The ELIXIR Proteomics Community
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Presentation given during the ELIXIR UK meeting in Edinburgh (November 2017)
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The ELIXIR Proteomics Community
- 1. European Life Sciences Infrastructure for Biological Information www.elixir-europe.org The ELIXIR Proteomics “Community” Dr. Juan AntonioVizcaíno EMBL-EBI juan@ebi.ac.uk
- 2. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017 • 1-year Implementation study started on February, included in the Data platform (EMBL-EBI & ELIXIR- DE) • Strategy meeting “The future of proteomics in ELIXIR”, Tuebingen, Germany (March 1st -2nd) • Needs of the field in the context of ELIXIR were openly discussed and prioritised. Ongoing proteomics activities in ELIXIR
- 3. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017 White paper as the basis for this Community Vizcaíno et al., F1000Research, 2017
- 4. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017 • 11 ELIXIR nodes supported the application: • Germany (co-lead) (O. Kohlbacher) • Belgium (co-lead) (L. Martens) • Czech Republic • Denmark • Ireland • France • Netherlands • Spain • Sweden • United Kingdom • EMBL-EBI (co-lead) (Juan A. Vizcaíno) ELIXIR nodes supporting the new Community
- 5. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017 • PRIDE stores mass spectrometry (MS)-based proteomics data: • Peptide and protein expression data (identification and quantification) • Post-translational modifications • Mass spectra (raw data and peak lists) • Technical and biological metadata • Any other related information • Full support for tandem MS approaches • Any type of data can be stored • Leading ProteomeXchange. • From July 2017, an ELIXIR core resource European leadership: the world-leading PRIDE database http://www.ebi.ac.uk/pride/archive Martens et al., Proteomics, 2005 Vizcaíno et al., NAR, 2016
- 6. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017 ProteomeXchange: A Global, distributed proteomics database PASSEL (SRM data) PRIDE (MS/MS data) MassIVE (MS/MS data) Raw ID/Q Meta jPOST (MS/MS data) Mandatory raw data deposition since July 2015 http://www.proteomexchange.org Vizcaíno et al., Nat Biotechnol, 2014 Deutsch et al., NAR, 2017 • Goal: Development of a framework to allow standard data submission and dissemination pipelines between the main existing proteomics repositories.
- 7. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017 Origin: 1229 USA 902 Germany 618 China 583 United Kingdom 319 France 250 Netherlands 213 Canada 208 Switzerland 200 Australia 179 Spain 172 Austria 168 Denmark 138 Sweden 133 India 115 Japan 115 Belgium 98 Norway 75 Italy 69 Taiwan 57 Brazil 51 Israel 51 Singapore 43 Finland 44 Ireland… ProteomeXchange: 7,475 datasets up until September 1st 2017 Type: 4805 PRIDE partial 1552 PRIDE complete 649 MassIVE 117 PeptideAtlas/PASSEL complete 109 jPOST 243 reprocessed datasets Publicly Accessible: 4051 datasets, 54% of all 89% PRIDE 6% MassIVE 3% PASSEL 2% jPOST Top Species studied by at least 50 datasets: 2,787 Homo sapiens 958 Mus musculus 236 Saccharomyces cerevisiae 229 Arabidopsis thaliana 190 Rattus norvegicus 157 Escherichia coli 68 Bos taurus 62 Drosophila melanogaster ~ 1,100 species in total
- 8. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017 Stats: Data growth in EMBL-EBI resources Genomics Transcriptomics Metabolomics Proteomics
- 9. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017 •Develops data standards for proteomics. •Both data representation and annotation standards. •Involves data producers, database providers, software producers, publishers, everyone who wants to be involved… •Active Workgroups: MI, MS, PI, Mod and the new QC. •Inter-group activities: MIAPE and Controlled Vocabularies. •Started in 2002, so some experience already… •One annual meeting in March-April, regular phone calls. •Close interaction with the metabolomics community (MSI). http://www.psidev.info European leadership: HUPO Proteomics Standards Initiative
- 10. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017 Work plan
- 11. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017
- 12. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017 Concept of “proteoform” Smith et al., Nat Methods, 2013
- 13. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017
- 14. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017 Across-omics -> Proteogenomics approaches • Proteomics data is combined with genomics and/or transcriptomics information, typically by using sequence databases generated from DNA sequencing efforts, RNA-Seq experiments, Ribo-Seq approaches, and long- non-coding RNAs. Nesvizhskii, Nat Methods, 2014
- 15. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017
- 16. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017
- 17. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017 Purpose: • Develop robust, fully reproducible and automated proteomics analysis pipelines (DDA ‘shot-gun’ proteomics workflows). • Deployed in a cloud environment and reusable by the scientific community. Started in February (1 year), ELIXIR Implementation study: • EMBL-EBI (Proteomics & Cloud infrastructure Teams) • ELIXIR-DE (Kohlbacher EKUT , Eisenacher RUB) ELIXIR Implementation Study
- 18. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017
- 19. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017
- 20. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017
- 21. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017 Proposed work plan Priority to the three groups of activities should be assigned in agreement with the overall ELIXIR plan, involving the other use cases and platforms, so that the impact of the use case is maximized.
- 22. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017 Acknowledgements
- 23. Juan A. Vizcaíno juan@ebi.ac.uk ELIXIR UK All-Hands Meeting 2017 Edinburgh, 1 November 2017