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MIAPE Extractor Tutorial SHPP meeting, 28 Aug 2012 La Cristalera, Miraflores de la Sierra, Madrid Salvador Martínez de Bartolomé Izquierdo CNB-CSIC / ProteoRed [email protected]
MIAPE Extractor Tutorial
SHPP meeting, 28 Aug 2012La Cristalera, Miraflores de la Sierra, Madrid
Salvador Martínez de Bartolomé IzquierdoCNB-CSIC / ProteoRed
SHPP - Data deposition workflow
1. Convert raw files to mzML or mgf2. Get search engine results in mzIdentML format3. Use MIAPE Extractor to generate MIAPE MS and
MIAPE MSI (at the same time!!)4. Inspect your data using the MIAPE Extractor Charts5. Use MIAPE Extractor to export PRIDE XML file from
several MIAPE MS and MSI6. Upload PRIDE XML file to (PRIDE database /
ProteomeXchange consortium)
SHPP - Data deposition workflow
1. Convert raw files to mzML or mgf2. Get search engine results in mzIdentML format3. Use MIAPE Extractor to generate MIAPE MS and
MIAPE MSI (at the same time!!)4. Inspect your data using the MIAPE Extractor Charts5. Use MIAPE Extractor to export PRIDE XML file from
several MIAPE MS and MSI6. Upload PRIDE XML file to (PRIDE database /
ProteomeXchange consortium)
Convert raw files to mzML or mgf• Use of available converters but...maybe its not
neccessary to create a mzML
• See afterwards...
SHPP - Data deposition workflow
1. Convert raw files to mzML or mgf2. Get search engine results in mzIdentML format3. Use MIAPE Extractor to generate MIAPE MS and
MIAPE MSI (at the same time!!)4. Inspect your data using the MIAPE Extractor Charts5. Use MIAPE Extractor to export PRIDE XML file from
several MIAPE MS and MSI6. Upload PRIDE XML file to (PRIDE database /
ProteomeXchange consortium)
Get search engine results in mzIdentML format
• MIAPE Extractor works with mzIdentML 1.0 and 1.1
Get search engine results in mzIdentML format
• mzIdentML from MASCOT (v2.3 or later):
Get search engine results in mzIdentML format
• mzIdentML from MASCOT (v2.3 or later):
Get search engine results in mzIdentML format
• mzIdentML from phenyx:
Get search engine results in mzIdentML format
• mzIdentML from phenyx:
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
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?
SHPP - Data deposition workflow
1. Convert raw files to mzML or mgf2. Get search engine results in mzIdentML format3. Use MIAPE Extractor to generate MIAPE MS and
MIAPE MSI (at the same time!!)4. Inspect your data using the MIAPE Extractor Charts5. Use MIAPE Extractor to export PRIDE XML file from
several MIAPE MS and MSI6. Upload PRIDE XML file to (PRIDE database /
ProteomeXchange consortium)
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!!
Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI
Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI
Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI
Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI
Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI
Metadata from mzMLProteome Discoverer
1.3.0.0
Compass Xport 3.0.5
Thermo RAW
Waters RAW AB wiff AB t2d
Bruker / Agilent YEP
Thermo RAW
Bruker / Agilent YEP
namemanufacturerversion - S/N
analyserActivation / dissociation componentActivation typenameversionparameters
msConvert 3.0.3643
MIAPE MS section
Ion source
Post-source component
Instrument
Acquisition software
ContainedNot contained
Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI
Two options:• mzML + mzIdentML• mgf + mzIdentML
Poor MS metadata
No MS metadata
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
Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI
Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI
Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI
Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI
Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI
Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI
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??????
SHPP - Data deposition workflow
1. Convert raw files to mzML or mgf2. Get search engine results in mzIdentML format3. Use MIAPE Extractor to generate MIAPE MS and
MIAPE MSI (at the same time!!)4. Inspect your data using the MIAPE Extractor Charts5. Use MIAPE Extractor to export PRIDE XML file from
several MIAPE MS and MSI6. Upload PRIDE XML file to (PRIDE database /
ProteomeXchange consortium)
Inspect your data using the MIAPE Extractor Charts
Lets try with examples....
SHPP - Data deposition workflow
1. Convert raw files to mzML or mgf2. Get search engine results in mzIdentML format3. Use MIAPE Extractor to generate MIAPE MS and
MIAPE MSI (at the same time!!)4. Inspect your data using the MIAPE Extractor Charts5. Use MIAPE Extractor to export PRIDE XML file from
several MIAPE MS and MSI6. Upload PRIDE XML file to (PRIDE database /
ProteomeXchange consortium)
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
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
SHPP - Data deposition workflow
1. Convert raw files to mzML or mgf2. Get search engine results in mzIdentML format3. Use MIAPE Extractor to generate MIAPE MS and
MIAPE MSI (at the same time!!)4. Inspect your data using the MIAPE Extractor Charts5. Use MIAPE Extractor to export PRIDE XML file from
several MIAPE MS and MSI6. Upload PRIDE XML file to (PRIDE database /
ProteomeXchange consortium)
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/)
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: [email protected]• Pass: miapereport
– Use your own account and share MIAPE projects after its creation with [email protected]
