1. Data Standards Submission 1 st CHr-16 Workshop. Miraflores de la Sierra August, 28 th -29 th 2012 Alberto Medina

2. Summary 1.Data standards (just a quick view) 2.Trusted pipeline 3.Starting! 4.Other search engines

3. Summary 1.Data standards (just a quick view) 2.Trusted pipeline 3.Starting! 4.Other search engines

4. Data Standards – PSI framework Spanish Consortium Bioinformatics pipeline Mass Spectra Raw dataMzMl/TraML Protein/Pepti des Search Engines MzIdentml Quantitation Vendor/Free software MzQuantml Data Reporting – ProteoRed MIAPE Web toolkit MIAPE MS/MSI PRIDE Data Reporting – with stable release MIAPEQuant PRIDEQuan¿? Data validation and submission ProteomeXchange

5. External repositories Development of bioinformatic environment: Spanish HPP will join the different resources to provide an unique enquiring system PAtlas NProt GPMDB PRIDE UProt Upcoming Proteomics results Data standards submission (ProteomeXchange) + + Emsembl

6. Summary 1.Data standards (just a quick view) 2.Trusted pipeline 3.Starting! 4.Other search engines

7. Trusted pipeline Mass Spectra.mgf Identification Mascot Output file mzIdentML MIAPE Generation MIAPE MSMIAPE MSI

8. Trusted pipeline MIAPE MSMIAPE MSI PRIDE Generation PRIDE XML Stats (MIAPE Extractor) Charts and Reports Check and View PRIDE

9. Summary 1.Data standards (just a quick view) 2.Trusted pipeline 3.Starting! 4.Other search engines

10. Starting (1) Step 1) Element to achieve: Peak lists (acquired data). Issues: Several data formats (mgf, wiff, pkl, etc). Different Software packets. Translators. Goal: MGF file or mzML. Translators MSConvert, OpenMS, ABSciex MS Data Converter, CompassXport, ProCon.

11. Starting (2) Step 2) Element to achieve: Identification of Proteins and Peptides. Issues: Have your own Mascot Server. Release 2.3 in advance Other search engines (check section 4). Goal: Submit to Mascot peak list obtained in step 1.

12. Starting (3) Step 3) Element to achieve: Mascot results formatted as mzIdentML Issues: Version 2.3 is rather slow. It is not possible to do using batch mode. Goal: mzIdentML.

13. Starting (3)

14. MIAPE Generation 1.GO to ProteoRed MIAPE web toolkit site. www.proteored.org/MIAPE www.proteored.org/MIAPE 2.Click on Create MIAPE  Automatic 1.Download the application (Java application). 2.Run the application

15. MIAPE Generation

16. PRIDE Generation

18. PRIDE Visualization http://proteo.cnb.csic.es/prideviewer

19. PRIDE Submission http://www.ebi.ac.uk/pride/easySubmitData.do? http://www.ebi.ac.uk/pride/easySubmitData.do?

20. Exchanging through the cloud

21. MIAPE Extractor

22. A hopefully universe ProteoRed MIAPE repository MPWTK mzML mzIdentML MPWTK MIAPE Extractor PRIDE XML A B C

23. Summary 1.Data standards (just a quick view) 2.Trusted pipeline 3.Starting! 4.Other search engines

24. Other Search Engines Phenyx: Waiting new patch to save the results in a straighforward manner. Similar to Mascot export. X!Tandem: Full integrated thorugh X!Tandem results files. Sequest: It is possible to save the results formatted as mzIdentML through ProCon tool (runnable from Windows XP OS). http://www.medizinisches-proteom-center.de/ProCon We need some feedback from Sequest users. OMSSA: Not integrated, but it is possible to use mzIdentML-Parsers http://code.google.com/p/mzidentml-parsers/

25. Questions