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  • Correspondence
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ProteomeXchange provides globally coordinated proteomics data submission and dissemination

Nature Biotechnology volume 32, pages 223–226 (2014) Cite this article

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To the Editor

There is a growing trend toward public dissemination of proteomics data, which is facilitating the assessment, reuse, comparative analyses and extraction of new findings from published data1,2. This process has been mainly driven by journal publication guidelines and funding agencies. However, there is a need for better integration of public repositories and coordinated sharing of all the pieces of information needed to represent a full mass spectrometry (MS)–based proteomics experiment. An editorial in your journal in 2009, 'Credit where credit is overdue'3, exposed the situation in the proteomics field, where full data disclosure is still not common practice. Olsen and Mann4 identified different levels of information in the typical experiment: from raw data and going through peptide identification and quantification, protein identifications and protein ratios and the resulting biological conclusions. All of these levels should be captured and properly annotated in public databases, using the existing MS proteomics repositories for the MS data (raw data, identification and quantification results) and metadata, whereas the resulting biological information should be integrated in protein knowledge bases, such as UniProt5. A recent editorial6 in Nature Methods again highlighted the need for a stable repository for raw MS proteomics data. In this Correspondence, we report the first implementation of the ProteomeXchange consortium, an integrated framework for submission and dissemination of MS-based proteomics data.

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Figure 1: Representation of the ProteomeXchange workflow for MS/MS and SRM data.
The alternative text for this image may have been generated using AI.
Figure 2: Summary of the main metrics of ProteomeXchange submissions (as of February 2014).
The alternative text for this image may have been generated using AI.

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Acknowledgements

We thank all the members of the community who participated as stakeholders in the ProteomeXchange meetings. This work was supported by the EU FP7 grant ProteomeXchange (grant number 260558). J.A.V., A.C., F.R. and D.R. were also funded by the Wellcome Trust (grant number WT085949MA). E.W.D., Z.S. and T.F. are also funded in part by US National Institutes of Health/National Institute General Medical Sciences grant no. R01 GM087221, US National Science Foundation Major Research Instrumentation Program (grant number 0923536), and the Luxembourg Centre for Systems Biomedicine and the University of Luxembourg. M.E. is funded by Protein Unit for Research in Europe (PURE), a project of Nordrhein-Westfalen. L.G. was supported by the EU FP7 PRIME-XS project (grant number 262067). R.W. was supported by the UK Biotechnology and Biological Sciences Research Council 'PRIDE Converter' grant (reference BB/I024204/1). G.S.O. acknowledges support from US National Institute of Health grants RM-08-029, P30U54ES017885 and UL1RR24986.

Author information

Author notes

  1. Juan A Vizcaíno and Eric W Deutsch: These authors contributed equally to this work.

Authors and Affiliations

  1. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

    Juan A Vizcaíno, Rui Wang, Attila Csordas, Florian Reisinger, Daniel Ríos, José A Dianes, Rolf Apweiler & Henning Hermjakob

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

    Eric W Deutsch, Zhi Sun, Terry Farrah & Gilbert S Omenn

  3. Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, California, USA

    Nuno Bandeira

  4. Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland

    Pierre-Alain Binz & Ioannis Xenarios

  5. University of Lausanne, Lausanne, Switzerland, and Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland

    Ioannis Xenarios

  6. Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland

    Ioannis Xenarios

  7. Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany

    Martin Eisenacher & Gerhard Mayer

  8. Department of Biochemistry, Computational Proteomics Unit and Cambridge Centre for Proteomics, University of Cambridge, Cambridge, United Kingdom

    Laurent Gatto

  9. Integromics SL, Santiago Grisolia, Madrid, Spain

    Alex Campos

  10. Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA

    Robert J Chalkley

  11. Wiley-VCH Verlag, Weinheim, Germany

    Hans-Joachim Kraus

  12. ProteoRed-ISCIII, National Center for Biotechnology-CSIC, Madrid, Spain

    Juan Pablo Albar & Salvador Martinez-Bartolomé

  13. Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA

    Gilbert S Omenn

  14. Department of Medical Protein Research, VIB, Ghent, Belgium

    Lennart Martens

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

    Lennart Martens

  16. Institute of Integrative Biology, University of Liverpool, UK

    Andrew R Jones

Authors
  1. Juan A Vizcaíno
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  2. Eric W Deutsch
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  3. Rui Wang
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  4. Attila Csordas
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  5. Florian Reisinger
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  7. José A Dianes
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  8. Zhi Sun
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  9. Terry Farrah
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  10. Nuno Bandeira
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  11. Pierre-Alain Binz
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  13. Martin Eisenacher
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  14. Gerhard Mayer
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  15. Laurent Gatto
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  16. Alex Campos
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  17. Robert J Chalkley
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  18. Hans-Joachim Kraus
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  19. Juan Pablo Albar
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  20. Salvador Martinez-Bartolomé
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  21. Rolf Apweiler
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  22. Gilbert S Omenn
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  23. Lennart Martens
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  24. Andrew R Jones
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  25. Henning Hermjakob
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Corresponding author

Correspondence to Juan A Vizcaíno.

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The authors declare no competing financial interests.

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Vizcaíno, J., Deutsch, E., Wang, R. et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol 32, 223–226 (2014). https://doi.org/10.1038/nbt.2839

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