Location via proxy:   [ UP ]  
[Report a bug]   [Manage cookies]                
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.

  • Correspondence
  • Published:

ProHits: integrated software for mass spectrometry–based interaction proteomics

Nature Biotechnology volume 28, pages 1015–1017 (2010)Cite this article

Subjects

To the Editor:

Affinity purification coupled with mass spectrometric identification (AP-MS) is now a method of choice for charting novel protein-protein interactions and has been applied to a large number of both small-scale and high-throughput studies1. However, general and intuitive computational tools for sample tracking, AP-MS data analysis and annotation have not kept pace with rapid methodological and instrument improvements. To address this need, we have developed the ProHits laboratory information management system platform.

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

Relevant articles

Open Access articles citing this article.

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: Overview of ProHits.

References

  1. Gingras, A.C., Gstaiger, M., Raught, B. & Aebersold, R. Nat. Rev. Mol. Cell Biol 8, 645–654 (2007).

    Article  CAS  Google Scholar 

  2. Taylor, C.F. et al. (MIAPE). Nat. Biotechnol. 25, 887–893 (2007).

    Article  CAS  Google Scholar 

  3. Perkins, D.N., Pappin, D.J., Creasy, D.M. & Cottrell, J.S. Electrophoresis 20, 3551–3567 (1999).

    Article  CAS  Google Scholar 

  4. Craig, R. & Beavis, R.C. Bioinformatics 20, 1466–1467 (2004).

    Article  CAS  Google Scholar 

  5. Keller, A., Eng, J., Zhang, N., Li, X.J. & Aebersold, R. Mol. Syst. Biol. 1, 2005 0017 (2005).

    Article  Google Scholar 

  6. Ewing, R.M. et al. Mol. Syst. Biol. 3, 89 (2007).

    Article  Google Scholar 

  7. Orchard, S. et al. Nat. Biotechnol. 25, 894–898 (2007).

    Article  CAS  Google Scholar 

  8. Breitkreutz, B.J. et al. Nucleic Acids Res. 36, D637–640 (2008).

    Article  CAS  Google Scholar 

  9. Shannon, P. et al. Genome Res. 13, 2498–2504 (2003).

    Article  CAS  Google Scholar 

  10. Cottingham, K. J. Proteome Res. 8, 4887–4888 (2009).

    Article  CAS  Google Scholar 

  11. Hermjakob, H. et al. Nat. Biotechnol. 22, 177–183 (2004).

    Article  CAS  Google Scholar 

  12. Orchard, S. et al. Proteomics 7 Suppl 1, 28–34 (2007).

    Article  Google Scholar 

  13. Kerrien, S. et al. Nucleic Acids Res. 35, D561–565 (2007).

    Article  CAS  Google Scholar 

  14. Falkner, J.A., Hill, J.A. & Andrews, P.C. Proteomics 8, 1756–1757 (2008).

    Article  CAS  Google Scholar 

  15. Breitkreutz, A. et al. Science 328, 1043–1046 (2010).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank G. Bader, H. Hermjakob, S. Orchard, J.A. Vizcaíno, C. Le Roy, R. Beavis and members of the Tyers and Gingras laboratories for helpful discussions. We are grateful to D. Figeys, S. Angers, D. Fermin, T. LeBihan, F. Ellisma, C. Poitras and B. Coulombe for testing beta versions of ProHits. We thank W. Dunham, E. Deutsch, D. Fermin, T. Glatter, M. Goudreault, L. D'Ambrosio and R. Ewing for critical reading of the manuscript and instruction manual and L. Ng, J. Wei and N. Mohammad for IT support. Supported by grants from the CIHR (MOP-84314 to A.-C.G., MOP-12246 to M.T., MOP-81268 to B.R., GSP-36651 to T.P., J.L.W. and M.T., FRN 82940 to M.T. and a resource grant to T.P., A.-C.G., J.L.W. and M.T.), the NIH (5R01RR024031 to M.T., 1R01GM094231-01 to A.I.N. and A.-C.G., and CA-126239 to A.I.N.), MRI-ORF (T.P., J.L.W. and A.-C.G.), the Canada Foundation for Innovation (T.P., J.L.W., A.-C.G. and M.T.), and Genome Canada through Ontario Genomics Institute (T.P. and J.L.W.). We wish to acknowledge support from the Mount Sinai Hospital Foundation; Canada Research Chairs in Functional Genomics and Bioinformatics to M.T., in Proteomics and Molecular Medicine to B.R., and in Functional Proteomics to A.-C.G.; the Lea Reichmann Chair in Cancer Proteomics to A.-C.G. and a Scottish Universities Life Sciences Alliance Research Professorship and a Royal Society Wolfson Research Merit Award to M.T.

Author information

Authors and Affiliations

  1. Centre for Systems Biology, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada

    Guomin Liu, Jianping Zhang, Brett Larsen, Chris Stark, Ashton Breitkreutz, Zhen-Yuan Lin, Bobby-Joe Breitkreutz, Yongmei Ding, Karen Colwill, Adrian Pasculescu, Tony Pawson, Jeffrey L Wrana, Mike Tyers & Anne-Claude Gingras

  2. Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada

    Tony Pawson, Jeffrey L Wrana, Mike Tyers & Anne-Claude Gingras

  3. Departments of Pathology and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA

    Alexey I Nesvizhskii

  4. Ontario Cancer Institute and McLaughlin Centre for Molecular Medicine, Toronto, Ontario, Canada

    Brian Raught

  5. Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK

    Mike Tyers

Authors
  1. Guomin Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jianping Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Brett Larsen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Chris Stark
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ashton Breitkreutz
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Zhen-Yuan Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Bobby-Joe Breitkreutz
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Yongmei Ding
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Karen Colwill
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Adrian Pasculescu
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Tony Pawson
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Jeffrey L Wrana
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Alexey I Nesvizhskii
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Brian Raught
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Mike Tyers
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Anne-Claude Gingras
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Mike Tyers or Anne-Claude Gingras.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–21 (PDF 11136 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Liu, G., Zhang, J., Larsen, B. et al. ProHits: integrated software for mass spectrometry–based interaction proteomics. Nat Biotechnol 28, 1015–1017 (2010). https://doi.org/10.1038/nbt1010-1015

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt1010-1015

This article is cited by

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research