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:

PRIDE Inspector: a tool to visualize and validate MS proteomics data

Nature Biotechnology volume 30, pages 135–137 (2012)Cite this article

Subjects

Access through your institution
Buy or subscribe

To the Editor:

Despite the increasing popularity of MS-based proteomics and the overall tendency in the life sciences toward open sharing of biological data, relatively little proteomics data are currently available in the public domain. This situation is changing, however, thanks to stricter data-sharing guidelines by scientific journals and funding agencies. Some proteomics journals (e.g., Proteomics and Molecular and Cellular Proteomics; MCP) recommend, and in some concrete cases mandate, public deposition of MS data in support of manuscripts. Journals from the Nature group also strongly recommend submission of proteomics data to repositories like PRIDE2, PeptideAtlas3 and Tranche4 (http://www.nature.com/authors/policies/availability.html).

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

Relevant articles

Open Access articles citing this article.

Access options

Access through your institution

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: PRIDE Inspector helps to perform every stage of the PRIDE submission workflow.
Figure 2: Screenshots showing some of the graphical features of PRIDE Inspector.

References

  1. Anonymous. Nat. Biotechnol. 27, 579 (2009).

  2. Vizcaino, J.A. et al. Nucleic Acids Res. 38, D736–D742 (2010).

    Article  CAS  Google Scholar 

  3. Deutsch, E.W., Lam, H. & Aebersold, R. EMBO Rep. 9, 429–434 (2008).

    Article  CAS  Google Scholar 

  4. Hill, J.A., Smith, B.E., Papoulias, P.G. & Andrews, P.C. J. Proteome Res. 9, 2809–2811 (2010).

    Article  CAS  Google Scholar 

  5. Barsnes, H., Vizcaino, J.A., Eidhammer, I. & Martens, L. Nat. Biotechnol. 27, 598–599 (2009).

    Article  CAS  Google Scholar 

  6. Searle, B.C. Proteomics 10, 1265–1269 (2010).

    Article  CAS  Google Scholar 

  7. Medina-Aunon, J.A., Carazo, J.M. & Albar, J.P. Proteomics 11, 334–337 (2011).

    Article  CAS  Google Scholar 

  8. Martens, L. et al. Mol. Cell Proteomics 10, R110000133 (2011).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  10. Nesvizhskii, A.I. & Aebersold, R. Mol. Cell. Proteomics 4, 1419–1440 (2005).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the Wellcome Trust (grant number WT085949MA) and EMBL core funding. R.G.C. is supported by EU FP7 grant SLING (grant number 226073). J.A.V. is supported by the EU FP7 grants LipidomicNet (grant number 202272) and ProteomeXchange (grant number 260558). A.F. was partially supported by the Spanish network COMBIOMED (RD07/0067/0006, ISCIII-FIS). L.M. would like to acknowledge support from the EU FP7 PRIME-XS grant (grant number 262067).

Author information

Authors and Affiliations

  1. EMBL Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

    Rui Wang, Antonio Fabregat, Daniel Ríos, David Ovelleiro, Joseph M Foster, Richard G Côté, Johannes Griss, Attila Csordas, Yasset Perez-Riverol, Florian Reisinger, Henning Hermjakob & Juan Antonio Vizcaíno

  2. Department of Medicine I, Medical University of Vienna, Vienna, Austria

    Johannes Griss

  3. Department of Proteomics, Center for Genetic Engineering and Biotechnology, Cubanacán, Playa, Ciudad de la Habana, Cuba

    Yasset Perez-Riverol

  4. Department of Medical Protein Research, Ghent, Belgium

    Lennart Martens

  5. Department of Biochemistry, Ghent University, Ghent, Belgium

    Lennart Martens

Authors
  1. Rui Wang
    View author publications

    Search author on:PubMed Google Scholar

  2. Antonio Fabregat
    View author publications

    Search author on:PubMed Google Scholar

  3. Daniel Ríos
    View author publications

    Search author on:PubMed Google Scholar

  4. David Ovelleiro
    View author publications

    Search author on:PubMed Google Scholar

  5. Joseph M Foster
    View author publications

    Search author on:PubMed Google Scholar

  6. Richard G Côté
    View author publications

    Search author on:PubMed Google Scholar

  7. Johannes Griss
    View author publications

    Search author on:PubMed Google Scholar

  8. Attila Csordas
    View author publications

    Search author on:PubMed Google Scholar

  9. Yasset Perez-Riverol
    View author publications

    Search author on:PubMed Google Scholar

  10. Florian Reisinger
    View author publications

    Search author on:PubMed Google Scholar

  11. Henning Hermjakob
    View author publications

    Search author on:PubMed Google Scholar

  12. Lennart Martens
    View author publications

    Search author on:PubMed Google Scholar

  13. Juan Antonio Vizcaíno
    View author publications

    Search author on:PubMed Google Scholar

Corresponding author

Correspondence to Juan Antonio Vizcaíno.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–24 and Supplementary Notes (PDF 5343 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Wang, R., Fabregat, A., Ríos, D. et al. PRIDE Inspector: a tool to visualize and validate MS proteomics data. Nat Biotechnol 30, 135–137 (2012). https://doi.org/10.1038/nbt.2112

Download citation

  • Published:

  • Issue date:

  • DOI: https://doi.org/10.1038/nbt.2112

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