PRIDE and ProteomeXchange

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1 PRIDE and ProteomeXchange Henning Hermjakob Head of Molecular Systems European Bioinformatics Institute Director of Bioinformatics National Center for Protein Sciences, Beijing

2 Data resources at EMBL-EBI Genes, genomes & variation European Nucleotide Archive Ensembl European Variation Archive Ensembl Genomes European Genome-phenome Archive GWAS Catalog Metagenomics portal Gene, protein & metabolite expression Systems RNA Central Array Express Expression Atlas Metabolights PRIDE BioModels BioSamples Enzyme Portal IntAct Reactome Protein sequences, families & motifs InterPro Pfam UniProt Molecular structures Literature & ontologies Europe PubMed Central BioStudies Gene Ontology Experimental Factor Ontology Protein Data Bank in Europe Electron Microscopy Data Bank Chemical biology ChEMBL SureChEMBL ChEBI

2016 update of the PRIDE database and its

3 A Proteomics Workflow Sample Raw data Id/Quant Analysis Res Metadata Vizcaíno JA, et al update of the PRIDE database and its related tools. Nucleic Acids Res Jan4;44(D1):D

data) PRIDE (MS/MS data) >150 datasets/month since July

4 ProteomeXchange: A Global, distributed proteomics database Raw ID/Q Meta PASSEL (SRM data) MassIVE (MS/MS data) PRIDE (MS/MS data) >150 datasets/month since July 2015 JPost (MS/MS data) Mandatory raw data deposition since July 2015

5 Origin: ProteomeXchange: 3,802 datasets up until April 1 st, USA 465 Germany 342 United Kingdom 264 China 194 France 158 Netherland 136 Canada 126 Switzerland 107 Denmark 104 Spain 99 Australia 95 Japan 72 Belgium 68 Austria 63 Sweden 61 India 51 Norway 43 Taiwan 30 Italy 29 Brazil 28 Singapore 28 Finland 27 Ireland 27 Russia 26 Israel Datasets/year: 2012: : : : : 452 Data volume: Total: ~150 TB Number of all files: ~400,000 PXD001860: ~ 12 TB PXD : ~ 4 TB PXD ~2.4 TB PXD ~1.6 TB Top Species studied by at least 20 datasets: 1526 Homo sapiens 485 Mus musculus 150 Saccharomyces cerevisiae 121 Arabidopsis thaliana 102 Rattus norvegicus 86 Escherichia coli 44 Bos taurus 35 Drosophila melanogaster 32 Glycine max ~ 700 species in total

8 Funding All ProteomeXchange partners are independently funded Basic institutional core funding Research grants PRIDE: 2 FTE EMBL-EBI core funding 2 FTE Wellcome Trust PRIDE 2 FTE BBSRC BBR 0.2 de.nbi (proto-elixir) Key development phase was enabled by EU ProteomeXchange grant (number ) with funding to both EU and US partners Challenge: Scarce international funding Two failed applications to joint NSF/BBSRC call 8

9 Usage Ca. 2,000 data submitters per year, defined through intensive contact. Ca. 5,000 data access users/year, defined through distinct IP addresses in web logs. Dataset level metrics through log analysis - challenging Downloads Hits/ No files = dataset Dataset Title PXD /91 = 350 Single muscle fiber proteomics reveals unexpected mitochondrial specialization PXD /26 = 188 Building high-quality assay libraries for targeted analysis of SWATH MS data PXD /32 = 139 Phospho-iTRAQ PXD /50 = 133 Yersinia enterocolitica SOR17 PXD /2 = 133 Proteomic analysis of accessory gland in sexually mature Eriocheir sinensis PXD /2383=20 A draft map of the human proteome 9

10 Usage Ca. 2,000 data submitters per year, defined through intensive contact. Ca. 5,000 data access users/year, defined through distinct IP addresses in web logs. Strong culture of data citation in Proteomics 10

11 11

12 12 Data Re-Use: Anecdotal Evidence

13 Systematic Tracking of Data Re-use: OmicsDI

14 Data Re-Use

15 Data re-use

Contingency Planning In proteomics, contingency planning is not hypothetical: NCBI Peptidome closed in 2011: Managed process, data remains accessible on FTP server Data transferred to EBI PRIDE,

16 Contingency Planning In proteomics, contingency planning is not hypothetical: NCBI Peptidome closed in 2011: Managed process, data remains accessible on FTP server Data transferred to EBI PRIDE, recurated Tranche closed in 01/2013 Heavily used repository, built on Bittorrent technology Became unreliable in 2012 Closed in 1/2013 MassIVE and PeptideAtlas tried to rescue data, largely unsuccessful There are now dead data links in the public literature 16

17 17 Best intentions one for all, all for one

18 Acknowledgements ProteomeXchange partners, in particular: Eric Deutsch, ISB, Seattle Nuno Bandeira, UCSD Yasushi Ishihama, jpost Andy Jones, U Liverpool Lennart Martens, U Gent Pierre-Alain Binz, SIB, Geneva Martin Eisenacher, MPC, Bochum Ruedi Aebersold, ETH Zurich Laurent Gatto, U Cambridge Editors Mike Dunn, Proteomics Achim Kraus, Proteomics Ralph Bradshaw, MCP PRIDE team Juan Antonio Vizcaino Attila Csordas Johannes Griss, EBI/U Vienna Tobias Ternent Yasset Perez Riverol Mingze Bai Noemi del Toro Ayllon Funding: All data providers! Wellcome Trust PRIDE EU FW7 ProteomeXchange BBSRC BBR Process BBSRC BBR ProteoGenomics NIH BD2K Center of UCLA, Grant number 1U54GM

19 ? If the Human Genome Project had not followed an open data release policy, what would we be searching our spectra against today? proteomexchange.org psidev.info

20 Proteomics Minimum Data Requirements 20

21 The HUPO Proteomics Standards Initiative Controlled vocabulary: 2013 mzml: spectra, 2011 mzidentml: identification, 2012 mzquantml: quantitation, 2013 qcml: quality control, 2014 mztab: summary, 2014

Data Deposition Requirements In particular, novel protein sequences

org); molecular interactions in an IMEx partner database (imex.sf.

If a manuscript is accepted by the journal, all mass spectra

22 Data Deposition Requirements In particular, novel protein sequences should be deposited in UniProt ( molecular interactions in an IMEx partner database (imex.sf.net); and protein identification data in PRIDE ( World-2DPAGE ( or a comparable database. If a manuscript is accepted by the journal, all mass spectra contributing to the described work must be deposited in electronic form by the time of publication at a publicly accessible site that is independent of the authors' control. 22

23 ProteomeXchange data flow Receiving repositories Peptide Atlas PRIDE (MS/MS data) Results Raw Data* Metadata / Manuscript MassIVE (MS/MS data) PASSEL (SRM data) ProteomeCentral UniProt/ nextprot Other DBs Researcher s results Reprocessed results Journals GPMDB Other DBs Raw data* Metadata

24 Curators! Attila Csordas Tobias Ternent 24

25 History 2005: First PRIDE Publication ProteomeXchange concept published 2011: Peptidome (NCBI) closes 2011: EU ProteomeXchange grant start DB partners PRIDE, PeptideAtlas (ISB, Seattle) 2012: ProteomeXchange production start 2013: Tranche closes 2014: ProteomeXchange grant ends 2014: Massive (UCSD) joins 2015: Mandatory submissions by MCP 2016: jpost (Japan) joins 25

Introduction to EMBL-EBI.

Introduction to EMBL-EBI. Introduction to EMBL-EBI www.ebi.ac.uk What is EMBL-EBI? Part of EMBL Austria, Belgium, Croatia, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, the Netherlands,