ProteomeXchange provides globally coordinated proteomics data submission and dissemination

Juan A Vizcaíno¹, Eric W Deutsch², Rui Wang³, Attila Csordas³, Florian Reisinger³, Daniel Ríos³, José A Dianes³, Zhi Sun⁴, Terry Farrah⁴, Nuno Bandeira⁵, Pierre-Alain Binz⁶, Ioannis Xenarios⁷, Martin Eisenacher⁸, Gerhard Mayer⁸, Laurent Gatto⁹, Alex Campos¹⁰, Robert J Chalkley¹¹, Hans-Joachim Kraus¹², Juan Pablo Albar¹³, Salvador Martinez-Bartolomé¹³, Rolf Apweiler³, Gilbert S Omenn¹⁴, Lennart Martens¹⁵, Andrew R Jones¹⁶, Henning Hermjakob³

Affiliations

¹ 1] European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. [2].
² 1] Institute for Systems Biology, Seattle, Washington, USA. [2].
³ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
⁴ Institute for Systems Biology, Seattle, Washington, USA.
⁵ Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, California, USA.
⁶ Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
⁷ 1] Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland. [2] University of Lausanne, Lausanne, Switzerland, and Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland. [3] Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
⁸ Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany.
⁹ Computational Proteomics Unit and Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
¹⁰ Integromics SL, Santiago Grisolia, Madrid, Spain.
¹¹ Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA.
¹² Wiley-VCH Verlag, Weinheim, Germany.
¹³ ProteoRed-ISCIII, National Center for Biotechnology-CSIC, Madrid, Spain.
¹⁴ 1] Institute for Systems Biology, Seattle, Washington, USA. [2] Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
¹⁵ 1] Department of Medical Protein Research, VIB, Ghent, Belgium. [2] Department of Biochemistry, Ghent University, Ghent, Belgium.
¹⁶ Institute of Integrative Biology, University of Liverpool, UK.

PMID: 24727771
PMCID: PMC3986813
DOI: 10.1038/nbt.2839

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

Juan A Vizcaíno et al. Nat Biotechnol. 2014 Mar.

. 2014 Mar;32(3):223-6.

doi: 10.1038/nbt.2839.

Authors

Affiliations

¹ 1] European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. [2].
² 1] Institute for Systems Biology, Seattle, Washington, USA. [2].
³ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
⁴ Institute for Systems Biology, Seattle, Washington, USA.
⁵ Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, California, USA.
⁶ Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
⁷ 1] Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland. [2] University of Lausanne, Lausanne, Switzerland, and Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland. [3] Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
⁸ Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany.
⁹ Computational Proteomics Unit and Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
¹⁰ Integromics SL, Santiago Grisolia, Madrid, Spain.
¹¹ Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA.
¹² Wiley-VCH Verlag, Weinheim, Germany.
¹³ ProteoRed-ISCIII, National Center for Biotechnology-CSIC, Madrid, Spain.
¹⁴ 1] Institute for Systems Biology, Seattle, Washington, USA. [2] Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
¹⁵ 1] Department of Medical Protein Research, VIB, Ghent, Belgium. [2] Department of Biochemistry, Ghent University, Ghent, Belgium.
¹⁶ Institute of Integrative Biology, University of Liverpool, UK.

PMID: 24727771
PMCID: PMC3986813
DOI: 10.1038/nbt.2839

No abstract available

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Conflict of interest statement

Competing financial interests

The authors have no competing financial or commercial interests.

Figures

**Figure 1**
Representation of the ProteomeXchange workflow for MS/MS and SRM data. *Raw data represents mass spectrometer output files.

**Figure 2**
Summary of the main metrics of ProteomeXchange submissions (by August 2013). The number of data sets is indicated for submission type, data access status and for the top species and countries represented.

See this image and copyright information in PMC

References

1. Hahne H, Kuster B. Mol Cell Proteomics. 2012;11:1063–1069. - PMC - PubMed
1. Matic I, Ahel I, Hay RT. Nat Methods. 2012;9:771–772. - PMC - PubMed
1. Nat Biotechnol. 2009;27:579. Editors. - PubMed
1. Olsen JV, Mann M. Sci Signal. 2011;4:pe7. - PubMed
1. The UniProt Consortium. Nucleic Acids Res. 2012;40:D71–75. - PMC - PubMed

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ProteomeXchange provides globally coordinated proteomics data submission and dissemination

Affiliations

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

Authors

Affiliations

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources