PRIDE and ProteomeXchange – Making proteomics data accessible and reusable
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The document discusses ProteomeXchange (PX), a consortium that aims to make proteomics data accessible and reusable. PX includes repositories like PRIDE, PeptideAtlas, and MassIVE. It allows standard data submission between repositories through a common identifier space. The document outlines the PX submission workflow, describes components like the PX submission tool and PRIDE Inspector. It also provides statistics on data available through PX, with over 1,300 datasets contributed primarily from human, mouse and yeast studies. Future plans include better integration of proteomics resources to facilitate data reuse.
PRIDE and ProteomeXchange – Making proteomics data accessible and reusable
- 1. PRIDE and ProteomeXchange – Making proteomics data accessible and reusable Dr. Yasset Perez-Riverol Twitter: @ypriverol Github: ypriverol Bioinformatician - PRIDE Group Proteomics Services Team EMBL-EBI Hinxton, Cambridge, UK
- 2. Proteomics Services, EBI-EMBL Yasset Perez-Riverol yperez@ebi.ac.uk Protein Sequences IntAct Interactions PRIDE MS/MS Data Uniprot BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014) Reactome Pathways Biomodels
- 3. Overview • The ProteomeXchange (PX) consortium • PRIDE and ProteomeXchange Yasset Perez-Riverol yperez@ebi.ac.uk BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014) • PRIDE Components. • Current and future developments.
- 4. 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 MassIVE (UCSD, San Diego). • Common identifier space (PXD identifiers) • Two supported data workflows: MS/MS and SRM. • Main objective: Make data available and reusable. http://www.proteomexchange.org Yasset Perez-Riverol yperez@ebi.ac.uk BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014)
- 5. ProteomeXchange data workflow Results Raw Data* Yasset Perez-Riverol yperez@ebi.ac.uk ProteomeCentral PRIDE (MS/MS data) BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014) Metadata / Manuscript Journals UniProt/ neXtProt Peptide Atlas Other DBs Receiving r e positories PASSEL (SRM data) Other DBs GPMDB Researcher’s results Reprocessed results Raw data* Metadata MassIVE (MS/MS data) Vizcaíno et al., Nat Biotechnol, 2014
- 6. Yasset Perez-Riverol yperez@ebi.ac.uk BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014) MassIVE (UCSD) http://proteomics.ucsd.edu/service/massive/ • Just joined ProteomeXchange on June 2014
- 7. http://www.peptideatlas.org/passel/ Yasset Perez-Riverol yperez@ebi.ac.uk • Suitable for SRM assays • Part of PeptideAtlas set of resources. BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014) Farrah et al., Proteomics, 2012 PASSEL: repository for SRM data
- 8. Pride: Protein identification Database http://www.ebi.ac.uk/pride/archive/ Yasset Perez-Riverol yperez@ebi.ac.uk Vizcaíno et al., N. A Research, 2014 BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014)
- 9. PX Submission workflow for MS/MS data 1. Mass spectrometer output files: raw data (binary files) or Yasset Perez-Riverol yperez@ebi.ac.uk peak list spectra in a standardized format (mzML, mzXML). BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014) 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 based on Ontologies and Controlled Vocabularies. 4. Other files: Optional files: a. QUANT: Quantification related results e. FASTA b. PEAK: Peak list files c. OTHER: Any other file type Published Raw Files Other files Ternent et al., Proteomics, 2014
- 10. Complete submissions using mzIdentML Yasset Perez-Riverol yperez@ebi.ac.uk An increasing number of tools support export to mzIdentML 1.1 BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014) Search Engine Results + MS files Search engines mzIdentML - 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. Metadata • Key-Value pairs Protein • Table-based Peptide • Table-based PSM • Table-based Small Molecule • Table-based Yasset Perez-Riverol yperez@ebi.ac.uk • Basic information about experiment and sample • Basic information about protein identifications • Information about quantified peptides • Information about identified spectra • Basic information about identified small molecules BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014) mzTab http://mztab.googlecode.com J. Griss et al., MCP, 2014
- 12. PRIDE Components: Submission Process PRIDE Converter PRIDE Inspector PX Submission Tool Yasset Perez-Riverol yperez@ebi.ac.uk BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014)
- 13. PRIDE Components: 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. Yasset Perez-Riverol yperez@ebi.ac.uk BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014) Published Raw Other files http://www.proteomexchange.org/submission PX submission tool
- 14. Available for complete submissions Yasset Perez-Riverol yperez@ebi.ac.uk BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014) 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 Quantitation (work in progress) https://github.com/PRIDE-Toolsuite/
- 15. Pride Components: Pipelines and Visualization Yasset Perez-Riverol yperez@ebi.ac.uk BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014) Submission validation Pipeline • QC of files submitted. • Metadata check. Submission pipeline. • Add Project to Database (files location, general statistics, metadata) Publication pipeline • Conversion of files to mztab • Conversion spectra peaks to mgf • Index de information in Solr server
- 16. Pride Components: Services & Web components Yasset Perez-Riverol yperez@ebi.ac.uk BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014)
- 17. ProteomeCentral: Portal for all PX datasets http://proteomecentral.proteomexchange.org/cgi/GetDataset Yasset Perez-Riverol yperez@ebi.ac.uk BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014)
- 18. ProteomeXchange: 1329 datasets up until October 2014 Yasset Perez-Riverol yperez@ebi.ac.uk BioHackthon 2014 Miyagi, Japan (Nov 9-14, 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
- 19. Journals and Data Deposition Yasset Perez-Riverol yperez@ebi.ac.uk Journal BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014) Number of Submissions
- 20. Yasset Perez-Riverol yperez@ebi.ac.uk BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014) Data Access ? Total Numbers
- 21. Future developments • Make the data reusable. • Integration of different Protein expression resources • PRIDE • PeptideAtlas • ProteomicsDB • Human Proteome Map Yasset Perez-Riverol yperez@ebi.ac.uk BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014) PXD Identifier Hits Dataset title PXD000561 153512 A draft map of the human proteome PXD000865 51639 Mass spectrometry based draft of the human proteome
- 22. Web Services PROXI PROXI PROXI PROXI PROXI Yasset Perez-Riverol yperez@ebi.ac.uk BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014) PROXI Clients Repositories & Databases Registry Data Perez-Riverol Y, Proteomics, 20014
- 23. 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) • Data depostion enables and promotes data reuse. • ProteomeXchange is open to new members. Yasset Perez-Riverol yperez@ebi.ac.uk BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014)
- 24. Acknowledgements PRIDE Team Juan A. Vizcaino (Group Leader) Attila Csordas Rui Wang Florian Reisinger Jose A. Dianes Tobias Ternent Yasset Perez-Riverol Noemi del Toro Henning Hermjakob Yasset Perez-Riverol yperez@ebi.ac.uk PeptideAtlas Team (ISB, Seattle) Eric Deutsch Terry Farrah Zhi Sun MAssIVE Nuno Bandeira And many other PX partners and stakeholders BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014)
- 25. Yasset Perez-Riverol yperez@ebi.ac.uk BioHackthon 2014 Miyagi, Japan (Nov 9-14, 2014) Questions?