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 Martínez de Bartolomé Izquierdo CNB-CSIC / ProteoRed
MIAPE Extractor Tutorial SHPP meeting, 28 Aug 2012 La
Cristalera, Miraflores de la Sierra, Madrid Salvador Martnez de
Bartolom Izquierdo CNB-CSIC / ProteoRed
[email protected]
Slide 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)
Slide 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)
Slide 4
Convert raw files to mzML or mgf Use of available converters
but...maybe its not neccessary to create a mzML See
afterwards...
Slide 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)
Slide 6
Get search engine results in mzIdentML format MIAPE Extractor
works with mzIdentML 1.0 and 1.1
Slide 7
Get search engine results in mzIdentML format mzIdentML from
MASCOT (v2.3 or later):
Slide 8
Get search engine results in mzIdentML format mzIdentML from
MASCOT (v2.3 or later):
Slide 9
Get search engine results in mzIdentML format mzIdentML from
phenyx:
Slide 10
Get search engine results in mzIdentML format mzIdentML from
phenyx:
Slide 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
Slide 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?
Slide 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)
Slide 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!!
Slide 15
Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI
Slide 16
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Metadata from mzML Contained Not contained
Slide 20
Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI Two
options: mzML + mzIdentML mgf + mzIdentML Poor MS metadata No MS
metadata
Slide 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
Slide 22
Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI
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Slide 31
MIAPE projects names consensus: SHPP + Cell Line + Other exper.
feature(s) SHPP Lab Jurkat SDSPage RIPA Suggestions??????
Slide 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)
Slide 33
Inspect your data using the MIAPE Extractor Charts Lets try
with examples....
Slide 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)
Slide 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
Slide 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
Slide 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)
Slide 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/
Slide 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:
[email protected] Pass: miapereport Use your own account
and share MIAPE projects after its creation with
[email protected]