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![Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2016
Hinxton, 8 December 2016
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D
From original publication [13] Reconstructed ProteomeXchange data
1. Thermo RAW data / UDP
2. Mirion Software (JLU)
1. Thermo RAW data / UDP
2. Convert to imzML
3. Upload to PRIDE
(EBI, Cambridge, UK)
4. Download from PRIDE
5. Display in MSiReader
- Vendor-independent data format
- Freely available software (open source)
- ‘open data‘ – free to reuse
- Anybody can do this!
A public repository for mass spectrometry imaging data
Römpp et al., 2015
PRIDE
database
European
Bioinformatics
Institute,
Cambridge, UK
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4. Download](https://image.slidesharecdn.com/03pridepx-161209110126/75/Pride-and-ProteomeXchange-31-2048.jpg)
Uploaded byJuan Antonio Vizcaino
Pride and ProteomeXchange
The document discusses PRIDE, a proteomics data repository at EMBL-EBI. It describes how PRIDE stores mass spectrometry proteomics data, its role within the ProteomeXchange consortium, and how researchers can submit data to PRIDE including the use of mzIdentML and PRIDE tools.
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Pride and ProteomeXchange
- 1. PRIDE resources andProteomeXchange Dr. Juan Antonio Vizcaíno Proteomics Team Leader EMBL-EBI Hinxton, Cambridge, UK
- 2. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 Data resources at EMBL-EBI Genes, genomes & variation ArrayExpress Expression Atlas PRIDE InterPro Pfam UniProt ChEMBL ChEBI Molecular structures Protein Data Bank in Europe Electron Microscopy Data Bank European Nucleotide Archive European Variation Archive European Genome-phenome Archive Gene & protein expression Protein sequences, families & motifs Chemical biology Reactions, interactions & pathways IntAct Reactome MetaboLights Systems BioModels Enzyme Portal BioSamples Ensembl Ensembl Genomes GWAS Catalog Metagenomics portal Europe PubMed Central Gene Ontology Experimental Factor Ontology Literature & ontologies
- 3. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 • PRIDE Archive (in the context of ProteomeXchange and the PSI standards) • How to submit data to PRIDE: PRIDE tools • How to access data in PRIDE Archive • PRIDE Cluster and PRIDE Proteomes Overview
- 4. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 • PRIDE Archive (in the context of ProteomeXchange and the PSI standards) • How to submit data to PRIDE: PRIDE tools • How to access data in PRIDE Archive • PRIDE Cluster and PRIDE Proteomes Overview
- 5. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 • PRIDE stores mass spectrometry (MS)-based proteomics data: • Peptide and protein expression data (identification and quantification) • Post-translational modifications • Mass spectra (raw data and peak lists) • Technical and biological metadata • Any other related information • Full support for tandem MS approaches • Any type of data can be stored. PRIDE (PRoteomics IDEntifications) Archive http://www.ebi.ac.uk/pride/archive Martens et al., Proteomics, 2005 Vizcaíno et al., NAR, 2016
- 6. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 Data content in PRIDE Archive • Submission driven resource • PRIDE is split in datasets (group of assays) • An assay represents one MS run (in most cases). • No data reprocessing at present. PRIDE aims to represent the author’s view on the data • Supported formats: PRIDE XML and mzIdentML. • Raw data is also now stored
- 7. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 ProteomeXchange: A Global, distributed proteomics database PASSEL (SRM data) PRIDE (MS/MS data) MassIVE (MS/MS data) Raw ID/Q Meta jPOST (MS/MS data) Mandatory raw data deposition since July 2015 • Goal: Development of a framework to allow standard data submission and dissemination pipelines between the main existing proteomics repositories. http://www.proteomexchange.org New in 2016 Vizcaíno et al., Nat Biotechnol, 2014 Deutsch et al., NAR, 2017, in press
- 8. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 ProteomeCentral Metadata / Manuscript Raw Data Results Journals Peptide Atlas Receiving repositories PRIDE Researcher’s results Raw data Metadata PASSEL Research groups Reanalysis of datasets MassIVE jPOST MS/MS data (as complete submissions) Any other workflow (mainly partial submissions) DATASETS SRM data Reprocessed results MassIVE ProteomeXchange data workflow Vizcaíno et al., Nat Biotechnol, 2014 Deutsch et al., NAR, 2017, in press
- 9. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 ProteomeCentral Metadata / Manuscript Raw Data Results Journals UniProt/ neXtProtPeptide Atlas Other DBs Receiving repositories PRIDE GPMDBResearcher’s results Raw data Metadata PASSEL proteomicsDB Research groups Reanalysis of datasets MassIVE jPOST MS/MS data (as complete submissions) Any other workflow (mainly partial submissions) DATASETS OmicsDI Integration with other omics datasets SRM data Reprocessed results MassIVE ProteomeXchange data workflow
- 10. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 PRIDE: Source of MS proteomics data • PRIDE Archive already provides or will soon provide MS proteomics data to other EMBL-EBI resources such as UniProt, Ensembl and the Expression Atlas. http://www.ebi.ac.uk/pride
- 11. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 • PRIDE Archive (in the context of ProteomeXchange and the PSI standards) • How to submit data to PRIDE: PRIDE tools • How to access data in PRIDE Archive • A sneak peak to other PRIDE resources Overview
- 12. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 ProteomeCentral Metadata / Manuscript Raw Data Results Journals Peptide Atlas Receiving repositories PRIDE Researcher’s results Raw data Metadata PASSEL Research groups Reanalysis of datasets MassIVE jPOST MS/MS data (as complete submissions) Any other workflow (mainly partial submissions) DATASETS SRM data Reprocessed results MassIVE ProteomeXchange data workflow
- 13. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 Complete Partial 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.
- 14. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 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 not so detailed
- 15. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 How to perform a complete PX submission to PRIDE • Decide between a complete/partial submission • File conversion/export to mzIdentML (or PRIDE XML) • File check before submission (PRIDE Inspector) • Experimental annotation and actual file submission (PX submission tool) • Post-submission steps
- 16. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 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 the mzIdentML data standard (or PRIDE XML). 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
- 17. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 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 the mzIdentML data standard (or PRIDE XML). 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 (the list can be extended): 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
- 18. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 PRIDE Components: Data Submission Process PRIDE Converter 2 PRIDE Inspector PX Submission Tool mzIdentML PRIDE XML In addition to PRIDE Archive, the PRIDE team develops and maintains different tools and software libraries to facilitate the handling and visualisation of MS proteomics data and the submission process
- 19. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 Tools ‘RESULT’ file generation Final ‘RESULT’ file mzIdentML ‘RESULT’ Native file export to mzIdentML Spectra files (mzML, mzXML, mzData, mgf, pkl, ms2, dta, apl) Mascot ProteinPilot Scaffold PEAKS MSGF+ Others Native File export
- 20. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 Complete submissions Search Engine Results + MS files Search engines mzIdentML - Mascot - MSGF+ - MyriMatch and related tools from D. Tabb’s lab - OpenMS - PEAKS - PeptideShaker - ProCon (ProteomeDiscoverer, Sequest) - Scaffold - TPP via the idConvert tool (ProteoWizard) - ProteinPilot (from version 5.0) - X!Tandem native conversion (Beta, PILEDRIVER) - Others: library for X!Tandem conversion, lab internal pipelines, … - Crux - Soon: ProteomeDiscoverer (Thermo) An increasing number of tools support export to mzIdentML 1.1 - Referenced spectral files need to be submitted as well (all open formats are supported). Updated list: http://www.psidev.info/tools-implementing-mzIdentML#.
- 21. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 Tools ‘RESULT’ file generation Final ‘RESULT’ file mzTab ‘RESULT’ Coming soon: Support for mzTab Spectra files (mzML, mzXML, mzData, mgf, pkl, ms2, dta, apl) Mascot MaxQuant Others Native File export
- 22. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 PRIDE Components: Submission Process PRIDE Converter 2 PRIDE Inspector PX Submission Tool mzIdentML PRIDE XML 2
- 23. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 PRIDE Inspector Toolsuite Wang et al., Nat. Biotechnology, 2012 Perez-Riverol et al., MCP, 2016 PRIDE Inspector PRIDE Inspector 2 supports: - PRIDE XML - mzIdentML + all types of spectra files - mzML - mzTab identification and Quantification (+ all types of spectra files) https://github.com/PRIDE-Toolsuite/
- 24. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 PRIDE Inspector Toolsuite PRIDE Inspector 2 https://github.com/PRIDE-Toolsuite/ New visualisation functionality for Protein Groups
- 25. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 PRIDE Components: Submission Process PRIDE Converter 2 PRIDE Inspector PX Submission Tool mzIdentML PRIDE XML 3
- 26. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 PX Submission Tool Desktop application for data submissions to ProteomeXchange via PRIDE • Implemented in Java 7 • Streamlines the submission process • Capture mappings between files • Retain metadata • Fast file transfer with Aspera (FASP® transfer technology) – FTP also available • Command line option Submission tool screenshot
- 27. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 PX submission tool: screenshots
- 28. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 PRIDE Archive – over 5,000 datasets from over 51 countries and 2,000 groups • USA – 814 datasets • Germany – 528 • UK – 338 • China – 328 • France – 222 • Netherlands – 175 • Canada - 137 Data volume: • Total: ~275 TB • Number of all files: ~560,000 • PXD000320-324: ~ 4 TB • PXD002319-26 ~2.4 TB • PXD001471 ~1.6 TB • 1,973 datasets i.e. 52% of all are publicly accessible • ~90% of all ProteomeXchange datasets YearSubmissions All submissions Complete PRIDE Archive growth In the last 12 months: ~165 submitted datasets per month Top Species studied by at least 100 datasets: 2,010 Homo sapiens 604 Mus musculus 191 Saccharomyces cerevisiae 140 Arabidopsis thaliana 127 Rattus norvegicus >900 reported taxa in total
- 29. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 Public data release: when does it happen? • When the author tells us to do it (the authors can do it by themselves) • When we find out that a dataset has been published • We look for PXD identifiers in PubMed abstracts. • If your PXD identifier is not in the abstract, a paper may have been published and the data is still private. Let us know! • New web form in the PRIDE web to facilitate the process
- 30. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 Partial submissions can be used to store other data types • Everything can be stored, not only MS/MS data: very flexible mechanism to be able to capture all types of datasets. • PRIDE does not actively store SRM data (PASSEL). • Top down proteomics datasets. • Mass Spectrometry Imaging datasets. • Data independent acquisition techniques: e.g. SWATH-MS, MSE, HD-MSE, etc.
- 31. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 C D From original publication [13] Reconstructed ProteomeXchange data 1. Thermo RAW data / UDP 2. Mirion Software (JLU) 1. Thermo RAW data / UDP 2. Convert to imzML 3. Upload to PRIDE (EBI, Cambridge, UK) 4. Download from PRIDE 5. Display in MSiReader - Vendor-independent data format - Freely available software (open source) - ‘open data‘ – free to reuse - Anybody can do this! A public repository for mass spectrometry imaging data Römpp et al., 2015 PRIDE database European Bioinformatics Institute, Cambridge, UK 3. Upload 4. Download
- 32. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 • PRIDE Archive (in the context of ProteomeXchange and the PSI standards) • How to submit data to PRIDE: PRIDE tools • How to access data in PRIDE Archive • PRIDE Cluster and PRIDE Proteomes Overview
- 33. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 Ways to access data in PRIDE Archive • PRIDE web interface • File repository • REST web service • PRIDE Inspector tool
- 34. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 PRIDE Archive web interface
- 35. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 PRIDE Archive web interface (2)
- 36. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 ProteomeCentral Metadata / Manuscript Raw Data Results Journals Peptide Atlas Receiving repositories PRIDE Researcher’s results Raw data Metadata PASSEL Research groups Reanalysis of datasets MassIVE jPOST MS/MS data (as complete submissions) Any other workflow (mainly partial submissions) DATASETS SRM data Reprocessed results MassIVE ProteomeXchange data workflow
- 37. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 ProteomeCentral: Centralised portal for all PX datasets http://proteomecentral.proteomexchange.org/cgi/GetDataset
- 38. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 RSS feed and Twitter for following announcements of public datasets http://groups.google.com/group/proteomexchange/feed/rss_v2_0_msgs.xml @proteomexchange
- 39. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 • PRIDE Archive (in the context of ProteomeXchange and the PSI standards) • How to submit data to PRIDE: PRIDE tools • How to access data in PRIDE Archive • PRIDE Cluster and PRIDE Proteomes Overview
- 40. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 Added value resources: PRIDE Cluster and PRIDE Proteomes • Condensed and across-data set, QC-filtered view on PRIDE data. • PRIDE Cluster: Peptide centric. • PRIDE Proteomes: Protein centric (identification data)
- 41. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 PRIDE Cluster • Provide an aggregated peptide centric view of PRIDE Archive. • Hypothesis: same peptide will generate similar MS/MS spectra across experiments. • New version of spectral clustering algorithm to reliably group spectra coming from the same peptide. • Enables QC of peptide-spectrum matches (PSMs). Infer reliable identifications by comparing submitted identifications of spectra within a cluster. After clustering, a representative spectrum is built for all peptides consistently identified across different datasets. Used to build spectral libraries (for 16 species). Griss et al., Nat. Methods, 2013 Griss et al., Nat. Methods, 2016
- 42. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 Example: one perfect cluster - 880 PSMs give the same peptide ID - 4 species - 28 datasets - Same instruments http://www.ebi.ac.uk/pride/cluster/
- 43. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 PRIDE Cluster as a Public Data Mining Resource 43 • http://www.ebi.ac.uk/pride/cluster • Spectral libraries for 16 species. • All clustering results, as well as specific subsets of interest available. • Source code (open source) and Java API
- 44. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 PRIDE Proteomes web interface: identification info Unique/Shared Peptides Mass spec-based sequence coverage PTM detected ( ) Observed tissues Biological vs Sample Prep PTMs http://wwwdev.ebi.ac.uk/pride/proteomes/
- 45. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 • Main characteristics of PRIDE Archive and ProteomeXchange • PX/PRIDE submission workflow for MS/MS data • PRIDE Inspector • PX submission tool • PRIDE/ProteomeXchange has become the de facto standard for data submission and data availability in proteomics • PRIDE Proteomes and PRIDE Cluster: new resources Conclusions
- 46. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 PRIDE resources
- 47. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 Do you want to know a bit more…? http://www.slideshare.net/JuanAntonioVizcaino
- 48. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 Aknowledgements: People Attila Csordas Tobias Ternent Gerhard Mayer (de.NBI) Johannes Griss Yasset Perez-Riverol Manuel Bernal-Llinares Andrew Jarnuczak Enrique Perez Former team members, especially Rui Wang, Florian Reisinger, Noemi del Toro, Jose A. Dianes & Henning Hermjakob Acknowledgements: The PRIDE Team All data submitters !!! @pride_ebi
- 49. Juan A. Vizcaíno juan@ebi.ac.uk WTProteomics Bioinformatics Course 2016 Hinxton, 8 December 2016 Questions?