Transcript of MIAPE Extractor Tutorial SHPP meeting, 28 Aug 2012 La Cristalera, Miraflores de la Sierra, Madrid...
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- MIAPE Extractor Tutorial SHPP meeting, 28 Aug 2012 La
Cristalera, Miraflores de la Sierra, Madrid Salvador Martnez de
Bartolom Izquierdo CNB-CSIC / ProteoRed
smartinez@proteored.org
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- 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)
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- 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)
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- Convert raw files to mzML or mgf Use of available converters
but...maybe its not neccessary to create a mzML See
afterwards...
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- 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)
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- Get search engine results in mzIdentML format MIAPE Extractor
works with mzIdentML 1.0 and 1.1
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- Get search engine results in mzIdentML format mzIdentML from
MASCOT (v2.3 or later):
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- Get search engine results in mzIdentML format mzIdentML from
MASCOT (v2.3 or later):
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- Get search engine results in mzIdentML format mzIdentML from
phenyx:
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- Get search engine results in mzIdentML format mzIdentML from
phenyx:
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- 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
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- 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?
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- 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)
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- 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!!
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- Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI
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- Metadata from mzML Contained Not contained
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- Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI Two
options: mzML + mzIdentML mgf + mzIdentML Poor MS metadata No MS
metadata
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- 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
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- Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI
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- MIAPE projects names consensus: SHPP + Cell Line + Other exper.
feature(s) SHPP Lab Jurkat SDSPage RIPA Suggestions??????
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- 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)
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- Inspect your data using the MIAPE Extractor Charts Lets try
with examples....
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- 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)
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- 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
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- 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
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- 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)
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- 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/
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- 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
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