Skip to main content
SpringerLink
Log in

A cross-platform toolkit for mass spectrometry and proteomics

  • Correspondence
  • Published:

From Nature Biotechnology

View current issue Submit your manuscript

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: Design of ProteoWizard.

References

  1. Schwanhausser, B. et al. Nature 473, 337–342 (2011).

    Article  Google Scholar 

  2. Raj, L. et al. Nature 475, 231–234 (2011).

    Article  CAS  Google Scholar 

  3. Bouwmeester, T. et al. Nat. Cell Biol. 6, 97–105 (2004).

    Article  CAS  Google Scholar 

  4. Patterson, S.D. Nat. Biotechnol. 21, 221–222 (2003).

    Article  CAS  Google Scholar 

  5. Askenazi, M., Parikh, J.R. & Marto, J.A. Nat. Methods 6, 240–241 (2009).

    Article  CAS  Google Scholar 

  6. Pedrioli, P.G. et al. Nat. Biotechnol. 22, 1459–1466 (2004).

    Article  CAS  Google Scholar 

  7. Orchard, S. et al. Proteomics 10, 1895–1898 (2010).

    Article  CAS  Google Scholar 

  8. Kessner, D., Chambers, M., Burke, R., Agus, D. & Mallick, P. Bioinformatics 24, 2534–2536 (2008).

    Article  CAS  Google Scholar 

  9. Sturm, M. et al. BMC Bioinformatics 9, 163 (2008).

    Article  Google Scholar 

  10. Apache.Software.Foundation 2004. http://www.apache.org/licenses/LICENSE-2.0.html.

  11. Martens, L. et al. Mol. Cell. Proteomics 10, R110 000133 (2011).

    Article  Google Scholar 

  12. Eisenacher, M. Methods Mol. Biol. 696, 161–177 (2011).

    Article  CAS  Google Scholar 

  13. Benton, H.P., Wong, D.M., Trauger, S.A. & Siuzdak, G. Anal. Chem. 80, 6382–6389 (2008).

    Article  CAS  Google Scholar 

  14. Luethy, R. et al. J. Proteome Res. 7, 4031–4039 (2008).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work is supported by the Wunderkinder Foundation, Redstone Family Foundation and Canary Foundation, and the National Cancer Institute and US National Institutes of Health grants and contracts P41 RR011823, CCNE-TR 5U54CA119367, CCNE-T 1U54CA151459, PSOC-MCSTART 5U54CA143907, R01CA126218 and U24CA126479. R.L.M. and C.P. have been supported by National Science Foundation MRI grant No. 0923536. L.G. has been supported by the European Union 7th Framework Program PRIME-XS project, grant agreement number 262067. The authors also thank the ProteoWizard developer community and TPP developer community for their contributions to the project and manuscript.

Author information

Author notes

  1. Matthew C Chambers, Brendan Maclean and Robert Burke: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, USA

    Matthew C Chambers & David L Tabb

  2. Department of Genome Sciences, University of Washington, Seattle, Washington, USA

    Brendan Maclean, Jarrett Egertson, Nicholas Shulman, Barbara Frewen, Tahmina A Baker & Michael MacCoss

  3. Center for Applied Molecular Medicine, University of Southern California, Los Angeles, California, USA

    Robert Burke, Daniel L Ruderman, Katherine Hoff, Darren Kessner, Lisa Flashner, Kian Kani, Jonathan E Katz, David B Agus & Parag Mallick

  4. Canary Center for Cancer Early Detection, Stanford University, Stanford, California, USA

    Dario Amodei & Parag Mallick

  5. Department of Stress & Developmental Biology, Leibniz Institute for Plant Biochemistry, Halle (Saale), Germany

    Steffen Neumann

  6. Proteomics Services, Cambridge Centre for Proteomics, Cambridge, England

    Laurent Gatto

  7. Genome Biology, EMBL Heidelberg, Germany

    Bernd Fischer

  8. Insilicos, Seattle, Washington, USA

    Brian Pratt & Natalie Tasman

  9. Institute for Systems Biology, Seattle, Washington, USA

    Mi-Youn Brusniak, Christopher Paulse, Eric W Deutsch & Robert L Moritz

  10. Matrix Science, Boston, Massachusetts, USA

    David Creasy

  11. USC Stevens Institute for Innovation, University of Southern California, Los Angeles, California, USA

    Chris Moulding & Krisztina Holly

  12. AB SCIEX, Foster City, California, USA

    Sean L Seymour, Lydia M Nuwaysir & Brent Lefebvre

  13. Agilent Technologies, Santa Clara, California, USA

    Frank Kuhlmann & Joe Roark

  14. Bruker Daltonik GmbH, Bremen, Germany

    Paape Rainer & Suckau Detlev

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

    Tina Hemenway & Andreas Huhmer

  16. Waters Corporation, Manchester, UK

    James Langridge

  17. LabKey Software, Seattle, Washington, USA

    Brian Connolly, Trey Chadick & Josh Eckels

Authors
  1. Matthew C Chambers
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Brendan Maclean
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Robert Burke
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Dario Amodei
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Daniel L Ruderman
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Steffen Neumann
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Laurent Gatto
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Bernd Fischer
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Brian Pratt
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Jarrett Egertson
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Katherine Hoff
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Darren Kessner
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Natalie Tasman
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Nicholas Shulman
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Barbara Frewen
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Tahmina A Baker
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Mi-Youn Brusniak
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Christopher Paulse
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. David Creasy
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. Lisa Flashner
    View author publications

    You can also search for this author in PubMed Google Scholar

  21. Kian Kani
    View author publications

    You can also search for this author in PubMed Google Scholar

  22. Chris Moulding
    View author publications

    You can also search for this author in PubMed Google Scholar

  23. Sean L Seymour
    View author publications

    You can also search for this author in PubMed Google Scholar

  24. Lydia M Nuwaysir
    View author publications

    You can also search for this author in PubMed Google Scholar

  25. Brent Lefebvre
    View author publications

    You can also search for this author in PubMed Google Scholar

  26. Frank Kuhlmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  27. Joe Roark
    View author publications

    You can also search for this author in PubMed Google Scholar

  28. Paape Rainer
    View author publications

    You can also search for this author in PubMed Google Scholar

  29. Suckau Detlev
    View author publications

    You can also search for this author in PubMed Google Scholar

  30. Tina Hemenway
    View author publications

    You can also search for this author in PubMed Google Scholar

  31. Andreas Huhmer
    View author publications

    You can also search for this author in PubMed Google Scholar

  32. James Langridge
    View author publications

    You can also search for this author in PubMed Google Scholar

  33. Brian Connolly
    View author publications

    You can also search for this author in PubMed Google Scholar

  34. Trey Chadick
    View author publications

    You can also search for this author in PubMed Google Scholar

  35. Krisztina Holly
    View author publications

    You can also search for this author in PubMed Google Scholar

  36. Josh Eckels
    View author publications

    You can also search for this author in PubMed Google Scholar

  37. Eric W Deutsch
    View author publications

    You can also search for this author in PubMed Google Scholar

  38. Robert L Moritz
    View author publications

    You can also search for this author in PubMed Google Scholar

  39. Jonathan E Katz
    View author publications

    You can also search for this author in PubMed Google Scholar

  40. David B Agus
    View author publications

    You can also search for this author in PubMed Google Scholar

  41. Michael MacCoss
    View author publications

    You can also search for this author in PubMed Google Scholar

  42. David L Tabb
    View author publications

    You can also search for this author in PubMed Google Scholar

  43. Parag Mallick
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Parag Mallick.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Text 1–3, Supplementary Examples 1–5 and Supplementary Tables 1–4 (PDF 1272 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Chambers, M., Maclean, B., Burke, R. et al. A cross-platform toolkit for mass spectrometry and proteomics. Nat Biotechnol 30, 918–920 (2012). https://doi.org/10.1038/nbt.2377

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt.2377

  • Springer Nature America, Inc.

This article is cited by

Search

Navigation