1. MIAPE Extractor Tutorial SHPP meeting, 28 Aug 2012 La Cristalera, Miraflores de la Sierra, Madrid Salvador Martínez de Bartolomé Izquierdo CNB-CSIC / ProteoRed smartinez@proteored.org

2. SHPP - Data deposition workflow 1.Convert raw files to mzML or mgf 2.Get search engine results in mzIdentML format 3.Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI (at the same time!!) 4.Inspect your data using the MIAPE Extractor Charts 5.Use MIAPE Extractor to export PRIDE XML file from several MIAPE MS and MSI 6.Upload PRIDE XML file to (PRIDE database / ProteomeXchange consortium)

3. SHPP - Data deposition workflow 1.Convert raw files to mzML or mgf 2.Get search engine results in mzIdentML format 3.Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI (at the same time!!) 4.Inspect your data using the MIAPE Extractor Charts 5.Use MIAPE Extractor to export PRIDE XML file from several MIAPE MS and MSI 6.Upload PRIDE XML file to (PRIDE database / ProteomeXchange consortium)

4. Convert raw files to mzML or mgf Use of available converters but...maybe its not neccessary to create a mzML See afterwards...

5. SHPP - Data deposition workflow 1.Convert raw files to mzML or mgf 2.Get search engine results in mzIdentML format 3.Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI (at the same time!!) 4.Inspect your data using the MIAPE Extractor Charts 5.Use MIAPE Extractor to export PRIDE XML file from several MIAPE MS and MSI 6.Upload PRIDE XML file to (PRIDE database / ProteomeXchange consortium)

6. Get search engine results in mzIdentML format MIAPE Extractor works with mzIdentML 1.0 and 1.1

7. Get search engine results in mzIdentML format mzIdentML from MASCOT (v2.3 or later):

8. Get search engine results in mzIdentML format mzIdentML from MASCOT (v2.3 or later):

9. Get search engine results in mzIdentML format mzIdentML from phenyx:

10. Get search engine results in mzIdentML format mzIdentML from phenyx:

11. Get search engine results in mzIdentML format mzIdentML from phenyx: PROBLEM!!!! The generated mzIdentML has not proteins!!!!! We are waiting for an update from Genebio

12. Get search engine results in mzIdentML format mzIdentML from Sequest: We have used Proteomics Conversion Tool (ProCon) We experimented some problems. Just worked in Windows XP Any help from Thermo users? Maybe Oscar Gallardo?

13. SHPP - Data deposition workflow 1.Convert raw files to mzML or mgf 2.Get search engine results in mzIdentML format 3.Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI (at the same time!!) 4.Inspect your data using the MIAPE Extractor Charts 5.Use MIAPE Extractor to export PRIDE XML file from several MIAPE MS and MSI 6.Upload PRIDE XML file to (PRIDE database / ProteomeXchange consortium)

14. Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI (at the same time!!) One MIAPE MS per raw file (fraction/band/replicate) One MIAPE MSI per mzIdentML (per search engine output) Create MIAPE MS and MSI (spectra file + mzIdentML) at the same time! Otherwise, PRIDE XML cannot be exported correctly!!

15. Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI

19. Metadata from mzML Contained Not contained

20. Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI Two options: mzML + mzIdentML mgf + mzIdentML Poor MS metadata No MS metadata

21. Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI Two options: mzML + mzIdentML + MS metadata mgf + mzIdentML + MS metadata Heavy (GB) and complicated lighter and easier

22. Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI

31. MIAPE projects names consensus: SHPP + Cell Line + Other exper. feature(s) “SHPP Lab Jurkat SDSPage RIPA” Suggestions??????

32. SHPP - Data deposition workflow 1.Convert raw files to mzML or mgf 2.Get search engine results in mzIdentML format 3.Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI (at the same time!!) 4.Inspect your data using the MIAPE Extractor Charts 5.Use MIAPE Extractor to export PRIDE XML file from several MIAPE MS and MSI 6.Upload PRIDE XML file to (PRIDE database / ProteomeXchange consortium)

33. Inspect your data using the MIAPE Extractor Charts Lets try with examples....

34. SHPP - Data deposition workflow 1.Convert raw files to mzML or mgf 2.Get search engine results in mzIdentML format 3.Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI (at the same time!!) 4.Inspect your data using the MIAPE Extractor Charts 5.Use MIAPE Extractor to export PRIDE XML file from several MIAPE MS and MSI 6.Upload PRIDE XML file to (PRIDE database / ProteomeXchange consortium)

35. Use MIAPE Extractor to export PRIDE XML file from several MIAPE MS and MSI Now is just possible to create a PRIDE XML file from a MIAPE MS and MSI pair Shot-gun experiments containing several fractions/bands/replicates One PRIDE XML file for each fraction/band/replicate

36. Use MIAPE Extractor to export PRIDE XML file from several MIAPE MS and MSI The idea is to implement a PRIDE XML exporter from the MIAPE Extractor Charts, creating a PRIDE XML file from each experiment (level 2), and include the FDR filters (or others) that have been applied to the data in the file(s). TO DO

37. SHPP - Data deposition workflow 1.Convert raw files to mzML or mgf 2.Get search engine results in mzIdentML format 3.Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI (at the same time!!) 4.Inspect your data using the MIAPE Extractor Charts 5.Use MIAPE Extractor to export PRIDE XML file from several MIAPE MS and MSI 6.Upload PRIDE XML file to (PRIDE database / ProteomeXchange consortium)

38. Upload PRIDE XML file to (PRIDE database / ProteomeXchange consortium) - Once the data is enough curated - Centralize deposition task? - Follow EBI PRIDE (http://www.ebi.ac.uk/pride/) or ProteomeXchange (http://www.proteomexchange.org/)http://www.ebi.ac.uk/pride/http://www.proteomexchange.org/

39. How to share data between us How can I see the MIAPE data from other labs? – Use a common account in the MIAPE Extractor: Usuario: sphpp-report@proteored.org Pass: miapereport – Use your own account and share MIAPE projects after its creation with sphpp-report@proteored.org