Proteomexchange

Short presentation given during one of the workshops at ASMS 2016 at San Antonio

1. ProteomeXchange Dr. Juan Antonio Vizcaíno EMBL-EBI Hinxton , Cambridge, UK

2. ProteomeXchange Consortium Goal: Development of a framework to allow standard data submission and dissemination pipelines between the main existing proteomics repositories. Includes PeptideAtlas (ISB, Seattle), PRIDE (Cambridge, UK) and (very recently) MassIVE (UCSD, San Diego) . Common identifier space (PXD identifiers) Two supported data workflows: MS/MS and SRM . Data from all approaches can be submitted. Main objective: Make life easier for researchers http :/ /www.proteomexchange.org Vizcaíno et al. , Nat Biotechnol , 2014

3. ProteomeCentral Metadata / Manuscript Raw Data* Results Journals UniProt/ neXtProt Peptide Atlas Other DBs Receiving repositories PASSEL (SRM data) PRIDE (MS/MS data) Other DBs GPMDB Researcher’s results Reprocessed results Raw data* Metadata MassIVE (MS/MS data) ProteomeXchange data workflow

4. Origin: 885 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 … ProteomeXchange: 3,802 datasets up until 1 st April, 2016 Type: 2429 PRIDE partial 1016 PRIDE complete 250 MassIVE 84 PeptideAtlas /PASSEL complete 23 Reprocessed Publicly Accessible: 1973 datasets, 52% of all 91% PRIDE 5 % MassIVE 4% PASSEL Datasets/year: 2012: 102 2013: 527 2014: 963 2015: 1758 2016: 452 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

5. PRIDE Archive submitted datasets up until 1 st April, 2016 In the last year: ~ 150 submitted datasets per month Size: ~ 220TB

6. ProteomeCentral : Portal for all PX datasets http:// proteomecentral.proteomexchange.org/cgi/GetDataset

7. OmicsDI : Portal for omics datasets http:// www.ebi.ac.uk /Tools/ omicsdi / Aims to integrate of ‘ omics ’ datasets ( genomics , proteomics and metabolomics at present). Not only EBI resources are included. PRIDE Archive MassIVE PASSEL GPMDB MetaboLights Metabolomics Workbench GNPS EGA

8. Datasets are being downloaded …. Data download volume in 2015: ~ 200 TB

9. Data reuse is increasing Vaudel et al., Proteomics, 2016

10. Aknowledgements : People PRIDE team at EMBL-EBI Attila Csordas Tobias Ternent Noemi del Toro Gerhard Mayer (Bochum, de.NBI ) Johannes Griss Yasset Perez- Riverol Henning Hermjakob Former team members: Rui Wang, Florian Reisinger & Jose A. Dianes Acknowledgements PX partners Eric Deutsch and his team at ISB Nuno Bandeira and his team at UCSD Twitter: @ proteomexchange