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PRIDE and ProteomeXchange: Training webinar

The document discusses a training webinar about PRIDE and ProteomeXchange. It begins with instructions for participating in the webinar and an overview of data resources at EMBL-EBI. It then covers PRIDE's mission to archive proteomics data, the ProteomeXchange consortium for standardized data submission, and tools for submitting data to PRIDE including PRIDE Converter, PRIDE Inspector, and the ProteomeXchange submission tool.

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PRIDE and ProteomeXchange: Training webinar Dr. Juan Antonio Vizcaíno PRIDE Group Coordinator Proteomics Services Team EMBL-EBI Hinxton, Cambridge, UK juan@ebi.ac.uk
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 Welcome - webinar instructions • Gototraining works best in Chrome or IE – avoid Firefox due to audio issues with Macs. • To access the full features of Gototraining, use the desktop version by clicking “switch to desktop version”. • All microphones will be muted whilst the trainer is speaking. • If you have a question during this time or at the end, please use the chat box at the bottom of the gototraining box. • Please complete the feedback survey which will launch at the end of the webinar.
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 Mass Spectrometry (MS)-based proteomics 7 • Many different workflows. • Discovery mode: • Bottom-up proteomics • Data dependent acquisition • Data independent acquisition • Top down proteomics • Targeted mode: • SRM (Selected Reaction Monitoring)
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 Mass Spectrometry (MS)-based proteomics 8 • Many different workflows. • Discovery mode: • Bottom-up proteomics • Data dependent acquisition • Data independent acquisition • Top down proteomics • Targeted mode: • SRM (Selected Reaction Monitoring)
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 MS proteomics: tandem MS (bottom-up) MS/MS matching identifies peptides, not proteins. Proteins are inferred from the peptide sequences.
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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.
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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.
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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.
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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 EBI Expression Atlas. http://www.ebi.ac.uk/pride/archive
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 Data content in PRIDE Archive • Dataset submission driven resource. • PRIDE is organised 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. • Main supported formats: PRIDE XML and mzIdentML. • Raw data is also now stored.
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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.
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 PRIDE Components: Submission Process PRIDE Converter 2 PRIDE Inspector PX Submission Tool mzIdentML PRIDE XML 1
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 PX Data workflow for MS/MS data Search Engine Results + MS files PRIDE Converter 2 PRIDE XML Coté & Griss et al., MCP, 2012 Other tools available: - PRIDE Converter - PLGS (Waters) - Proteios - EasyProt - hEIDI - OmicsHub (Integromics) - PeptideShaker (Compomics) PRIDE Converter 2 https://github.com/PRIDE-Toolsuite/pride-converter-2 - ‘Bulk’ conversion possible: Command Line mode - Virtually no limit in file sizes.
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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#.
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 PRIDE Components: Submission Process PRIDE Converter 2 PRIDE Inspector PX Submission Tool mzIdentML PRIDE XML 2
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 PRIDE Inspector Toolsuite Wang et al., Nat. Biotechnology, 2012 Perez-Riverol et al., MCP, 2016, in press PRIDE Inspector PRIDE Inspector Toolsuite supports: - PRIDE XML - mzIdentML + all types of spectra files - mzML - mzTab identification and Quantification + all types of spectra files https://github.com/PRIDE-Toolsuite/
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 PRIDE Inspector Toolsuite https://github.com/PRIDE-Toolsuite/ New visualisation functionality for Protein Groups PRIDE Inspector Toolsuite
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 PRIDE Inspector Toolsuite PRIDE Inspector Toolsuite Private review of files submitted to PRIDE https://github.com/PRIDE-Toolsuite/
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 PRIDE Components: Submission Process PRIDE Converter 2 PRIDE Inspector PX Submission Tool mzIdentML PRIDE XML 3
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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.
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 PX submission tool: step by step
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 PX submission tool: screenshots
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 PRIDE Archive submitted datasets up until 1st November, 2015 • 1,259 submitted datasets by November 1st • 923 submitted datasets in 2014 • In the last 6 months, 155 submitted datasets per month • Size: ~ 160 TB.
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 PRIDE: Size comparison with other EBI resources (May 2015) 1.E+07 1.E+08 1.E+09 1.E+10 1.E+11 1.E+12 1.E+13 1.E+14 1.E+15 1.E+16 1.E+17 2004 2006 2008 2010 2012 2014 2016 bytes date Data accumulation by resource Metabolites PRIDE EGA ENA (less AE) AE Chart generated by Guy Cochrane
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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,…
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 RSS feed for public datasets http://groups.google.com/group/proteomexchange/feed/rss_v2_0_msgs.xml
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 Ways to access data in PRIDE Archive • PRIDE web interface • File repository • REST web service • PRIDE Inspector tool
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 PRIDE Archive web interface
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 PRIDE Archive web interface (2)
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 ProteomeCentral: Portal for all PX datasets http://proteomecentral.proteomexchange.org/cgi/GetDataset
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 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
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 2015 overview of PRIDE resources
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 PRIDE Proteomes and PRIDE Cluster • 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/
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 • Main characteristics of PRIDE Archive and ProteomeXchange (PX) • 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 Conclusions
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 Do you want to know a bit more…? http://www.slideshare.net/JuanAntonioVizcaino
Juan A. Vizcaíno juan@ebi.ac.uk Training webinar 25 November 2015 Aknowledgements: People Attila Csordas Tobias Ternent Noemi del Toro Gerhard Mayer (Bochum, de.NBI) Johannes Griss Yasset Perez-Riverol Henning Hermjakob Former team members: Rui Wang, Florian Reisinger and Jose A. Dianes Acknowledgements: The PRIDE Team
• 9 December – UniProt website updates • 16 December – Ensembl release 83 All webinars @ 4:00pm GMT time unless stated For details see: http://www.ebi.ac.uk/training/webinars Future webinars:

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PRIDE and ProteomeXchange: Training webinar

  • 1.
    PRIDE and ProteomeXchange:Training webinar Dr. Juan Antonio Vizcaíno PRIDE Group Coordinator Proteomics Services Team EMBL-EBI Hinxton, Cambridge, UK juan@ebi.ac.uk
  • 2.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 Welcome - webinar instructions • Gototraining works best in Chrome or IE – avoid Firefox due to audio issues with Macs. • To access the full features of Gototraining, use the desktop version by clicking “switch to desktop version”. • All microphones will be muted whilst the trainer is speaking. • If you have a question during this time or at the end, please use the chat box at the bottom of the gototraining box. • Please complete the feedback survey which will launch at the end of the webinar.
  • 3.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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
  • 4.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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
  • 5.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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
  • 6.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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
  • 7.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 Mass Spectrometry (MS)-based proteomics 7 • Many different workflows. • Discovery mode: • Bottom-up proteomics • Data dependent acquisition • Data independent acquisition • Top down proteomics • Targeted mode: • SRM (Selected Reaction Monitoring)
  • 8.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 Mass Spectrometry (MS)-based proteomics 8 • Many different workflows. • Discovery mode: • Bottom-up proteomics • Data dependent acquisition • Data independent acquisition • Top down proteomics • Targeted mode: • SRM (Selected Reaction Monitoring)
  • 9.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 MS proteomics: tandem MS (bottom-up) MS/MS matching identifies peptides, not proteins. Proteins are inferred from the peptide sequences.
  • 10.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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
  • 11.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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.
  • 12.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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.
  • 13.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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
  • 14.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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.
  • 15.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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 EBI Expression Atlas. http://www.ebi.ac.uk/pride/archive
  • 16.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 Data content in PRIDE Archive • Dataset submission driven resource. • PRIDE is organised 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. • Main supported formats: PRIDE XML and mzIdentML. • Raw data is also now stored.
  • 17.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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
  • 18.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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
  • 19.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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
  • 20.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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
  • 21.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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
  • 22.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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.
  • 23.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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
  • 24.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 PRIDE Components: Submission Process PRIDE Converter 2 PRIDE Inspector PX Submission Tool mzIdentML PRIDE XML 1
  • 25.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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
  • 26.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 PX Data workflow for MS/MS data Search Engine Results + MS files PRIDE Converter 2 PRIDE XML Coté & Griss et al., MCP, 2012 Other tools available: - PRIDE Converter - PLGS (Waters) - Proteios - EasyProt - hEIDI - OmicsHub (Integromics) - PeptideShaker (Compomics) PRIDE Converter 2 https://github.com/PRIDE-Toolsuite/pride-converter-2 - ‘Bulk’ conversion possible: Command Line mode - Virtually no limit in file sizes.
  • 27.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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
  • 28.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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#.
  • 29.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 PRIDE Components: Submission Process PRIDE Converter 2 PRIDE Inspector PX Submission Tool mzIdentML PRIDE XML 2
  • 30.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 PRIDE Inspector Toolsuite Wang et al., Nat. Biotechnology, 2012 Perez-Riverol et al., MCP, 2016, in press PRIDE Inspector PRIDE Inspector Toolsuite supports: - PRIDE XML - mzIdentML + all types of spectra files - mzML - mzTab identification and Quantification + all types of spectra files https://github.com/PRIDE-Toolsuite/
  • 31.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 PRIDE Inspector Toolsuite https://github.com/PRIDE-Toolsuite/ New visualisation functionality for Protein Groups PRIDE Inspector Toolsuite
  • 32.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 PRIDE Inspector Toolsuite PRIDE Inspector Toolsuite Private review of files submitted to PRIDE https://github.com/PRIDE-Toolsuite/
  • 33.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 PRIDE Components: Submission Process PRIDE Converter 2 PRIDE Inspector PX Submission Tool mzIdentML PRIDE XML 3
  • 34.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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.
  • 35.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 PX submission tool: step by step
  • 36.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 PX submission tool: screenshots
  • 37.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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
  • 38.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 PRIDE Archive submitted datasets up until 1st November, 2015 • 1,259 submitted datasets by November 1st • 923 submitted datasets in 2014 • In the last 6 months, 155 submitted datasets per month • Size: ~ 160 TB.
  • 39.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 PRIDE: Size comparison with other EBI resources (May 2015) 1.E+07 1.E+08 1.E+09 1.E+10 1.E+11 1.E+12 1.E+13 1.E+14 1.E+15 1.E+16 1.E+17 2004 2006 2008 2010 2012 2014 2016 bytes date Data accumulation by resource Metabolites PRIDE EGA ENA (less AE) AE Chart generated by Guy Cochrane
  • 40.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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
  • 41.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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,…
  • 42.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 RSS feed for public datasets http://groups.google.com/group/proteomexchange/feed/rss_v2_0_msgs.xml
  • 43.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 Ways to access data in PRIDE Archive • PRIDE web interface • File repository • REST web service • PRIDE Inspector tool
  • 44.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 PRIDE Archive web interface
  • 45.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 PRIDE Archive web interface (2)
  • 46.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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
  • 47.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 ProteomeCentral: Portal for all PX datasets http://proteomecentral.proteomexchange.org/cgi/GetDataset
  • 48.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 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
  • 49.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 2015 overview of PRIDE resources
  • 50.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 PRIDE Proteomes and PRIDE Cluster • 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/
  • 51.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 • Main characteristics of PRIDE Archive and ProteomeXchange (PX) • 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 Conclusions
  • 52.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 Do you want to know a bit more…? http://www.slideshare.net/JuanAntonioVizcaino
  • 53.
    Juan A. Vizcaíno juan@ebi.ac.uk Trainingwebinar 25 November 2015 Aknowledgements: People Attila Csordas Tobias Ternent Noemi del Toro Gerhard Mayer (Bochum, de.NBI) Johannes Griss Yasset Perez-Riverol Henning Hermjakob Former team members: Rui Wang, Florian Reisinger and Jose A. Dianes Acknowledgements: The PRIDE Team
  • 54.
    • 9 December– UniProt website updates • 16 December – Ensembl release 83 All webinars @ 4:00pm GMT time unless stated For details see: http://www.ebi.ac.uk/training/webinars Future webinars: