the elixir proteomics community

European Life Sciences Infrastructure for Biological Informationwww.elixir-europe.org

The ELIXIR Proteomics “Community”

Dr. Juan Antonio Vizcaíno

[email protected]

Juan A. Vizcaí[email protected]

ELIXIR UK All-Hands Meeting 2017Edinburgh, 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



White paper as the basis for this Community

Vizcaíno et al., F1000Research, 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



• 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, 2005Vizcaíno et al., NAR, 2016



ProteomeXchange: A Global, distributed proteomics database

PASSEL (SRM data)

PRIDE (MS/MS data)

MassIVE(MS/MS data)

Raw

ID/Q

Met

a

jPOST(MS/MS data)

Mandatory raw data deposition since July 2015

http://www.proteomexchange.org

Vizcaíno et al., Nat Biotechnol, 2014Deutsch et al., NAR, 2017

• Goal: Development of a framework to allow standard datasubmission and dissemination pipelines between the mainexisting proteomics repositories.



Origin: 1229 USA902 Germany618 China583 United Kingdom319 France250 Netherlands213 Canada208 Switzerland 200 Australia179 Spain172 Austria168 Denmark138 Sweden 133 India 115 Japan115 Belgium98 Norway 75 Italy69 Taiwan57 Brazil51 Israel51 Singapore43 Finland44 Ireland…

ProteomeXchange: 7,475 datasets up until September 1st 2017

Type:4805 PRIDE partial

1552 PRIDE complete649 MassIVE117 PeptideAtlas/PASSEL

complete109 jPOST243 reprocessed datasets

Publicly Accessible: 4051 datasets, 54% of all 89% PRIDE

6% MassIVE3% PASSEL2% jPOST

Top Species studied by at least 50 datasets:2,787 Homo sapiens

958 Mus musculus236 Saccharomyces cerevisiae229 Arabidopsis thaliana190 Rattus norvegicus157 Escherichia coli

68 Bos taurus62 Drosophila melanogaster

~ 1,100 species in total



Stats: Data growth in EMBL-EBI resources

Genomics

Transcriptomics

Metabolomics

Proteomics



•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



Work plan



Concept of “proteoform”

Smith et al., Nat Methods, 2013



Across-omics -> Proteogenomics approaches

• Proteomics data is combined with genomics and/or transcriptomicsinformation, typically by using sequence databases generated from DNAsequencing efforts, RNA-Seq experiments, Ribo-Seq approaches, and long-non-coding RNAs.

Nesvizhskii, Nat Methods, 2014



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



Proposed work plan

Priority to the three groups of activities should be assigned inagreement with the overall ELIXIR plan, involving the otheruse cases and platforms, so that the impact of the use caseis maximized.



Acknowledgements