ProteomeXchange: data deposition and data retrieval made easy
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The ProteomeXchange consortium allows researchers to easily deposit and retrieve proteomics data. It includes repositories like PRIDE, PeptideAtlas, and recently MassIVE. The goal is to standardize submission and access across repositories through common identifiers and supported workflows. Over 1,300 datasets have been submitted, with many tools now supporting standard formats like mzIdentML for complete submissions. The most accessed datasets include large reference maps of the human proteome. Open source tools are improving submission and analysis of ProteomeXchange data.
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ProteomeXchange: data deposition and data retrieval made easy
- 1. ProteomeXchange: data deposition and data retrieval made easy Juan Antonio VIZCAINO, Ph.D. PRIDE Group coordinator Proteomics Services Group European Bioinformatics Institute Hinxton, Cambridge United Kingdom juan@ebi.ac.uk
- 2. Overview • The ProteomeXchange (PX) consortium • Highlights in the last year • PRIME-XS datasets
- 3. 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. • Main objective: Make life easier for researchers http://www.proteomexchange.org
- 4. ProteomeXchange data workflow ProteomeCentral Results Raw Data* Metadata / Manuscript PRIDE (MS/MS data) Journals UniProt/ neXtProt Peptide Atlas Other DBs Receiving repositories PASSEL (SRM data) Other DBs GPMDB Researcher’s results Reprocessed results Raw data* Metadata MassIVE (MS/MS data) Vizcaíno et al., Nat Biotechnol, 2014
- 5. MassIVE (UCSD) http://proteomics.ucsd.edu/service/massive/ • Just joined ProteomeXchange on June 2014 • Only partial submissions. A few datasets so far.
- 6. Overview • The ProteomeXchange (PX) consortium • Highlights in the last year • PRIME-XS datasets
- 7. PX Data workflow for MS/MS data 1. Mass spectrometer output files: raw data (binary files) or peak list spectra in a standardized format (mzML, mzXML). 2. Result files: a. Complete submissions: Result files can be converted to PRIDE XML or the mzIdentML data standard. b. Partial submissions: For workflows not yet supported by PRIDE, search engine output files will be stored and provided in their original form. 3. Metadata: Sufficiently detailed description of sample origin, workflow, instrumentation, submitter. 4. Other files: Optional files: a. QUANT: Quantification related results e. FASTA b. PEAK: Peak list files f. SP_LIBRARY c. GEL: Gel images d. OTHER: Any other file type Published Raw Files Other files
- 8. Complete vs Partial submissions: processed results For complete submissions, it is possible to connect the spectra with the identification processed results and they can be visualized. PRIDE XML, mzIdentML supported mzTab to come Complete Partial
- 9. Complete vs Partial submissions: experimental metadata Complete Partial General experimental metadata about the projects is similar. However, at the assay level information, in partial submissions is less annotated
- 10. Complete submissions using mzIdentML Search Engine Results + MS files Search engines mzIdentML An increasing number of tools support export to mzIdentML 1.1 - Mascot - MSGF+ - Myrimatch and related tools from D. Tabb’s lab - OpenMS - PEAKS - ProCon (ProteomeDiscoverer, Sequest) - Scaffold - TPP via the idConvert tool (ProteoWizard) - ProteinPilot (planned by the end of 2014) - Others: library for X!Tandem conversion, lab internal pipelines, … - Referenced spectral files need to be submitted as well (all open formats are supported). Updated list: http://www.psidev.info/tools-implementing-mzIdentML#.
- 11. Tools ‘RESULT’ file generation Final ‘RESULT’ file mzIdentML ‘RESULT’ Now: native file export Spectra files Mascot ProteinPilo t Scaffold PEAKS MSGF+ Others Native File export
- 12. Original data files ‘RESULT’ file generation Final ‘RESULT’ file Search output files Spectra files PRIDE XML ‘RESULT’ Before: file conversion using PRIDE Converter File conversion PRIDE Converter
- 13. PRIDE Inspector 2 Wang et al., Nat. Biotechnology, 2012 PRIDE Inspector 2.0 PRIDE Inspector 2.0 supports: - PRIDE XML - mzIdentML + all types of spectra files - mzML - mzTab (work in progress) http://code.google.com/p/pride-toolsuite/ wiki/PRIDEInspector
- 14. PX submission tool: data submission Published Raw Other files http://www.proteomexchange.org/submission PX submission tool • Capture the mappings between the different types of files. • Add the mandatory metadata annotation. • Make the file upload process straightforward to the submitter (It transfers all the files using Aspera or FTP). • Command line alternative: some scripting is needed.
- 15. Uploading large datasets: Aspera - Aspera is the default file transfer protocol to PRIDE: - PX Submission tool - Command line - Up to 50X faster than FTP File transfer speed should not be a problem!!
- 16. Tutorial manuscript detailing the process Example dataset: PXD000764 - Title: “Discovery of new CSF biomarkers for meningitis in children” - 12 runs: 4 controls and 8 infected samples - Identification and quantification data http://www.proteomexchange.org/submission Ternent et al., Proteomics, 2014
- 17. ProteomeXchange: 1329 datasets up until October 2014 Origin: 271 USA 166 Germany 115 United Kingdom 73 Switzerland 70 China 68 Netherlands 67 France 55 Canada 44 Spain 42 Belgium 33 Sweden 31 Australia 31 Denmark 31 Japan 20 India 20 Norway 19 Taiwan 17 Ireland 16 Austria 14 Finland 14 Italy 12 Republic of Korea 11 Brazil 9 Russia 8 Israel 7 Singapore … Type: 437 PRIDE complete 792 PRIDE partial 63 PeptideAtlas/PASSEL complete 14 MassIVE 23 reprocessed Publicly Accessible: 691 datasets, 52% of all 86% PRIDE 12% PASSEL 2% MassIVE Top Species studied by at least 10 datasets: 577 Homo sapiens 165 Mus musculus 56 Saccharomyces cerevisiae 53 Arabidopsis thaliana 29 Rattus norvegicus 22 Escherichia coli 17 Bos taurus 16 Mycobacterium tuberculosis 13 Oryza sativa 13 Drosophila melanogaster 13 Glycine max ~ 290 species in total Data volume: Total: ~55 TB Number of all files: ~131,000 PXD000320-324: ~ 5 TB PXD000065: ~ 1.4TB Datasets/year: 2012: 102 2013: 527 2014: 700
- 18. Overview • The ProteomeXchange (PX) consortium • Highlights in the last year • PRIME-XS datasets
- 19. PX submission tool: PRIME-XS tags 37 Datasets in total (both public and private at present): - 20 from the Netherlands - 4 from UK - 2 from Austria, Belgium, Denmark, Spain and Switzerland - 1 from France and USA.
- 20. PRIME-XS are now tagged in PRIDE PRIME-XS datasets are now tagged and can be browsed as a group http://www.ebi.ac.uk/pride/archive/simpleSearch?q=prime-xs
- 21. ProteomeCentral: Portal for all PX datasets http://proteomecentral.proteomexchange.org/cgi/GetDataset
- 22. Which are the most accessed datasets? PXD Identifier Total Hits Dataset title Publication PXD000561 153512 A draft map of the human proteome Kim et al., Nature,2014. PMID: 24870542 PXD000851 111587 Membrane proteomic analysis of colorectal cancer tissue Kume et al., MCP, 2014. PMID:24687888 PXD000865 51639 Mass spectrometry based draft of the human proteome Wilhelm et al., 2014, Nature, PMID:24870543
- 23. Total Numbers Which are the most accessed datasets?
- 24. Find the desired PRIDE project … … inspect the project details …. Reshake PRIDE data in PeptideShaker … and start re-analyzing the data! http://peptide-shaker.googlecode.com Vaudel M, Burkhart J, Zahedi RP, Berven FS, Sickmann A, Martens L, Barsnes H. Nature Biotechnology (in press)
- 25. A little bit of perspective Berlin 2011 Mallorca 2012 Annecy 2013 Split 2013
- 26. A little bit of perspective 2011 2012 2013 2014 PRIDE Inspector PX Submission Tool mzIdentML mzQuantML PRIDE/PX datasets qcML mzTab PRIDE web (2011) PRIDE Converter PRIDE Converter 2 PRIDE Inspector 2 PRIDE web (2014)
- 27. Conclusions • ProteomeXchange is widely used. – PRIDE contains most of the MS/MS datasets. – It has now a new consortium member: MassIVE (UCSD). – Around half of the datasets are already public. • Different open source tools available to facilitate the process: – File transfer speed should not be a problem (Aspera support)
- 28. Aknowledgements: People Attila Csordas Tobias Ternent Noemi del Toro Rui Wang Florian Reisinger Jose A. Dianes Johannes Griss Steven Lewis Yasset Perez-Riverol Henning Hermjakob All previous team members ProteomeXchange partners
- 29. Acknowledgements: Funding @pride_ebi pride-ebi@ebi.ac.uk pride-support@ebi.ac.uk http://www.proteomexchange.org http://code.google.com/p/pride-converter-2/