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A quantitative analysis software tool for mass spectrometry–based proteomics

Nature Methods volume 5, pages 319–322 (2008)Cite this article

Abstract

We describe Census, a quantitative software tool compatible with many labeling strategies as well as with label-free analyses, single-stage mass spectrometry (MS1) and tandem mass spectrometry (MS/MS) scans, and high- and low-resolution mass spectrometry data. Census uses robust algorithms to address poor-quality measurements and improve quantitative efficiency, and it can support several input file formats. We tested Census with stable-isotope labeling analyses as well as label-free analyses.

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Figure 1: Schematic detailing the quantitative analysis capabilities of Census.
Figure 2: Use of high mass accuracy for improved quantification with Census.
Figure 3: Expected and measured relative abundances of technical replicates of a 10-protein mix dataset using Census.

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References

  1. Makarov, A. et al. Anal. Chem. 78, 2113–2120 (2006).

    Article  CAS  Google Scholar 

  2. Olsen, J.V. et al. Mol. Cell. Proteomics 4, 2010–2021 (2005).

    Article  CAS  Google Scholar 

  3. Yates, J.R., Cociorva, D., Liao, L. & Zabrouskov, V. Anal. Chem. 78, 493–500 (2006).

    Article  CAS  Google Scholar 

  4. Denison, C. et al. Mol. Cell. Proteomics 4, 246–254 (2005).

    Article  CAS  Google Scholar 

  5. Dieguez-Acuna, F.J. et al. Mol. Cell. Proteomics 4, 1459–1470 (2005).

    Article  CAS  Google Scholar 

  6. Foster, L.J., Hoog, C.L.d. & Mann, M. Proc. Natl. Acad. Sci. 100, 5813–5818 (2003).

    Article  CAS  Google Scholar 

  7. Venable, J.D., Wohlschlegel, J., McClatchy, D.B., Park, S.K. & Yates, J.R. III. Anal. Chem. 79, 3056–3064 (2007).

    Article  CAS  Google Scholar 

  8. Eng, J.K., McCormack, A.L. & Yates, J.R., III . J. Am. Soc. Mass Spectrom. 5, 976–989 (1994).

    Article  CAS  Google Scholar 

  9. Sadygov, R.G. & Yates, J.R., III . Anal. Chem. 75, 3792–3798 (2003).

    Article  CAS  Google Scholar 

  10. Tabb, D.L., Saraf, A. & Yates, J.R., III . Anal. Chem. 75, 6415–6421 (2003).

    Article  CAS  Google Scholar 

  11. Geer, L.Y. et al. J. Proteome Res. 3, 958–964 (2004).

    Article  CAS  Google Scholar 

  12. Ong, S.E. & Mann, M. Nat. Chem. Biol. 1, 252–262 (2005).

    Article  CAS  Google Scholar 

  13. Domon, B. & Aebersold, R. Science 312, 212–217 (2006).

    Article  CAS  Google Scholar 

  14. MacCoss, M.J., Wu, C.C. & Yates, J.R., III . Anal. Chem. 75, 6912–6921 (2003).

    Article  CAS  Google Scholar 

  15. Venable, J.D., Dong, M.Q., Wohlschlegel, J., Dillin, A. & Yates, J.R. Nat. Methods 1, 39–45 (2004).

    Article  CAS  Google Scholar 

  16. Owens, K.G. Appl. Spectrosc. Rev. 27, 1–49 (1992).

    Article  Google Scholar 

  17. Arnott, D. et al. Mol. Cell. Proteomics 1, 148–156 (2002).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank J. Wohlschlegel and D. Cociorva for their comments and discussions about the manuscript, M. MacCoss for his insights and work developing RelEx, S. Agarwalla and D. McMullan for sample preparation. S.K.P. is supported by US National Institutes of Health (NIH) National Institute of Allergy and Infectious Diseases (UOM/DMID-BAA-03). J.D.V. is supported by a National Research Service Award (NIH) fellowship. T.X. is supported by NIH (DE016267). J.R.Y. is supported by NIH (P41 RR011823, R01 MH067880 and R01 HL079442).

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Author notes

  1. Sung Kyu Park and John D Venable: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, SR11, La Jolla, 92014, California, USA

    Sung Kyu Park, John D Venable, Tao Xu & John R Yates III

Authors
  1. Sung Kyu Park
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  2. John D Venable
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  3. Tao Xu
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  4. John R Yates III
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Contributions

S.K.P. developed the algorithm and applications; J.D.V. prepared yeast cell lysates, 10 protein standard mixtures, iTRAQ samples and developed algorithms; T.X. contributed to discussions on algorithms; J.R.Y. led and coordinated the project.

Corresponding author

Correspondence to John R Yates III.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8, Supplementary Tables 1–6, Supplementary Methods (PDF 673 kb)

Supplementary Data

Quantitative analysis results obtained from Census for 1:1 mixture of unlabeled and metabolically 15N labeled yeast standards. (ZIP 145 kb)

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Park, S., Venable, J., Xu, T. et al. A quantitative analysis software tool for mass spectrometry–based proteomics. Nat Methods 5, 319–322 (2008). https://doi.org/10.1038/nmeth.1195

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