Skip to main content

Thank you for visiting nature.com. 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.

  • Brief Communication
  • Published:

Identification of cross-linked peptides from large sequence databases

Nature Methods volume 5, pages 315–318 (2008)Cite this article

A Corrigendum to this article was published on 01 August 2008

This article has been updated

Abstract

NOTE: In the version of this Brief Communication initially published, an author name (Lukas Mueller) was incorrect. The correct author name is Lukas N Mueller. The error has been corrected in the HTML and PDF versions of the article.

We describe a method to identify cross-linked peptides from complex samples and large protein sequence databases by combining isotopically tagged cross-linkers, chromatographic enrichment, targeted proteomics and a new search engine called xQuest. This software reduces the search space by an upstream candidate-peptide search before the recombination step. We showed that xQuest can identify cross-linked peptides from a total Escherichia coli lysate with an unrestricted database search.

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

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Workflow of cross-link search with xQuest in the ion-tag mode.
Figure 2: Linear discriminant analysis separates true positive MS2 assignments to standard protein cross-links from false positive hits in a large peptide-interaction database.
Figure 3: Inter-protein and intra-protein cross-links were identified from a total E. coli lysate, searched against the total E. coli protein database.

Similar content being viewed by others

Change history

  • 27 June 2008

    In the version of this Brief Communication initially published, an author name (Lukas Mueller) was incorrect. The correct author name is Lukas N Mueller. The error has been corrected in the HTML and PDF versions of the article.

References

  1. Young, M.M. et al. Proc. Natl. Acad. Sci. USA 97, 5802–5806 (2000).

    Article  CAS  Google Scholar 

  2. Sinz, A. J. Mass Spectrom. 38, 1225–1237 (2003).

    Article  CAS  Google Scholar 

  3. Seebacher, J. et al. J. Proteome Res. 5, 2270–2282 (2006).

    Article  CAS  Google Scholar 

  4. Ihling, C. et al. J. Am. Soc. Mass Spectrom. 17, 1100–1113 (2006).

    Article  CAS  Google Scholar 

  5. Muller, D.R. et al. Anal. Chem. 73, 1927–1934 (2001).

    Article  CAS  Google Scholar 

  6. Dihazi, G.H. & Sinz, A. Rapid Commun. Mass Spectrom. 17, 2005–2014 (2003).

    Article  CAS  Google Scholar 

  7. Huang, B.X., Kim, H.Y. & Dass, C. J. Am. Soc. Mass Spectrom. 15, 1237–1247 (2004).

    Article  CAS  Google Scholar 

  8. Novak, P. et al. Anal. Chem. 77, 5101–5106 (2005).

    Article  CAS  Google Scholar 

  9. Pearson, K.M., Pannell, L.K. & Fales, H.M. Rapid Commun. Mass Spectrom. 16, 149–159 (2002).

    Article  CAS  Google Scholar 

  10. Gao, Q. et al. Anal. Chem. 78, 2145–2149 (2006).

    Article  CAS  Google Scholar 

  11. Schilling, B., Row, R.H., Gibson, B.W., Guo, X. & Young, M.M. J. Am. Soc. Mass Spectrom. 14, 834–850 (2003).

    Article  CAS  Google Scholar 

  12. de Koning, L.J. et al. FEBS J. 273, 281–291 (2006).

    Article  CAS  Google Scholar 

  13. Back, J.W., de Jong, L., Muijsers, A.O. & de Koster, C.G. J. Mol. Biol. 331, 303–313 (2003).

    Article  CAS  Google Scholar 

  14. Sinz, A., Kalkhof, S. & Ihling, C. J. Am. Soc. Mass Spectrom. 16, 1921–1931 (2005).

    Article  CAS  Google Scholar 

  15. Trester-Zedlitz, M. et al. J. Am. Chem. Soc. 125, 2416–2425 (2003).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

O.R. was supported by fellowships of the Deutsche Forschungsgemeinschaft and the Roche Research Foundation; M.B. was supported by a long-term fellowship of the European Molecular Biology Organization and a Marie Curie fellowship of the European Commission. A.S. was supported in part by a grant from F. Hoffmann–La Roche Ltd provided to the Competence Center for Systems Physiology and Metabolic Disease. The work was supported in part with Federal funds from the US National Heart, Lung and Blood Institute, National Institutes of Health (contract N01-HV-28179) and with funds from ETH Zurich.

Author information

Authors and Affiliations

  1. Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Wolfgang-Pauli Strasse 16, Zurich, 8093, Switzerland

    Oliver Rinner, Thomas Walzthoeni, Lukas N Mueller, Martin Beck, Alexander Schmidt, Markus Mueller & Ruedi Aebersold

  2. Institute for Systems Biology, 1441 North 34th Street, Seattle, 98103, Washington, USA

    Jan Seebacher & Ruedi Aebersold

  3. University of Innsbruck, Innrain 52, Innsbruck, A-6020, Austria

    Thomas Walzthoeni

  4. Faculty of Science, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland

    Alexander Schmidt & Ruedi Aebersold

Authors
  1. Oliver Rinner
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jan Seebacher
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Thomas Walzthoeni
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Lukas N Mueller
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Martin Beck
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Alexander Schmidt
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Markus Mueller
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Ruedi Aebersold
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

O.R. was responsible for most of the software design and programming, conducted most of the experiments and most of the data evaluation; J.S. synthesized the cross-linker and contributed to software design; T.W. contributed to scoring, data evaluation and part of experiments; L.N.M. analyzed and aligned MS1 data; M.B. performed part of experiments and evaluated data; A.S. designed mass spectrometric methods for analyzing cross-linked samples; M.M. contributed to scoring; R.A. coordinated the project, contributed ideas and concept.

Corresponding author

Correspondence to Ruedi Aebersold.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5, Supplementary Tables 1–2, Supplementary Results, Supplementary Discussion, Supplementary Methods (PDF 1982 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Rinner, O., Seebacher, J., Walzthoeni, T. et al. Identification of cross-linked peptides from large sequence databases. Nat Methods 5, 315–318 (2008). https://doi.org/10.1038/nmeth.1192

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nmeth.1192

This article is cited by

Search

Advanced search

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