An overview of the PRIDE ecosystem of resources and computational tools for mass spectrometry proteomics data
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The document provides an overview of the PRIDE ecosystem of resources and computational tools for mass spectrometry proteomics data. It describes PRIDE Archive and ProteomeXchange as repositories for proteomics data, as well as tools like PRIDE Inspector for visualizing and validating data. It also discusses how public proteomics data is increasingly being reused, and added-value resources like PRIDE Cluster and PRIDE Proteomes that provide aggregated views of proteomics data.
An overview of the PRIDE ecosystem of resources and computational tools for mass spectrometry proteomics data
- 1. An overview of the PRIDE ecosystem of resources and computational tools for mass spectrometry proteomics data Dr. Juan Antonio Vizcaíno EMBL-European Bioinformatics Institute Hinxton, Cambridge, UK
- 2. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 Overview • PRIDE Archive and ProteomeXchange • PRIDE tools • Reuse of public proteomics data • PRIDE added-value resources: PRIDE Cluster and PRIDE Proteomes
- 3. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 What is a proteomics publication in 2016? • Proteomics studies generate potentially large amounts of data and results. • Ideally, a proteomics publication needs to: • Summarize the results of the study • Provide supporting information for reliability of any results reported • Information in a publication: • Manuscript • Supplementary material • Associated data submitted to a public repository
- 4. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 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 PRIDE (PRoteomics IDEntifications) Archive http://www.ebi.ac.uk/pride/archive Martens et al., Proteomics, 2005 Vizcaíno et al., NAR, 2016
- 5. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 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 Deustch et al., NAR, 2017, in press
- 6. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 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 Deustch et al., NAR, 2017, in press
- 7. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 ProteomeCentral: Centralised portal for all PX datasets http://proteomecentral.proteomexchange.org/cgi/GetDataset
- 8. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 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 Deustch et al., NAR, 2017, in press
- 9. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 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 Vizcaíno et al., Nat Biotechnol, 2014 Deustch et al., NAR, 2017, in press
- 10. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 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 EBI Expression Atlas. http://www.ebi.ac.uk/pride/archive
- 11. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 PRIDE Archive – over 4,500 datasets from over 51 countries and 1,700 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
- 12. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 Overview • PRIDE Archive and ProteomeXchange • PRIDE tools • Reuse of public proteomics data • PRIDE added-value resources: PRIDE Cluster and PRIDE Proteomes
- 13. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 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
- 14. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 PRIDE Inspector Toolsuite Wang et al., Nat. Biotechnology, 2012 Perez-Riverol et al., Bioinformatics, 2015 Perez-Riverol et al., MCP, 2016 • PRIDE Inspector - standalone tool to enable visualisation and validation of MS data. • Build on top of ms-data-core-api - open source algorithms and libraries for computational proteomics. • Supported file formats: mzIdentML, mzML, mzTab (PSI standards), and PRIDE XML. • Broad functionality. https://github.com/PRIDE-Utilities/ms-data-core-api https://github.com/PRIDE-Toolsuite/pride-inspector Summary and QC charts Peptide spectra annotation and visualization
- 15. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 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
- 16. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 Overview • PRIDE Archive and ProteomeXchange • PRIDE tools • Reuse of public proteomics data • PRIDE added-value resources: PRIDE Cluster and PRIDE Proteomes
- 17. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 Datasets are being reused more and more…. Vaudel et al., Proteomics, 2016 Data download volume for PRIDE Archive in 2015: 198 TB 0 50 100 150 200 250 2013 2014 2015 2016 Downloads in TBs
- 18. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 Data sharing in Proteomics Vaudel et al., Proteomics, 2016
- 19. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 Draft Human proteome papers published in 2014 Wilhelm et al., Nature, 2014 Kim et al., Nature, 2014 •Two independent groups claimed to have produced the first complete draft of the human proteome by MS. • Some of their findings are controversial and need further validation… but generated a lot of discussion and put proteomics in the spotlight. •They used many different tissues. Nature cover 29 May 2014
- 20. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 Draft Human proteome papers published in 2014 Wilhelm et al., Nature, 2014 •Around 60% of the data used for the analysis comes from previous experiments, most of them stored in proteomics repositories such as PRIDE/ProteomeXchange, PASSEL or MassIVE. •They complement that data with “exotic” tissues.
- 21. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 Data sharing in Proteomics Vaudel et al., Proteomics, 2016
- 22. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 Examples of repurposing in proteogenomics
- 23. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 Public datasets from different omics: OmicsDI http://www.ebi.ac.uk/Tools/omicsdi/ • Aims to integrate of ‘omics’ datasets (proteomics, transcriptomics, metabolomics and genomics at present). PRIDE MassIVE jPOST PASSEL GPMDB ArrayExpress Expression Atlas MetaboLights Metabolomics Workbench GNPS EGA Perez-Riverol et al., Nat Biotechnol, in press
- 24. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 OmicsDI: Portal for omics datasets
- 25. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 OmicsDI: Portal for omics datasets
- 26. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 Overview • PRIDE Archive and ProteomeXchange • PRIDE tools • Reuse of public proteomics data • PRIDE added-value resources: PRIDE Cluster and PRIDE Proteomes
- 27. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 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)
- 28. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 Data sharing in Proteomics Vaudel et al., Proteomics, 2016
- 29. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 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
- 30. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 Example: one perfect cluster - 880 PSMs give the same peptide ID - 4 species - 28 datasets - Same instruments http://wwwdev.ebi.ac.uk/pride/cluster/
- 31. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 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/
- 32. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 Conclusions • PRIDE Archive and ProteomeXchange have become the standard platform for public data deposition in proteomics. • PRIDE Inspector: support for data standards. • PX submission tool. • Reuse of public proteomics data is increasing: many opportunities for data miners. • OmicsDI: new platform to identify public datasets coming from different omics technologies (more possibilities for data reuse!). • PRIDE Cluster and PRIDE Proteomes.
- 33. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 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 @proteomexchange
- 34. Juan A. Vizcaíno [email protected] Mass Spectrometry and Proteomics Congress 2016 London, 15 November 2016 Questions? http://www.slideshare.net/JuanAntonioVizcaino