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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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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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.
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The authors declare no competing financial interests.
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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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DOI: https://doi.org/10.1038/nmeth.1714
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