Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Digestion and depletion of abundant proteins improves proteomic coverage

An Addendum to this article was published on 27 February 2014


Two major challenges in proteomics are the large number of proteins and their broad dynamic range in the cell. We exploited the abundance-dependent Michaelis-Menten kinetics of trypsin digestion to selectively digest and deplete abundant proteins with a method we call DigDeAPr. We validated the depletion mechanism with known yeast protein abundances, and we observed greater than threefold improvement in low-abundance human-protein identification and quantitation metrics. This methodology should be broadly applicable to many organisms, proteases and proteomic pipelines.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Schematic and description of the DigDeAPr method.
Figure 2: Analysis of proteomic metric improvements from DigDeAPr on HEK cell lysates.
Figure 3: Analysis of proteomic metrics relevant to MS- and MS/MS-based quantitation.


  1. Cravatt, B.F., Simon, G.M. & Yates, J.R. III. Nature 450, 991–1000 (2007).

    CAS  Article  Google Scholar 

  2. Nilsson, T. et al. Nat. Methods 7, 681–685 (2010).

    CAS  Article  Google Scholar 

  3. Washburn, M.P., Wolters, D. & Yates, J.R. III. Nat. Biotechnol. 19, 242–247 (2001).

    CAS  Article  Google Scholar 

  4. MacCoss, M.J. et al. Proc. Natl. Acad. Sci. USA 99, 7900–7905 (2002).

    CAS  Article  Google Scholar 

  5. Choudhary, G., Wu, S.L., Shieh, P. & Hancock, W.S. J. Proteome Res. 2, 59–67 (2003).

    CAS  Article  Google Scholar 

  6. Swaney, D.L., Wenger, C.D. & Coon, J.J. J. Proteome Res. 9, 1323–1329 (2010).

    CAS  Article  Google Scholar 

  7. Tran, B.Q. et al. J. Proteome Res. 10, 800–811 (2011).

    CAS  Article  Google Scholar 

  8. Manza, L.L., Stamer, S.L., Ham, A.J., Codreanu, S.G. & Liebler, D.C. Proteomics 5, 1742–1745 (2005).

    CAS  Article  Google Scholar 

  9. Wu, C.C., MacCoss, M.J., Howell, K.E. & Yates, J.R. III. Nat. Biotechnol. 21, 532–538 (2003).

    CAS  Article  Google Scholar 

  10. Blonder, J., Chan, K.C., Issaq, H.J. & Veenstra, T.D. Nat. Protoc. 1, 2784–2790 (2006).

    CAS  Article  Google Scholar 

  11. Wu, C. et al. Nat. Methods 9, 822–824 (2012).

    CAS  Article  Google Scholar 

  12. Picotti, P., Aebersold, R. & Domon, B. Mol. Cell. Proteomics 6, 1589–1598 (2007).

    CAS  Article  Google Scholar 

  13. Liu, H., Sadygov, R.G. & Yates, J.R. III. Anal. Chem. 76, 4193–4201 (2004).

    CAS  Article  Google Scholar 

  14. Jmeian, Y. & El Rassi, Z. Electrophoresis 30, 249–261 (2009).

    CAS  Article  Google Scholar 

  15. Liebler, D.C. & Ham, A.J. Nat. Methods 6, 785 (2009).

    CAS  Article  Google Scholar 

  16. McDonald, W.H. et al. Rapid Commun. Mass Spectrom. 18, 2162–2168 (2004).

    CAS  Article  Google Scholar 

  17. Xu, T. et al. Mol. Cell. Proteomics 5, S174 (2006).

    Google Scholar 

  18. Tabb, D.L., McDonald, W.H. & Yates, J.R. III. J. Proteome Res. 1, 21–26 (2002).

    CAS  Article  Google Scholar 

  19. Cociorva, D., Tabb, D.L. & Yates, J.R. Curr. Protoc. Bioinformatics 16, 13.4 (2007).

    Google Scholar 

  20. Wong, C.C., Cociorva, D., Venable, J.D., Xu, T. & Yates, J.R. III. J. Am. Soc. Mass Spectrom. 20, 1405–1414 (2009).

    CAS  Article  Google Scholar 

  21. Park, S.K., Venable, J.D., Xu, T. & Yates, J.R. III. Nat. Methods 5, 319–322 (2008).

    CAS  Article  Google Scholar 

  22. Fonslow, B.R. et al. J. Proteome Res. 10, 3690–3700 (2011).

    CAS  Article  Google Scholar 

Download references


This project was supported by the US National Center for Research Resources (5P41RR011823-17), National Institute of General Medical Sciences (8P41GM103533-17), National Institute of Diabetes and Digestive and Kidney Diseases (R01DK074798), National Heart, Lung, and Blood Institute (RFP-NHLBI-HV-10-5) and National Institute of Mental Health (R01MH067880). We thank J.N. Savas, C.M. Delahunty and J.K. Diedrich for comments on the manuscript.

Author information

Authors and Affiliations



B.R.F. designed experiments, performed experiments, analyzed data and wrote the manuscript. B.D.S. prepared HEK cell lysates and provided conceptual advice. K.J.W. prepared yeast lysates. T.X., J.C. and S.K.P. developed software for data analysis. J.R.Y. wrote the manuscript and provided conceptual guidance.

Corresponding author

Correspondence to John R Yates III.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8 and Supplementary Notes 1–6 (PDF 726 kb)

Supplementary Data

Protein and peptide raw data and comparisons from yeast and HEK-cell control and DigDeAPr analyses. (XLSX 49758 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Fonslow, B., Stein, B., Webb, K. et al. Digestion and depletion of abundant proteins improves proteomic coverage. Nat Methods 10, 54–56 (2013).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing