Presentation given during the ELIXIR UK meeting in Edinburgh (November 2017)

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