Abstract
Quantitative mass spectrometry–based proteomics is highly versatile but not easily multiplexed. Isobaric labeling strategies allow mass spectrometry–based multiplexed proteome quantification; however, ratio distortion owing to protein quantification interference is a common effect. We present a two-proteome model (mixture of human and yeast proteins) in a sixplex isobaric labeling system to fully document the interference effect, and we report that applying triple-stage mass spectrometry (MS3) almost completely eliminates interference.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Aebersold, R. & Mann, M. Nature 422, 198–207 (2003).
Ross, P.L. et al. Mol. Cell Proteomics 3, 1154–1169 (2004).
Dayon, L. et al. Anal. Chem. 80, 2921–2931 (2008).
Thompson, A. et al. Anal. Chem. 75, 1895–1904 (2003).
Choe, L. et al. Proteomics 7, 3651–3660 (2007).
Bantscheff, M. et al. Mol. Cell Proteomics 7, 1702–1713 (2008).
Karp, N.A. et al. Mol. Cell Proteomics 9, 1885–1897 (2010).
Ow, S.Y. et al. J. Proteome Res. 8, 5347–5355 (2009).
Shirran, S.L. & Botting, C.H. J. Proteomics 73, 1391–1403 (2010).
Villén, J. & Gygi, S.P. Nat. Protoc. 3, 1630–1638 (2008).
Olsen, J.V. et al. Nat. Methods 4, 709–712 (2007).
Elias, J.E. & Gygi, S.P. Nat. Methods 4, 207–214 (2007).
Huttlin, E.L. et al. Cell 143, 1174–1189 (2010).
Beausoleil, S.A. et al. Proc. Natl. Acad. Sci. USA 101, 12130–12135 (2004).
Eng, J.K., McCormack, A.L. & Yates, J.R. III. J. Am. Soc. Mass Spectrom. 5, 976–989 (1994).
Acknowledgements
This work was supported in part by US National Institutes of Health grants (HG3456 and GM67945) to S.P.G.
Author information
Authors and Affiliations
Contributions
L.T., S.P.G. and W.H. designed experiments, analyzed data and wrote the paper. L.T. and W.H. performed experiments. R.R. developed software for data analysis.
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Supplementary information
Supplementary Text and Figures
Supplementary Figures 1–6 and Supplementary Table 1 (PDF 831 kb)
Supplementary Data
All yeast and human identification and quantification data. (XLSX 57496 kb)
Rights and permissions
About this article
Cite this article
Ting, L., Rad, R., Gygi, S. et al. MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat Methods 8, 937–940 (2011). https://doi.org/10.1038/nmeth.1714
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/nmeth.1714
