author inPubMed Google Scholar * Michael S Westphall View author

publications You can also search for this author inPubMed Google Scholar * Joshua J Coon View author publications You can also search for this author inPubMed Google Scholar 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. ETHICS DECLARATIONS 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). SUPPLEMENTARY INFORMATION SUPPLEMENTARY TEXT AND FIGURES Supplementary Figures

1–9, Supplementary Table 1, Supplementary Note, Supplementary Protocol (PDF 1940 kb) RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE 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 Download citation * Received: 17 March 2011 * Accepted: 19 August 2011 * Published: 02 October 2011 * Issue Date: November 2011 * DOI:

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