PRIDE resources and ProteomeXchange
Dr. Juan Antonio Vizcaíno
PRIDE Group Coordinator
Proteomics Services Team
EMBL-EBI
Hi...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Data resources at EMBL-...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
• PRIDE Archive (in the...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
• PRIDE Archive (in the...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
ProteomeXchange Consort...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
• PRIDE stores mass spe...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PRIDE Mission
• To arch...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PRIDE Mission
• To arch...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Data content in PRIDE A...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
What is a proteomics pu...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Journal Submission Reco...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PRIDE: Source of MS pro...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
ProteomeXchange Consort...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
ProteomeCentral
Metadat...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
• PRIDE Archive (in the...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
ProteomeCentral
Metadat...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Complete
Partial
Comple...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Complete vs Partial sub...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
How to perform a comple...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PX Data workflow for MS...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PX Data workflow for MS...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PRIDE Components: Submi...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Search
output
files
Spe...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Tools ‘RESULT’ file gen...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Complete submissions
Se...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PRIDE Components: Submi...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PRIDE Inspector Toolsui...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PRIDE Inspector 2
PRIDE...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PRIDE Components: Submi...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
• Capture the mappings ...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PX submission tool: scr...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Fast file transfer with...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Manuscript published de...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PRIDE Archive: Number o...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
ProteomeXchange: 2,774 ...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Public data release: wh...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Partial submissions can...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
C
D
From original publi...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
• PRIDE Archive (in the...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Data access to PRIDE Ar...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
ProteomeCentral
Metadat...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
ProteomeCentral: Portal...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
RSS feed for public dat...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Ways to access data in ...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PRIDE Archive web inter...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PRIDE Archive web inter...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Vaudel M, Barsnes H, Be...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Find the desired PRIDE ...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
• PRIDE Archive (in the...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PRIDE resources
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PRIDE
Archive
Aggr
egat...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Sneak peak
• Provide an...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PRIDE Cluster - Concept...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PRIDE Cluster - Concept...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PRIDE Cluster Home page...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PRIDE Cluster: result o...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Examples: one perfect c...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Examples: one perfect c...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Examples: one perfect c...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Examples: very good clu...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Examples: very good clu...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Examples: one perfect c...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PRIDE Cluster – Spectra...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PRIDE Proteomes: reusin...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
PRIDE: Using it for giv...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Examples: one perfect c...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
• Main characteristics ...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Do you want to know a b...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Aknowledgements: People...
Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2015
Hinxton, 10 December 2015
Questions?
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PRIDE-ProteomeXchange

Lecture of the PRIDE resources and ProteomeXchange for the Wellcome Trust Proteomics Bioinformatics Course 2015
Published on: Mar 4, 2016
Published in: Science      
Source: www.slideshare.net


Transcripts - PRIDE-ProteomeXchange

  • 1. PRIDE resources and ProteomeXchange Dr. Juan Antonio Vizcaíno PRIDE Group Coordinator Proteomics Services Team EMBL-EBI Hinxton, Cambridge, UK
  • 2. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Data resources at EMBL-EBI Genes, genomes & variation RNA Central Array Express Expression Atlas Metabolights 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 & metabolite 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 WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 • 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 WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 • 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 WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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
  • 6. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 • 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) database http://www.ebi.ac.uk/pride/archive Martens et al., Proteomics, 2005 Vizcaíno et al., NAR, 2013
  • 7. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PRIDE Mission • To archive all types of proteomics mass spectrometry data for the purpose of supporting reproducible research, allowing the application of quality control metrics and enabling the reuse of these data by other researchers. • To integrate MS-based data in a protein-centric manner to provide information on protein variants, modifications, and expression. • To provide mass spectrometry based expression data to the Expression Atlas.
  • 8. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PRIDE Mission • To archive all types of proteomics mass spectrometry data for the purpose of supporting reproducible research, allowing the application of quality control metrics and enabling the reuse of these data by other researchers. • To integrate MS-based data in a protein-centric manner to provide information on protein variants, modifications, and expression. • To provide mass spectrometry based expression data to the Expression Atlas.
  • 9. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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
  • 10. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 What is a proteomics publication in 2015? • 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
  • 11. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Journal Submission Recommendations • Journal guidelines recommend submission to proteomics repositories:  Proteomics  Nature Biotechnology  Nature Methods  Molecular and Cellular Proteomics • Funding agencies are enforcing public deposition of data to maximize the value of the funds provided.
  • 12. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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
  • 13. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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
  • 14. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 ProteomeCentral Metadata / Manuscript Raw Data* Results Journals UniProt/ neXtProt Peptide Atlas Other DBs Receiving repositories PASSEL (SRM data) PRIDE (MS/MS data) Other DBs GPMDB Researcher’s results Reprocessed results Raw data* Metadata MassIVE (MS/MS data) Vizcaíno et al., Nat Biotechnol, 2014 ProteomeXchange data workflow
  • 15. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 • 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
  • 16. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 ProteomeCentral Metadata / Manuscript Raw Data* Results Journals UniProt/ neXtProt Peptide Atlas Other DBs Receiving repositories PASSEL (SRM data) PRIDE (MS/MS data) Other DBs GPMDB Researcher’s results Reprocessed results Raw data* Metadata MassIVE (MS/MS data) Vizcaíno et al., Nat Biotechnol, 2014 ProteomeXchange data workflow
  • 17. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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.
  • 18. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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
  • 19. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 How to perform a complete PX submission to PRIDE • Decide between a complete/partial submission. • File conversion/export to PRIDE XML or mzIdentML • File check before submission (PRIDE Inspector) • Experimental annotation and actual file submission (PX submission tool) • Post-submission steps
  • 20. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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
  • 21. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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 (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
  • 22. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PRIDE Components: Submission Process PRIDE Converter 2 PRIDE Inspector PX Submission Tool mzIdentML PRIDE XML 1
  • 23. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Search output files Spectra files Original data files ‘RESULT’ file generation Final ‘RESULT’ file PRIDE XML ‘RESULT’ Before: only file conversion to PRIDE XML File conversion PRIDE Converter Other tools, e.g. hEIDI Barsnes et al., Nat Biotechnol, 2009 Cote et al., MCP, 2012
  • 24. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Tools ‘RESULT’ file generation Final ‘RESULT’ file mzIdentML ‘RESULT’ Now: native file export to mzIdentML Spectra files (mzML, mzXML, mzData, mgf, pkl, ms2, dta, apl) Mascot ProteinPilo t Scaffold PEAKS MSGF+ Others Native File export
  • 25. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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 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#.
  • 26. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PRIDE Components: Submission Process PRIDE Converter 2 PRIDE Inspector PX Submission Tool mzIdentML PRIDE XML 2
  • 27. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PRIDE Inspector Toolsuite Wang et al., Nat. Biotechnology, 2012 Perez-Riverol et al., MCP, 2016, in press PRIDE Inspector PRIDE Inspector 2 supports: - PRIDE XML - mzIdentML + all types of spectra files - mzML - mzTab identification and Quantification https://github.com/PRIDE-Toolsuite/
  • 28. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PRIDE Inspector 2 PRIDE Inspector 2 https://github.com/PRIDE-Toolsuite/ New visualisation functionality for Protein Groups
  • 29. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PRIDE Components: Submission Process PRIDE Converter 2 PRIDE Inspector PX Submission Tool mzIdentML PRIDE XML 3
  • 30. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 • 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). PX submission tool Published Raw Other files http://www.proteomexchange.org/submission PX submission tool • Command line alternative: Using the Aspera file transfer protocol.
  • 31. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PX submission tool: screenshots
  • 32. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Fast file transfer with 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!!
  • 33. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Manuscript published detailing the process Ternent et al., Proteomics, 2014http://www.proteomexchange.org/submission 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
  • 34. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PRIDE Archive: Number of submitted datasets in 2015 0 20 40 60 80 100 120 140 160 180 200 Number of submitted datasets to PRIDE Archive per month (November 1st 2015)
  • 35. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 ProteomeXchange: 2,774 datasets up until 1st September, 2015 Type: 1681 PRIDE partial 813 PRIDE complete 173 MassIVE 84 PeptideAtlas/PASSEL complete 23 Reprocessed Publicly Accessible: 1372 datasets, 49% of all 90% PRIDE 6% PASSEL 4% MassIVE Data volume: Total: ~150 TB Number of all files: ~400,000 PXD000320-324: ~ 4 TB PXD002319-26 ~2.4 TB PXD001471 ~1.6 TB Datasets/year: 2012: 102 2013: 527 2014: 963 2015: 1182 Top Species studied by at least 20 datasets: 1080 Homo sapiens 335 Mus musculus 110 Saccharomyces cerevisiae 98 Arabidopsis thaliana 75 Rattus norvegicus 58 Escherichia coli 29 Bos taurus 23 Glycine max 20 Caenorhabditis elegans 20 Oryza sativa ~ 500 species in total Origin: 714 USA 313 Germany 252 United Kingdom 163 China 146 France 121 Netherlands 108 Switzerland 103 Canada 81 Denmark 73 Spain 68 Japan 67 Australia 63 Sweden 57 Belgium 43 Austria 39 India 34 Taiwan 33 Norway 26 Italy 24 Ireland 24 Finland 21 Republic of Korea 20 Brazil 20 Russia 18 Israel 18 Singapore …
  • 36. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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
  • 37. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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 store SRM data (it goes to PASSEL) • Top down proteomics datasets. • Mass Spectrometry Imaging datasets. • Data independent acquisition techniques: e.g. SWATH-MS datasets.
  • 38. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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
  • 39. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 • 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 WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Data access to PRIDE Archive • Look for particular datasets of interest: • For data reuse: which particular proteins and peptides (including PTMs) have been detected. • Data reinterpretation or re-analysis. • Validation of the experimental results reported. • Specific use cases for proteomics: spectral libraries, fragmentation models, SRM transitions,…
  • 41. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 ProteomeCentral Metadata / Manuscript Raw Data* Results Journals UniProt/ neXtProt Peptide Atlas Other DBs Receiving repositories PASSEL (SRM data) PRIDE (MS/MS data) Other DBs GPMDB Researcher’s results Reprocessed results Raw data* Metadata MassIVE (MS/MS data) Vizcaíno et al., Nat Biotechnol, 2014 ProteomeXchange data workflow
  • 42. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 ProteomeCentral: Portal for all PX datasets http://proteomecentral.proteomexchange.org/cgi/GetDataset
  • 43. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 RSS feed for public datasets http://groups.google.com/group/proteomexchange/feed/rss_v2_0_msgs.xml
  • 44. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Ways to access data in PRIDE Archive • PRIDE web interface • File repository • REST web service • PRIDE Inspector tool
  • 45. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PRIDE Archive web interface
  • 46. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PRIDE Archive web interface (2)
  • 47. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Vaudel M, Barsnes H, Berven FS, Sickmann A, Martens L: Proteomics 2011;11(5):996-9. https://github.com/compomics/searchgui https://github.com/compomics/peptide-shaker Vaudel M, Burkhart J, Zahedi RP, Berven FS, Sickmann A, Martens L, Barsnes H: Nature Biotechnology 2015; 33(1):22-24. CompOmics Open Source Analysis Pipeline
  • 48. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Find the desired PRIDE project … … and start re-analyzing the data! … inspect the project details …. Reshake PRIDE data!
  • 49. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 • 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
  • 50. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PRIDE resources
  • 51. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PRIDE Archive Aggr egati on PRIDE Cluster Basic QC checks for PSMs Reprocessed datasets Original Submissions Link to the original evidence For original results PRIDE Proteomes
  • 52. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Sneak peak • Provide an aggregated and QC filtered peptide-centric and protein centric view on PRIDE Archive data. http://www.ebi.ac.uk/pride/cluster/http://wwwdev.ebi.ac.uk/pride/proteomes/
  • 53. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PRIDE Cluster - Concept • Use spectral clustering to reliably group spectra coming from the same peptide • Infer reliable identifications by comparing submitted identifications of spectra within a cluster • Increases quality through data increase (taking advantage of the wealth of data in PRIDE). • Inherently adapts to new (labelling) techniques Griss et al., Nat Methods, 2013
  • 54. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PRIDE Cluster - Concept Griss et al., Nat Methods, 2013 NMMAACDPR NMMAACDPR PPECPDFDPPR NMMAACDPR Consensus spectrum PPECPDFDPPR NMMAACDPR NMMAACDPR Threshold: At least 10 spectra in a cluster and ratio >70%. Originally submitted identified spectra
  • 55. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PRIDE Cluster Home page http://www.ebi.ac.uk/pride/cluster/#/
  • 56. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PRIDE Cluster: result of searches http://www.ebi.ac.uk/pride/cluster/#/ A couple of examples …
  • 57. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Examples: one perfect cluster - 880 PSMs give the same peptide ID - 4 species - 28 datasets - Same instruments
  • 58. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Examples: one perfect cluster (2)
  • 59. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Examples: one perfect cluster (3) What does that peptide sequence correspond to?
  • 60. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Examples: very good cluster
  • 61. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Examples: very good cluster (2)
  • 62. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Examples: one perfect cluster (3) What does that peptide sequence correspond to?
  • 63. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PRIDE Cluster – Spectral libraries http://www.ebi.ac.uk/pride/cluster/#/libraries
  • 64. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PRIDE Proteomes: reusing PRIDE Cluster data • Condensed and cross-dataset view of PRIDE Archive for identification data: • Data filtering of PSMs is performed at the level of the submitted data. • PSMs are grouped as peptide sequences. • The peptide sequences are remapped to a recent version of UniProtKB (at present UniProtKB “complete proteome”). • Linked to the original supporting evidence. • “PRIDE Cluster” used as an extra evidence for the PSMs. http://wwwdev.ebi.ac.uk/pride/proteomes/
  • 65. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PRIDE: Using it for giving reliability to IDs Link to PRIDE Cluster web http://wwwdev.ebi.ac.u k/pride/proteomes/
  • 66. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Examples: one perfect cluster - 880 PSMs give the same peptide ID - 4 species - 28 datasets - Same instruments
  • 67. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 • 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
  • 68. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Do you want to know a bit more…? http://www.slideshare.net/JuanAntonioVizcaino
  • 69. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Aknowledgements: People Attila Csordas Tobias Ternent Noemi del Toro Johannes Griss Yasset Perez-Riverol Henning Hermjakob All past team members, especially Rui Wang, Florian Reisinger and Jose A. Dianes All ProteomeXchange partners, especially Eric Deutsch and Nuno Bandeira Acknowledgements: The PRIDE Team and collaborators
  • 70. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Questions?

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