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PRIDE associated tools: Practical exercise 1

PRIDE associated tools: Practical exercise 1. Juan Antonio VIZCAINO. PRIDE team, Proteomics Services Group PANDA group European Bioinformatics Institute Hinxton , Cambridge United Kingdom. Overview …. Submission of data: PRIDE Converter Visualization of data: PRIDE Inspector:

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PRIDE associated tools: Practical exercise 1

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  1. PRIDE associated tools: Practical exercise 1 Juan Antonio VIZCAINO PRIDE team, Proteomics Services Group PANDA group European Bioinformatics Institute Hinxton, Cambridge United Kingdom

  2. Overview … • Submission of data: PRIDE Converter • Visualization of data: PRIDE Inspector: • Review functionality • Charts • Practical exercise 1

  3. MS Proteomics Typical Workflow TDMDNQIVVSDYAQMDRLFDQAFGLPR AKPLMELIERDESTNVDMSLAQRDIVVQETMEDIDK NGMFFSTYDR GTAGNALMDGASQL Sequence Database Peptides Search Engine MS/MS spectra IPI00302927 IPI00025512 IPI00002478 IPI00185600 IPI00014537 IPI00298497 IPI00329236 IPI00002232 PRIDE stores: 1) Peptide Identifications 2) Protein Identifications 3) Mass spectra 4) Valuable additional metadata Proteins

  4. DATA SUBMISSION TO PRIDE (Submission-driven resource)

  5. PRIDE Submission Workflow Search Engine PRIDE XML PRIDE Converter Mascot (.dat), Sequest (.out) SpectrumMill (.spo) pep.xml, prot.xml

  6. DATA SUBMISSION TO PRIDE USING PRIDE CONVERTER

  7. Stand-alone tool for creating PRIDE XML files (the format needed for performing a PRIDE submission) It can support a variety of popular proteomics data formats Metadata must be provided using CVs/ontologies. GUI based tool, easy to use PRIDE Converter http://code.google.com/p/pride-converter

  8. Why? Submission made easier: PRIDE Converter http://code.google.com/p/pride-converter Barsneset al., Nat. Biotechnology, 2009

  9. PRIDE Converter – interface details

  10. From PRIDE Converter to PRIDE FTP

  11. The need for new tool Search Engine PRIDE Converter Mascot (.dat), Sequest (.out) SpectrumMill (.spo) pep.xml, prot.xml • Visualize/Check data • Support for reviewers/ editors • More flexible than the web interface • Initial assessment on data quality

  12. Stand-alone GUI based tool for visualising and doing a initial analysis of PRIDE XML files and data already in PRIDE via the PRIDE public DB instance. Also private review of data is possible. Still under active development (latest version is 1.2.4). At present it also supports mzML. http://code.google.com/p/pride-toolsuite/wiki/PRIDEInspector PRIDE Inspector Wang et al., Nat. Biotechnology, 2012

  13. How does PRIDE Inspector look like? • Fast loading of large mzML and PRIDE XML files. • Direct access to all PRIDE public database experiments. • Private user download facility.

  14. Experimental Metadata View (1) General

  15. Experimental Metadata View (2) Sample Protocol

  16. Experimental Metadata View (3) Data processing Instrument

  17. Protein Centric View Selected Protein Peptides identify the same protein Spectrum for selected peptide

  18. Protein Centric View (2) Selected Protein Peptides identify the same protein Sequence viewer

  19. Peptide Centric View Peptides PTMs Amino Acid Highlighting

  20. Spectrum Centric View Spectrum details

  21. Summary Chart View

  22. Summary Chart View (extended)

  23. Who can use PRIDE Inspector? • Researchers to check their data before they submit it to PRIDE • Journal’s reviewers and editors in the review process

  24. PRIDE web page: PRIDE Inspector Web Start http://www/ebi.ac.uk/pride

  25. PRIDE Inspector Web Start For each submission (private data), a unique URL is generated and it can be included in your manuscript submission: http://www.ebi.ac.uk:21390/pride/jsp/pages/jnlp/jnlp.jsp?username=review53187&password= - *_3XR8G

  26. PRIDE tools and search engine exercise

  27. Workflow MS experiment Your own workflow:MS/MSdata processingpeak list generation mgf Search engine omx omssa_results_2780 PRIDE Converter PRIDE XML PRIDEXML PRIDE Inspector PRIDE

  28. You will use the data generated using the OMSSA search engine (imagine that they are the results of your search) You will learn how to use PRIDE Converter (tool for performing submissions to PRIDE) You will learn how to use PRIDE Inspector (tool for the visualization and analysis of proteomics data) In this exercise…

  29. We need to do this: Perform submission of the data to PRIDE Use PRIDE Inspector to visualize and analyse it We will use PRIDE Converter: we need to provide enough metadata to allow the reuse of the data. 1) Converting the .omx OMSSA file to PRIDE XML

  30. DATA SUBMISSION TO PRIDE USING PRIDE CONVERTER

  31. Why? Submission made easier: PRIDE Converter http://code.google.com/p/pride-converter

  32. We need to do this: Perform submission of the data to PRIDE Use PRIDE Inspector to visualize and analyse it We will use PRIDE Converter: we need to provide enough metadata to allow the reuse of the data. 1) Converting the .omx OMSSA file to PRIDE XML

  33. Time to Work on it…

  34. DATA VISUALIZATION AND ANALYSIS USING PRIDE INSPECTOR

  35. We will have a look at the new results that have been generated using OMSSA. We will browse the metadata, proteins, peptides and spectra. We will have a quick look at the quality charts, generated in order to make an initial assessment of data quality at different levels. 2) Visualizing and analysing the data (PRIDE Inspector)

  36. How does PRIDE Inspector look like? • Fast loading of large mzML and PRIDE XML files.

  37. Time to Work on it…

  38. Using PRIDE Converter you are able to annotate the data and get it ready for submission to PRIDE Using PRIDE Inspector, you are able to visualize and perform a first analysis of the results. You have learnt some of the variables that can affect the final results of a proteomics experiment (list of proteins) Conclusions

  39. PRIDE Converter 2 (beta available) http://code.google.com/p/pride-converter-2

  40. The PRIDE Team Attila Csordas David Ovelleiro Richard Côté Rui Wang Daniel Ríos FlorianReisinger Gavin O’Kelly MelihBirim Joe Foster Johannes Griss Samuel Wein Antonio Fabregat Juan Antonio Vizcaíno Henning Hermjakob

  41. Questions?

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