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ProteomeXchange: Data Deposition … but where? Questions about submission: Which repository should I submit to? Should I submit to more than one? Do I need.

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Presentation on theme: "ProteomeXchange: Data Deposition … but where? Questions about submission: Which repository should I submit to? Should I submit to more than one? Do I need."— Presentation transcript:

1 ProteomeXchange: Data Deposition … but where? Questions about submission: Which repository should I submit to? Should I submit to more than one? Do I need to submit raw data? Questions about deposited data: How do I find all datasets on Human hepatocytes? Do PRIDE and PeptideAtlas both have this dataset? Do they interpret it differently? Question about repository stability Peptidome closed in 2011 Tranche closed in 01/2013 Will the data remain publicly available?

2 ProteomeXchange: Different Views of one Dataset Proteome Central Metadata / Manuscript Raw Data Results Journals UniProt/ NextProt Peptide AtlasOther DBs Receiving repositories PASSEL (SRM data) PRIDE (MS/MS data) Other DBs GPMDBCOPaKB

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6 Origin: 66 USA 51 Germany 33 United Kingdom 29 Switzerland 25 Netherlands 24 France 22 Belgium 18 China 13 Spain 12 Australia 12 Japan 9 Canada 8 Sweden 5 Denmark 5 Russia 4 Ireland 4 Italy 4 Austria 4 Israel 4 India 4 Taiwan 3 Poland 2 Singapore 2 Republic of Korea 2 Brazil 2 Portugal ProteomeXchange: Current status Type: 137 PRIDE complete 204 PRIDE partial 32 PeptideAtlas/PASSEL complete Processed/month: 2012 2 March 1 May 2 June 5 July 10 August 21 September 18 October 15 November 32 December 2013 20 January 32 February 30 March 39 April 42 May 38 June 75 July Access: 27% PRIDE public 8% PASSEL public 64% PRIDE private 1% PASSEL private Data size: Total: 25 TB Largest project: 4 TB, >10, 000 files, 5 identifiers Datasets >100 GB: 59 Number of all files: >63,000 Top Species studied by at least 7 datasets: 150 Homo sapiens 44 Mus musculus 14 Arabidopsis thaliana 13 Saccharomyces cerevisiae 8 Rattus norvegicus 7 Escherichia coli 7 Mycobacterium tuberculosis ~ 120 species in total

7 Will my data still be there in five years? Databases depend on continued funding Tranche repository ceased operations recently Serious data loss Peptidome ceased operations in 2011 No data loss, data still available from NCBI ftp … and from PRIDE: Csordas A, et al. From Peptidome to PRIDE: Public proteomics data migration at a large scale. Proteomics. 2013 Mar 27. ProteomeXchange PRIDE, PeptideAtlas have been around since 2005 PRIDE Institutional funding to ensure basic operations while needed by community Hardware support: Two independent London data centers, eight year UK support Wellcome Trust PRIDE funding just renewed: from 1/1/2014 for four years Potential future ProteomeXchange partners: MassIVE (Nuno Bandeira, UCSD) Imported all recoverable Tranche data Beijing Proteomics Center Active collaboration is key for “mutual backup” in case of funding loss

8 Acknowledgements ProteomeXchange partners, particularly: Eric Deutsch, ISB, Seattle Andy Jones, U Liverpool Lennart Martens, U Gent Pierre-Alain Binz, SIB, Geneva Martin Eisenacher, MPC, Bochum Ruedi Aebersold, ETH Zurich Juan Pablo Albar, CSIC, Madrid Laurent Gatto, U Cambridge Nuno Bandeira, UCSD Editors Mike Dunn, Proteomics Achim Kraus, Proteomics Ralph Bradshaw, MCP Bill Hancock, JPR Funding EU FW7 ProteomeXchange Wellcome Trust PRIDE NIH - NHLBI Proteomics Centers All data providers!

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


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