Plasma Proteome Project...Hupo Plasma Proteome Project workshop Bethesda, July 2003, Henning...
Transcript of Plasma Proteome Project...Hupo Plasma Proteome Project workshop Bethesda, July 2003, Henning...
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PlasmaProteomeProject
Data Capture and Data Analysis
Hupo Plasma Proteome Project workshopBethesda, July 2003, Henning Hermjakob, EBI
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PlasmaProteomeProject
Aims•Ensure data comparability to allow
•Comparative analysis of results•Presentation of results•User-friendly public access to results
•Ensure data quality
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PlasmaProteomeProject
Overview•Data submission review
•Submission tools•Database standardization•Representation of PTMs•Future perspectives
•Data analysis
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PlasmaProteomeProject
Data submission tools•Excel spreadsheets
•Easy, accessible technology•More effort for central analysis•Sent out in June:
•Protein summary•Abundance summary•Resources summary
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PlasmaProteomeProject
Data submission tools•XML-based:
•Better data integration•Easier central analysis•Better for data presentation• Input tools: Pedro•Experimental status
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PlasmaProteomeProject
Database standardisation•Comparison of results obtained from searches against different databases is difficult
•Proposal: Define one default database as a basis for all searches
•Proposal: IPI
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PlasmaProteomeProject
International Protein Index (IPI)•Merged set of all major protein sequence data sources
•First created for:Initial sequencing and analysis of the human genome.Lander, ES., et al., Nature. 2001 Feb 15;409(6822):860-921.
•Monthly updated•Stable, versioned identifiers•Detailed documentation•Statistics: 56530 human entries as of July 2.•http://www.ebi.ac.uk/IPI
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PlasmaProteomeProject
IPI formats•Fasta format:
>IPI:IPI00000005.1|SWISS-PROT:P01111-3|REFSEQ_NP:NP_002515|TREMBL:P54111| REFSEQ_XP:XP_032698;XP_001317|ENSEMBL:ENSP00000261444 Tax_Id=9606 Transforming protein N-Ras MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG QEEYSAMRDQYMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDL PTRTVDTKQAHELAKSYGIPFIETSAKTRQGVEDAFYTLVREIRQYRMKKLNSSDDGTQG CMGLPCVVM
•Swiss-Prot style format
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PlasmaProteomeProject
IPI algorithm outline•Expand all annotated SP splice variants into separate entries
•Inter-database similarity searches•Clustering based on pairwise reciprocal best matches and subfragment matches (95% cutoff)
•Each cluster represents one IPI entry•Identifier tracking based on cluster member accession numbers
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PlasmaProteomeProject
Representation of PTMs•How much detail do we need?•High-detail proposal: PSI PTM classification:
•Controlled vocabulary for PTMs in GO format•Covers both general (“phosphorylation”) and detailed PTMs
•Fully cross-referenced with RESID database
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PlasmaProteomeProject
Future work•Controlled vocabulary development:Hierarchical classification of experimental techniques
•Representation of complexes and interactions
•Partially done for Protein Interactions within HUPO Proteomics Standards Initiative
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PlasmaProteomeProject
Data analysis•How to verify protein identifications?•How to integrate cross-specimen, cross-laboratory, and cross-technology data?
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PlasmaProteomeProject
Acknowledgements•Richard Simpson, Ludwig Institute for Cancer Research
•Paul Kersey, EBI•Luisa Montecchi-Palazzi, University of Rome•Rolf Apweiler, EBI
•You!
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PlasmaProteomeProject
Questions for the
Data Management/Analysis
Breakout Session
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PlasmaProteomeProject
Data Management/Analysis Session•Timeline:
•XML schema by Monday, July 21•Preliminary data submissions until September 15
•Data mapping and joining•Comparative analysis until HUPO congress
•More detailed round for Jambouree Spring 2004
•HELP!!!!
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PlasmaProteomeProject
Data Management/Analysis Session•Format questions:
•Shared database possible?•Which one?•PTM representation?
•Access to joint dataset:•Only for PPP consortium until Spring 2004?•To all as soon as possible?
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PlasmaProteomeProject
Data Management/Analysis Session•Quality checks:
•Which checks to run?•Who?•What needed?
•Analysis on joined set•Which questions do you want to ask?•Do you want to participate?• In which form?•Teaser: Clustering identification lists, do you get stronger correlation with samples or labs?
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PlasmaProteomeProject
Data Management group report•Modifications to the Excel forms:
•Add mass, pi, intensity (2D)•Confidence (high, low)
•XML preferred format, Excel ok
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PlasmaProteomeProject
Data Management group report•Data submission support:
•Univ. Manchester and Yale offer assistance with formatting/writing Mascot parser
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PlasmaProteomeProject
Data Management group report•Timeline:
•Next week: XML schema and documentation
•August 15: Test submission•September 15: Real submission•October 10: Preliminary analysis results
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PlasmaProteomeProject
Data Management group report•Analysis aims:
•How/Which proteins identified by abundance
•Consistency of identification•Comparison of samples•Comparison of methods•Consistency of abundance (by rank order)
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PlasmaProteomeProject
Data Management group report
•Open questions:•8 labs indicated “Seldi only”
•This data is not captured by the proposed spreadsheet•We need Seldi experts!
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PlasmaProteomeProject
Data Management group report
•Open questions:•Data release:
•Data will be anonymised, but be aware it can be “attributed” to sources by experts•Publications will be anonymous
•“First right” of publication for participants.