Skip to main content
SpringerLink
Log in

Multiplexed MS/MS for improved data-independent acquisition

  • Brief Communication
  • Published:

From Nature Methods

View current issue Submit your manuscript

Abstract

In mass spectrometry–based proteomics, data-independent acquisition (DIA) strategies can acquire a single data set useful for both identification and quantification of detectable peptides in a complex mixture. However, DIA data are noisy owing to a typical five- to tenfold reduction in precursor selectivity compared to data obtained with data-dependent acquisition or selected reaction monitoring. We demonstrate a multiplexing strategy, MSX, for DIA analysis that increases precursor selectivity fivefold.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1: Multiplexed data-independent acquisition with MSX.
Figure 2: Demultiplexing reduces chemical noise and improves selectivity.
Figure 3: Quantitation of the LVNELTEFAK peptide by MSX and MS1.

Similar content being viewed by others

Accession codes

Accessions

GenBank/EMBL/DDBJ

References

  1. Stahl, D.C., Swiderek, K.M., Davis, M.T. & Lee, T.D. J. Am. Soc. Mass Spectrom. 7, 532–540 (1996).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  3. Michalski, A., Cox, J. & Mann, M. J. Proteome Res. 10, 1785–1793 (2011).

    Article  CAS  Google Scholar 

  4. Wenner, B.R. & Lynn, B.C. J. Am. Soc. Mass Spectrom. 15, 150–157 (2004).

    Article  CAS  Google Scholar 

  5. Hoopmann, M.R., Finney, G.L. & MacCoss, M.J. Anal. Chem. 79, 5620–5632 (2007).

    Article  CAS  Google Scholar 

  6. Purvine, S., Eppel, J.T., Yi, E.C. & Goodlett, D.R. Proteomics 3, 847–850 (2003).

    Article  CAS  Google Scholar 

  7. Myung, S. et al. Anal. Chem. 75, 5137–5145 (2003).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  9. Panchaud, A. et al. Anal. Chem. 81, 6481–6488 (2009).

    Article  CAS  Google Scholar 

  10. Weisbrod, C.R., Eng, J.K., Hoopmann, M.R., Baker, T. & Bruce, J.E. J. Proteome Res. 11, 1621–1632 (2012).

    Article  CAS  Google Scholar 

  11. Gillet, L.C. et al. Mol. Cell Proteomics 11, O111.016717 (2012).

    Article  Google Scholar 

  12. Williams, E.R., Loh, S.Y., McLafferty, F.W. & Cody, R.B. Anal. Chem. 62, 698–703 (1990).

    Article  CAS  Google Scholar 

  13. MacLean, B. et al. Bioinformatics 26, 966–968 (2010).

    Article  CAS  Google Scholar 

  14. US National Institute of Standards and Technology. NIST Peptide Tandem Mass Spectral Libraries (eds. Stein, S.E. & Rudnick, P.A.) 〈http://peptide.nist.gov/〉 (2009; 24 May 2011 builds).

  15. Yost, R.A. & Enke, C.G. Anal. Chem. 51, 1251–1264 (1979).

    Article  CAS  Google Scholar 

  16. Frahm, J.L., Howard, B.E., Heber, S. & Muddiman, D.C. J. Mass Spectrom. 41, 281–288 (2006).

    Article  CAS  Google Scholar 

  17. Gay, S., Binz, P.A., Hochstrasser, D.F. & Appel, R.D. Electrophoresis 20, 3527–3534 (1999).

    Article  CAS  Google Scholar 

  18. Frewen, B.E., Merrihew, G.E., Wu, C.C., Noble, W.S. & MacCoss, M.J. Anal. Chem. 78, 5678–5684 (2006).

    Article  CAS  Google Scholar 

  19. Lawson, C.L. & Hanson, R.J. Solving Least Squares Problems (Society for Industrial and Applied Mathematics, Philadelphia, 1995).

  20. Chambers, M.C. et al. Nat. Biotechnol. 30, 918–920 (2012).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors acknowledge financial support from US National Institutes of Health grants R01 GM103551, P41 GM103533 and F31 AG037265.

Author information

Authors and Affiliations

  1. Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA

    Jarrett D Egertson, Gennifer E Merrihew, Brendan X MacLean, Ying S Ting, Donald M Marsh & Michael J MacCoss

  2. Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany

    Andreas Kuehn & Markus Kellmann

  3. Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA

    Nicholas W Bateman & Christine C Wu

  4. Thermo Fisher Scientific, San Jose, California, USA

    Jesse D Canterbury & Vlad Zabrouskov

Authors
  1. Jarrett D Egertson
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Andreas Kuehn
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gennifer E Merrihew
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Nicholas W Bateman
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Brendan X MacLean
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ying S Ting
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Jesse D Canterbury
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Donald M Marsh
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Markus Kellmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Vlad Zabrouskov
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Christine C Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Michael J MacCoss
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

A.K., C.C.W., J.D.C., J.D.E., M.J.M., M.K., V.Z. and Y.S.T. designed experiments. A.K., C.C.W., J.D.E., M.J.M., M.K., N.W.B. and V.Z. interpreted results. J.D.E. and M.J.M. wrote the manuscript. A.K. created a firmware modification for the Q-Exactive. A.K. and M.K. provided preliminary data. G.E.M., J.D.E. and N.W.B. performed experiments. B.X.M., D.M.M. and J.D.E. wrote software.

Corresponding author

Correspondence to Michael J MacCoss.

Ethics declarations

Competing interests

All authors received financial support from Thermo Fisher Scientific. A.K., J.D.C., M.K. and V.Z. are employees of Thermo Fisher Scientific, the company that markets and sells the mass spectrometry instrumentation used in this manuscript. Thermo Fisher will make the methods described herein available to their customers in version 2.2 SP1 of the Q-Exactive software.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8, Supplementary Tables 1 and 2, Supplementary Data and Supplementary Note (PDF 3353 kb)

Supplementary Video 1

Demonstration of multiplexed data-independent acquisition (MSX) and demultiplexing (MOV 5308 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Egertson, J., Kuehn, A., Merrihew, G. et al. Multiplexed MS/MS for improved data-independent acquisition. Nat Methods 10, 744–746 (2013). https://doi.org/10.1038/nmeth.2528

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nmeth.2528

  • Springer Nature America, Inc.

This article is cited by

Search

Navigation