AHUPO_Vizcaino_remote_presentation_082014
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ProteomeXchange: Update for the C-HPP Consortium. 10th C-HPP Workshop: “Proteome data management and identification of missing proteins". Bangkok, Thailand. 09/08/2015. Remote presentation.
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AHUPO_Vizcaino_remote_presentation_082014
- 1. ProteomeXchange: Update for the C-HPP Consortium Dr. Juan Antonio Vizcaíno PRIDE Group Coordinator Proteomics Services Team EMBL-EBI Hinxton, Cambridge, UK
- 2. Overview • The ProteomeXchange (PX) consortium • How to submit and access data in PX via PRIDE • How to access PX data Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014 • Miscellaneous • Your questions for the discussion
- 3. Overview • The ProteomeXchange (PX) consortium • How to submit and access data in PX via PRIDE • How to access PX data Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014 • Miscellaneous • Your questions for the discussion
- 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 (very recently) MassIVE (UCSD, San Diego). • EU FP7 CA (01/2011-> 06/2014). • Common identifier space (PXD identifiers) • Two supported data workflows: MS/MS and SRM. • Main objective: Make life easier for researchers http://www.proteomexchange.org Vizcaíno et al., Nat Biotechnol, 2014 Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014
- 5. ProteomeXchange data workflow Results Raw Data* Juan A. Vizcaíno juan@ebi.ac.uk PRIDE (MS/MS data) 10th C-HPP Workshop Bangkok, 9 August 2014 ProteomeCentral 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. MassIVE (UCSD) • Just joined ProteomeXchange on June 2014 • Similar role to PRIDE (although not yet formalised). Juan A. Vizcaíno juan@ebi.ac.uk http://proteomics.ucsd.edu/service/massive/ 10th C-HPP Workshop Bangkok, 9 August 2014
- 7. ProteomeXchange data workflow Results Raw Data* Juan A. Vizcaíno juan@ebi.ac.uk PRIDE (MS/MS data) 10th C-HPP Workshop Bangkok, 9 August 2014 ProteomeCentral 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
- 8. Overview • The ProteomeXchange (PX) consortium • How to submit and access data in PX via PRIDE • How to access PX data Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014 • Miscellaneous • Your questions for the discussion
- 9. PRIDE (PRoteomics IDEntifications) database http://www.ebi.ac.uk/pride Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014 • Focused on MS/MS approaches Martens et al., Proteomics, 2005 Vizcaíno et al., NAR, 2013
- 10. Manuscript just out detailing the process Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014 Ternent et al., Proteomics, 2014, in press http://www.proteomexchange.org/submission
- 11. • The challenge: PRIDE is an archival database, aiming to provide long term access to proteomics data from all workflows • Huge variety of proteomics workflows and file formats establishes a data management nightmare • Previously, we had to decline submissions since there were in formats we could not handle. • Solution: Complete and Partial submissions • Complete submission • All data in standard formats, accessible through PRIDE Inspector and web interface (not yet) • Results searchable in DB • Submission gets DOI • Metadata, raw data, results are mandatory in both cases, just not parsed for Juan A. Vizcaíno juan@ebi.ac.uk Complete vs Partial submissions 10th C-HPP Workshop Bangkok, 9 August 2014 partial submissions • Partial submission • Part of data in non-standard formats • Files are made available to download • Only metadata searchable • No DOI
- 12. PX Data workflow for MS/MS data Juan A. Vizcaíno juan@ebi.ac.uk 1. Mass spectrometer output files: raw data (binary files) or peak list spectra in a standardized format (mzML, mzXML). 10th C-HPP Workshop Bangkok, 9 August 2014 Raw Files
- 13. PX Data workflow for MS/MS data Juan A. Vizcaíno juan@ebi.ac.uk 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. 10th C-HPP Workshop Bangkok, 9 August 2014 Published Raw Files
- 14. Juan A. Vizcaíno juan@ebi.ac.uk Complete submissions An increasing number of tools support export to mzIdentML 1.1 10th C-HPP Workshop Bangkok, 9 August 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 Updated list: http://www.psidev.info/tools-implementing-mzIdentML#.
- 15. Available for complete submissions Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 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 Ident (work in progress) http://code.google.com/p/pride-toolsuite/ wiki/PRIDEInspector
- 16. PX Data workflow for MS/MS data Juan A. Vizcaíno juan@ebi.ac.uk 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. 10th C-HPP Workshop Bangkok, 9 August 2014 Published Raw Files
- 17. PX Data workflow for MS/MS data Juan A. Vizcaíno juan@ebi.ac.uk 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 10th C-HPP Workshop Bangkok, 9 August 2014 Published Raw Files Other files
- 18. PX submission tool • Capture the mappings between the different types of files. • Make the file upload process straightforward to the submitter (It transfers all the files using Aspera or FTP). Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014 Published Raw Other files http://www.proteomexchange.org/submission PX submission tool • Command line alternative: some scripting is needed
- 19. Fast file transfer with Aspera Part C: Difficulties in Connections: Q1. How to make the connections between local server and central DBs much faster and accessible (e.g. local server and ProteomeXchange)? Juan A. Vizcaíno juan@ebi.ac.uk - Aspera is the default file transfer protocol to PRIDE: - PX Submission tool - Command line - Up to 50X faster than FTP 10th C-HPP Workshop Bangkok, 9 August 2014 File transfer speed should not be a problem!!
- 20. PX submission tool Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014
- 21. PX submission tool: HPP tags Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014
- 22. • The challenge: PRIDE is an archival database, aiming to provide long term access to proteomics data from all workflows • Huge variety of proteomics workflows and file formats establishes a data management nightmare • Previously, we had to decline submissions since there were in formats we could not handle. • Solution: Complete and Partial submissions • Complete submission • All data in standard formats, accessible through PRIDE Inspector and web interface (not yet) • Results searchable in DB • Submission gets DOI • Metadata, raw data, results are mandatory in both cases, just not parsed for Juan A. Vizcaíno juan@ebi.ac.uk Complete vs Partial submissions 10th C-HPP Workshop Bangkok, 9 August 2014 partial submissions • Partial submission • Part of data in non-standard formats • Files are made available to download • Only metadata searchable • No DOI
- 23. • Everything can be stored, not only MS/MS data: very flexible mechanism to be able to capture all types of datasets • Top down proteomics datasets • Mass Spectrometry Imaging datasets • Data independent acquisition techniques: e.g. SWATH-MS datasets, among Juan A. Vizcaíno juan@ebi.ac.uk Partial submissions 10th C-HPP Workshop Bangkok, 9 August 2014 other DIA approaches
- 24. ProteomeXchange: 1,148 datasets up until August 2014 Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014 Origin: 235 USA 142 Germany 97 United Kingdom 67 Switzerland 64 Netherlands 62 China 60 France 48 Canada 43 Spain 36 Belgium 32 Sweden 29 Australia 26 Denmark 23 Japan 18 Taiwan 17 India 16 Ireland 14 Norway 14 Italy 12 Finland 11 Republic of Korea 10 Brazil 8 Austria 7 Israel 7 Singapore … Type: 386 PRIDE complete 687 PRIDE partial 51 PeptideAtlas/PASSEL complete 1 MassIVE 23 reprocessed Publicly Accessible: 544 datasets, 50% of all 90% PRIDE 10% PASSEL Top Species studied by at least 10 datasets: 510 Homo sapiens 142 Mus musculus 46 Saccharomyces cerevisiae 45 Arabidopsis thaliana 23 Rattus norvegicus 16 Escherichia coli 15 Bos taurus 15 Mycobacterium tuberculosis 13 Oryza sativa 12 Drosophila melanogaster 12 Glycine max ~ 265 species in total Data volume: Total: ~51 TB Number of all files: ~130,000 PXD000320-324: ~ 5 TB PXD000065: ~ 1.4TB Datasets/year: 2012: 102 2013: 527 2014: 519
- 25. Overview • The ProteomeXchange (PX) consortium • How to submit and access data in PX via PRIDE • How to access PX data Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014 • Miscellaneous • Your questions for the discussion
- 26. ProteomeXchange data workflow Results Raw Data* Juan A. Vizcaíno juan@ebi.ac.uk PRIDE (MS/MS data) 10th C-HPP Workshop Bangkok, 9 August 2014 ProteomeCentral 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
- 27. ProteomeCentral: Portal for all PX datasets http://proteomecentral.proteomexchange.org/cgi/GetDataset Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014
- 28. ProteomeCentral: Portal for all PX datasets http://proteomecentral.proteomexchange.org/cgi/GetDataset Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014
- 29. Get notified about new PX datasets - Subscribe to the RSS Feed to receive information about the new datasets: http://groups.google.com/group/proteomexchange/feed/ rss_v2_0_msgs.xml Juan A. Vizcaíno juan@ebi.ac.uk Proteome Central Researchers 10th C-HPP Workshop Bangkok, 9 August 2014
- 30. Reuse of datasets in PeptideAtlas can be tracked Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014
- 31. Overview • The ProteomeXchange (PX) consortium • How to submit and access data in PX via PRIDE • How to access PX data Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014 • Miscellaneous • Your questions for the discussion
- 32. HPP datasets are now tagged The Projects are now tagged and can be browsed as a group of data sets." " Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014 Tags for: HPP, C-HPP and B/D-HPP
- 33. HPP PX datasets Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014
- 34. HPP PX datasets: some numbers Since January 2014, we started capturing the PI information - 25 HPP datasets: 22 C-HPP and 3 B/D-HPP - Countries represented in C-HPP: Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014 - 5 Spain - 4 South Korea - 3 Brazil, China Only a small proportion of the datasets have been made publicly available, at least through ProteomeXchange
- 35. For the near future in PRIDE… • Complete data workflow for data visualization in PRIDE Archive web • Improvement of existing PRIDE REST API • Incorporation of reprocessed data in PRIDE (in collaboration with Prof. L. Martens (VIB/Ghent) and Dr. A. Jones (U. Liverpool) • Integration of the data in the EBI Molecular Atlas Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014
- 36. Conclusions • ProteomeXchange is widely used. It has now a new consortium member: MassIVE (UCSD). • PRIDE is getting a lot of data via ProteomeXchange. Pipeline in production since summer 2012. More than 1,100 datasets have been already submitted. • Half of them already public. • Different open source tools available to facilitate the process: • File transfer speed should not be a problem (Aspera support) Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014
- 37. Acknowledgements PRIDE Team Attila Csordas Rui Wang Florian Reisinger Jose A. Dianes Tobias Ternent Yasset Perez-Riverol Noemi del Toro Henning Hermjakob Juan A. Vizcaíno juan@ebi.ac.uk EU FP7 grant number 260558 10th C-HPP Workshop Bangkok, 9 August 2014 PeptideAtlas Team (ISB, Seattle) Eric Deutsch Terry Farrah Zhi Sun Andrew R. Jones Lennart Martens Juan Pablo Albar Martin Eisenacher Gil Omenn And many other PX partners and stakeholders
- 38. Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014 Questions?
- 39. Overview • The ProteomeXchange (PX) consortium • How to submit and access data in PX via PRIDE • How to access PX data Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014 • Miscellaneous • Your questions for the discussion
- 40. Questions for discussion Part A: Proteomic Dataset with PXD: Q1. How to make deposited through ProteomeXchange or published data available for the consortium members as well as public DB managers (GPMDB, neXtProt, PeptideAtlas and ProteinAtlas)? • There is plenty of documentation available: • http://www.proteomexchange.com/submission • PRIDE documentation • Original paper (PMID: 24727771) and submission tutorial paper (PMID: 25047258). • Resources need to be devoted to this… Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014
- 41. Questions for discussion Part A: Proteomic Dataset with PXD: Q2. What can we do for such inaccessible datasets in the public DB? • Contact the author directly and convince him/her to make a submission to ProteomeXchange. Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014
- 42. Questions for discussion Part A: Proteomic Dataset with PXD: Q3. Do we need to ask people to place a link with PXD identifier on the Wiki in order to see which chromosome team placed which datasets online (for sharing)? • NO, in the PX submission tool it is possible to specify the tags for HPP and/or C-HPP or B/D-HPP. • Visit ‘ProteomeCentral’ and look for them. • Visit PRIDE and look for them there (specific tags) Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014
- 43. HPP datasets are now tagged The Projects are now tagged and can be browsed as a group of data sets." " Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014 Tags for: HPP, C-HPP and B/D-HPP
- 44. Questions for discussion Part B: Proteogenomic Dataset: Q1. How to make easy access to or deposit proteogenomic dataset including RNAseq and other types of genetic data? • Not easy to do at present. • NCBI and EBI have created “BioSamples databases” to be able to link different studies performed using the same sample. • Proteomics data could be submitted to PRIDE/ProteomeXchange and RNAseq data to e.g. ArrayExpress (EBI), linked by the same sample number. • Sample IDs coming from the BioSamples DB to be integrated in the PX submission tool and in PRIDE (expected before the end of Juan A. Vizcaíno juan@ebi.ac.uk 10th C-HPP Workshop Bangkok, 9 August 2014 the year).
- 45. Biosamples DB Juan A. Vizcaíno juan@ebi.ac.uk http://www.ebi.ac.uk/biosamples/ 10th C-HPP Workshop Bangkok, 9 August 2014
- 46. Fast file transfer with Aspera Part C: Difficulties in Connections: Q1. How to make the connections between local server and central DBs much faster and accessible (e.g. local server and ProteomeXchange)? Juan A. Vizcaíno juan@ebi.ac.uk - Aspera is the default file transfer protocol to PRIDE: - PX Submission tool - Command line - Up to 50X faster than FTP 10th C-HPP Workshop Bangkok, 9 August 2014 File transfer speed should not be a problem!!