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Vizcaíno JA, Walzer M, Jiménez RC, et al. A community proposal to integrate proteomics activities in ELIXIR. F1000Res. 2017;6doi: 10.12688/f1000research.11751.1.
Vizcaíno, J. A., Walzer, M., Jiménez, R. C., Bittremieux, W., Bouyssié, D., Carapito, C., Corrales, F., Ferro, M., Heck, A. J. R., Horvatovich, P., Hubalek, M., Lane, L., Laukens, K., Levander, F., Lisacek, F., Novak, P., Palmblad, M., Piovesan, D., Pühler, A., Schwämmle, V., Valkenborg, D., van Rijswijk, M., Vondrasek, J., Eisenacher, M., Martens, L., & Kohlbacher, O. (2017). A community proposal to integrate proteomics activities in ELIXIR. F1000Research, 6. https://doi.org/10.12688/f1000research.11751.1
Vizcaíno, Juan Antonio, et al. "A community proposal to integrate proteomics activities in ELIXIR." F1000Research vol. 6 (2017). doi: https://doi.org/10.12688/f1000research.11751.1
Vizcaíno JA, Walzer M, Jiménez RC, Bittremieux W, Bouyssié D, Carapito C, Corrales F, Ferro M, Heck AJR, Horvatovich P, Hubalek M, Lane L, Laukens K, Levander F, Lisacek F, Novak P, Palmblad M, Piovesan D, Pühler A, Schwämmle V, Valkenborg D, van Rijswijk M, Vondrasek J, Eisenacher M, Martens L, Kohlbacher O. A community proposal to integrate proteomics activities in ELIXIR. F1000Res. 2017 Jun 13;6. doi: 10.12688/f1000research.11751.1. eCollection 2017. PMID: 28713550; PMCID: PMC5499783.
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F1000Res. 2017 Jun 13;6. doi: 10.12688/f1000research.11751.1. eCollection 2017.

A community proposal to integrate proteomics activities in ELIXIR.

F1000Research

Juan Antonio Vizcaíno, Mathias Walzer, Rafael C Jiménez, Wout Bittremieux, David Bouyssié, Christine Carapito, Fernando Corrales, Myriam Ferro, Albert J R Heck, Peter Horvatovich, Martin Hubalek, Lydie Lane, Kris Laukens, Fredrik Levander, Frederique Lisacek, Petr Novak, Magnus Palmblad, Damiano Piovesan, Alfred Pühler, Veit Schwämmle, Dirk Valkenborg, Merlijn van Rijswijk, Jiri Vondrasek, Martin Eisenacher, Lennart Martens, Oliver Kohlbacher

Affiliations

  1. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK.
  2. ELIXIR Hub, Cambridge, CB10 1SD, UK.
  3. Department of Mathematics and Computer Science, University of Antwerp, Antwerp, 2020, Belgium.
  4. French Proteomics Infrastructure ProFI, Grenoble, (EDyP U1038, CEA/Inserm/ Grenoble Alpes University) Toulouse (IPBS, Université de Toulouse, CNRS, UPS), Strasbourg (LSMBO, IPHC UMR7178, CNRS-Université de Strasbourg), France.
  5. ProteoRed, Proteomics Unit, Centro Nacional de Biotecnología (CSIC), Madrid, 28049, Spain.
  6. Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, 3548 CH, Netherlands.
  7. Netherlands Proteomics Center, Utretcht, 3584 CH, Netherlands.
  8. Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 9713 AV, Netherlands.
  9. Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 1, 117 20, Czech Republic.
  10. CALIPHO Group, SIB Swiss Institute of Bioinformatics, Geneva, 1015, Switzerland.
  11. Department of Human Protein Science, Faculty of Medicine, University of Geneva, Geneva, 1205, Switzerland.
  12. National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, Department of Immunotechnology, Lund University, Lund, 223 62, Sweden.
  13. Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, 1015, Switzerland.
  14. Computer Science Department, University of Geneva, Geneva, 1205, Switzerland.
  15. Institute of Microbiology, Czech Academy of Sciences, Prague 1, 117 20, Czech Republic.
  16. Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands.
  17. Department of Biomedical Sciences, University of Padova, Padova, I-35121, Italy.
  18. Center for Biotechnology, Bielefeld University, Bielefeld, 33615, Germany.
  19. Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, 5230, Denmark.
  20. Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Hasselt, 3500, Belgium.
  21. Center for Proteomics, University of Antwerp, Antwerpen, 2000, Belgium.
  22. Applied Bio & Molecular Systems, VITO, Mol, BE-2400, Belgium.
  23. Netherlands Metabolomics Centre, Utrecht, 3511 GC, Netherlands.
  24. Dutch Techcentre for Life Sciences / ELIXIR-NL, Utrecht, 3511 GC, Netherlands.
  25. Medical Bioinformatics, Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, 44801, Germany.
  26. VIB-UGent Center for Medical Biotechnology, Ghent, 9052, Belgium.
  27. Department of Biochemistry, Ghent University, Ghent, 9000, Belgium.
  28. Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, 72074, Germany.
  29. Center for Bioinformatics Tübingen, University of Tübingen, Tübingen, 72074, Germany.
  30. Quantitative Biology Center, University of Tübingen, Tübingen, 72074, Germany.
  31. Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany.

PMID: 28713550 PMCID: PMC5499783 DOI: 10.12688/f1000research.11751.1

Abstract

Computational approaches have been major drivers behind the progress of proteomics in recent years. The aim of this white paper is to provide a framework for integrating computational proteomics into ELIXIR in the near future, and thus to broaden the portfolio of omics technologies supported by this European distributed infrastructure. This white paper is the direct result of a strategy meeting on 'The Future of Proteomics in ELIXIR' that took place in March 2017 in Tübingen (Germany), and involved representatives of eleven ELIXIR nodes. These discussions led to a list of priority areas in computational proteomics that would complement existing activities and close gaps in the portfolio of tools and services offered by ELIXIR so far. We provide some suggestions on how these activities could be integrated into ELIXIR's existing platforms, and how it could lead to a new ELIXIR use case in proteomics. We also highlight connections to the related field of metabolomics, where similar activities are ongoing. This white paper could thus serve as a starting point for the integration of computational proteomics into ELIXIR. Over the next few months we will be working closely with all stakeholders involved, and in particular with other representatives of the proteomics community, to further refine this paper.

Keywords: bioinformatics infrastructure; computational proteomics; data standards; databases; mass spectrometry; multi-omics approaches.; proteomics; training

Conflict of interest statement

Competing interests: No competing interests were disclosed.

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