1 / 44

MIAPE Extractor Tutorial

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. SHPP - Data deposition workflow. Convert raw files to mzML or mgf

daryl
Download Presentation

MIAPE Extractor Tutorial

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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 • Convert raw files to mzML or mgf • Get search engine results in mzIdentML format • Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI (at the same time!!) • Inspect your data using the MIAPE Extractor Charts • Use MIAPE Extractor to export PRIDE XML file from several MIAPE MS and MSI • Upload PRIDE XML file to (PRIDE database / ProteomeXchange consortium)

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

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

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

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

  19. Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI Not contained Metadata from mzML 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

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

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

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

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

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

  28. Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI MIAPE projects names consensus: SHPP + Cell Line + Other exper. feature(s) “SHPP Lab Jurkat SDSPage RIPA” Suggestions??????

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

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

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

  32. 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

  33. 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

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

  35. 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/)

  36. Howto share data betweenus • How can I seethe MIAPE data fromotherlabs? • Use a commonaccount in the MIAPE Extractor: • Usuario: sphpp-report@proteored.org • Pass: miapereport • Use yourownaccount and share MIAPE projectsafteritscreationwithsphpp-report@proteored.org

More Related