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MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

Nature Methods volume 8, pages 937–940 (2011)Cite this article

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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.

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Figure 1: Isobaric labeling, interference and interference modeling.
Figure 2: Evaluation and attempted removal of the interference effect.
Figure 3: An MS3-based method eliminates the interference effect.

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Acknowledgements

This work was supported in part by US National Institutes of Health grants (HG3456 and GM67945) to S.P.G.

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Authors and Affiliations

  1. Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA

    Lily Ting, Ramin Rad, Steven P Gygi & Wilhelm Haas

Authors
  1. Lily Ting
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  2. Ramin Rad
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  3. Steven P Gygi
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  4. Wilhelm Haas
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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

Correspondence to Steven P Gygi or Wilhelm Haas.

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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)

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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

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