A community proposal to integrate proteomics activities in ELIXIR

Research output: Contribution to journalArticle

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.

Details

Authors
  • 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
  • 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
Organisations
External organisations
  • European Bioinformatics Institute
  • ELIXIR Hub, UK
  • University of Antwerp
  • Institut Gustave Roussy
  • Utrecht University
  • University of Groningen
  • Swiss Institute of Bioinformatics
  • University of Geneva Medical School
  • University of Geneva
  • Leiden University Medical Centre
  • University of Padova
  • Bielefeld University
  • University of Southern Denmark
  • Hasselt University
  • Flemish Institute for Technological Research
  • Netherlands Metabolomics Centre
  • Dutch Techcentre for Life Sciences
  • Ruhr-University Bochum
  • Ghent University
  • University of Tübingen
  • CSIC National Center for Biotechnology (CNB)
  • Academy of Sciences of the Czech Republic
  • Max Planck Institute for Developmental Biology
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Bioinformatics (Computational Biology)

Keywords

  • Bioinformatics infrastructure, Computational proteomics, Data standards, Databases, Mass spectrometry, Multi-omics approaches., Proteomics, Training
Original languageEnglish
Article number875
JournalF1000Research
Volume6
Publication statusPublished - 2017
Publication categoryResearch
Peer-reviewedYes