1. EBI is an Outstation of the European Molecular Biology Laboratory. PRIDE associated tools: Practical exercise 1 PRIDE team, Proteomics Services Group PANDA group European Bioinformatics Institute Hinxton, Cambridge United Kingdom Juan Antonio VIZCAINO

2. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Overview … Submission of data: PRIDE Converter Visualization of data: PRIDE Inspector: Review functionality Charts Practical exercise 1

3. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk MS Proteomics Typical Workflow Proteins MS/MS spectra Peptides Search Engine Sequence Database TDMDNQIVVSDYAQ MDRLFDQAFGLPR AKPLMELIERDESTN VDMSLAQRDIVVQET MEDIDK NGMFFSTYDR GTAGNALMDGASQL IPI00302927 IPI00025512 IPI00002478 IPI00185600 IPI00014537 IPI00298497 IPI00329236 IPI00002232 PRIDE stores: 1) Peptide Identifications 2) Protein Identifications 3) Mass spectra 4) Valuable additional metadata

4. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk DATA SUBMISSION TO PRIDE (Submission-driven resource)

5. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk PRIDE Submission Workflow 5 Search Engine Mascot (.dat), Sequest (.out) SpectrumMill (.spo) pep.xml, prot.xml PRIDE XML PRIDE Converter

6. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk DATA SUBMISSION TO PRIDE USING PRIDE CONVERTER

7. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk PRIDE Converter 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 http://code.google.com/p/pride-converter

8. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Why? Submission made easier: PRIDE Converter http://code.google.com/p/pride-converter Barsnes et al., Nat. Biotechnology, 2009

9. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk PRIDE Converter – interface details

10. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk From PRIDE Converter to PRIDE FTP

11. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk The need for new tool Search Engine 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 PRIDE Converter

12. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk PRIDE Inspector 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 Wang et al., Nat. Biotechnology, 2012

13. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk 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. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Experimental Metadata View (1) General

15. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Experimental Metadata View (2) Sample Protocol

16. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Experimental Metadata View (3) Instrument Data processing

17. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Protein Centric View Selected Protein Peptides identify the same protein Spectrum for selected peptide

18. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Protein Centric View (2) Selected Protein Peptides identify the same protein Sequence viewer

19. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Peptide Centric View Peptides Amino Acid Highlighting PTMs

20. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Spectrum Centric View Spectrum details

21. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Summary Chart View

22. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Summary Chart View (extended)

23. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk 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. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk PRIDE web page: PRIDE Inspector Web Start http://www/ebi.ac.uk/pride

25. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk 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=review 53187&password= - *_3XR8G

26. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk PRIDE tools and search engine exercise

27. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Workflow MS experiment mgf omx PRIDE XML PRIDE Converter Search engine PRIDE Inspector PRIDE Your own workflow: MS/MS data processing peak list generation omssa_results_2780 PRIDEXML

28. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk In this exercise… 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)

29. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk 1) Converting the.omx OMSSA file to PRIDE XML 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.

30. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk DATA SUBMISSION TO PRIDE USING PRIDE CONVERTER

31. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Why? Submission made easier: PRIDE Converter http://code.google.com/p/pride-converter

32. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk 1) Converting the.omx OMSSA file to PRIDE XML 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.

33. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Time to Work on it…

34. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk DATA VISUALIZATION AND ANALYSIS USING PRIDE INSPECTOR

35. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk 2) Visualizing and analysing the data (PRIDE Inspector) 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.

36. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk How does PRIDE Inspector look like? Fast loading of large mzML and PRIDE XML files.

37. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Time to Work on it…

38. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Conclusions 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)

39. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk PRIDE Converter 2 (beta available) http://code.google.com/p/pride-converter-2

40. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk The PRIDE Team Attila Csordas David Ovelleiro Richard Côté Rui Wang Daniel Ríos Florian Reisinger Gavin O’Kelly Melih Birim Joe Foster Johannes Griss Samuel Wein Antonio Fabregat Juan Antonio Vizcaíno Henning Hermjakob

41. EBI Roadshow Sofia, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Questions?