data standards submission 1 st chr-16 workshop. miraflores de la sierra august, 28 th -29 th 2012...
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![Page 1: Data Standards Submission 1 st CHr-16 Workshop. Miraflores de la Sierra August, 28 th -29 th 2012 Alberto Medina](https://reader035.vdocument.in/reader035/viewer/2022062517/56649edb5503460f94bea5b0/html5/thumbnails/1.jpg)
Data Standards Submission 1st CHr-16 Workshop.Miraflores de la SierraAugust, 28th-29th 2012 Alberto Medina
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Summary
1. Data standards (just a quick view)2. Trusted pipeline3. Starting!4. Other search engines
![Page 3: Data Standards Submission 1 st CHr-16 Workshop. Miraflores de la Sierra August, 28 th -29 th 2012 Alberto Medina](https://reader035.vdocument.in/reader035/viewer/2022062517/56649edb5503460f94bea5b0/html5/thumbnails/3.jpg)
Summary
1. Data standards (just a quick view)2. Trusted pipeline3. Starting!4. Other search engines
![Page 4: Data Standards Submission 1 st CHr-16 Workshop. Miraflores de la Sierra August, 28 th -29 th 2012 Alberto Medina](https://reader035.vdocument.in/reader035/viewer/2022062517/56649edb5503460f94bea5b0/html5/thumbnails/4.jpg)
Data Standards – PSI fram
ework
Spanish Consortium Bioinformatics pipeline
Mass Spectra
Raw data MzMl/TraML
Protein/Peptides
Search Engines MzIdentml
Quantitation
Vendor/Free software MzQuantml
Data Reporting – ProteoRed M
IAPE W
eb toolkit
MIAPE MS/MSI
PRIDE
Data Reporting –
with stable release
MIAPEQuant
PRIDEQuan¿?
Data validation and subm
ission
ProteomeXchange
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External repositories
Development of bioinformatic environment:Spanish HPP will join the different resources to provide an unique enquiring system
PAtlasNProt
GPMDB
PRIDE
UProtUpcoming
Proteomics results
Data standards submission
(ProteomeXchange)+ +Emsembl
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Summary
1. Data standards (just a quick view)2. Trusted pipeline3. Starting!4. Other search engines
![Page 7: Data Standards Submission 1 st CHr-16 Workshop. Miraflores de la Sierra August, 28 th -29 th 2012 Alberto Medina](https://reader035.vdocument.in/reader035/viewer/2022062517/56649edb5503460f94bea5b0/html5/thumbnails/7.jpg)
Trusted pipeline
Mass Spectra
.mgf
Identification
Mascot
Output file
mzIdentML
MIAPE Generation
MIAPE MS MIAPE MSI
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Trusted pipeline
MIAPE MS MIAPE MSI
PRIDE Generation
PRIDE XML
Stats (MIAPE Extractor)
Charts and Reports
Check and View PRIDE
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Summary
1. Data standards (just a quick view)2. Trusted pipeline3. Starting!4. Other search engines
![Page 10: Data Standards Submission 1 st CHr-16 Workshop. Miraflores de la Sierra August, 28 th -29 th 2012 Alberto Medina](https://reader035.vdocument.in/reader035/viewer/2022062517/56649edb5503460f94bea5b0/html5/thumbnails/10.jpg)
Starting (1)• Step 1)• Element to achieve: Peak lists (acquired data).• Issues:
• Several data formats (mgf, wiff, pkl, etc).• Different Software packets.• Translators.
• Goal: • MGF file or mzML.
• Translators• MSConvert, OpenMS, ABSciex MS Data Converter, CompassXport,
ProCon.
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Starting (2)• Step 2)• Element to achieve: Identification of Proteins and Peptides.• Issues:
• Have your own Mascot Server.• Release 2.3 in advance• Other search engines (check section 4).
• Goal: • Submit to Mascot peak list obtained in step 1.
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Starting (3)• Step 3)• Element to achieve: Mascot results formatted as mzIdentML• Issues:
• Version 2.3 is rather slow. • It is not possible to do using batch mode.
• Goal: • mzIdentML.
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Starting (3)
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MIAPE Generation
1. GO to ProteoRed MIAPE web toolkit site.www.proteored.org/MIAPE
2. Click on Create MIAPE Automatic
3. Download the application (Java application).
4. Run the application
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MIAPE Generation
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PRIDE Generation
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PRIDE Generation
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PRIDE Visualizationhttp://proteo.cnb.csic.es/prideviewer
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PRIDE Submissionhttp://www.ebi.ac.uk/pride/easySubmitData.do?
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Exchanging through the cloud
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MIAPE Extractor
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A hopefully universe
• ProteoRed MIAP
E repository
• MPWTK
• mzML
• mzIdentML
• MPWTK
• MIAPE
Extractor
• PRIDE XML
• A
• B
• C
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Summary
1. Data standards (just a quick view)2. Trusted pipeline3. Starting!4. Other search engines
![Page 24: Data Standards Submission 1 st CHr-16 Workshop. Miraflores de la Sierra August, 28 th -29 th 2012 Alberto Medina](https://reader035.vdocument.in/reader035/viewer/2022062517/56649edb5503460f94bea5b0/html5/thumbnails/24.jpg)
Other Search Engines• Phenyx:
• Waiting new patch to save the results in a straighforward manner. Similar to Mascot export.
• X!Tandem:• Full integrated thorugh X!Tandem results files.
• Sequest:• It is possible to save the results formatted as mzIdentML through
ProCon tool (runnable from Windows XP OS).http://www.medizinisches-proteom-center.de/ProConWe need some feedback from Sequest users.
• OMSSA:• Not integrated, but it is possible to use mzIdentML-Parsershttp://code.google.com/p/mzidentml-parsers/
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Questions