qconcat: from instrument to browser
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QConCAT: from instrument to browser
Neil Swainston, Daniel JamesonManchester Centre for Integrative Systems Biology
14 September 2009
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Overview
• Brief intro to the MCISB
• Data management infrastructure for quantitative proteomics (QconCAT)
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Experimental data infrastructure
Enzyme kineticsQuantitativemetabolomics
Quantitativeproteomics
SBML Model
Parameters(KM, Kcat)
Variables(metabolite, proteinconcentrations)
PRIDE MeMo SABIO-RK
Web serviceWeb serviceWeb service
MeMo-RK
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…from instrument to browser
• From an QconCAT informatics perspective, there are three steps…
1. Selection of QconCAT peptides2. Analysis and submission of data3. Browsing / querying
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Selection of QconCAT peptides
Q. Given a given protein, which peptides are suitable candidates for QconCAT peptides?
Must…• Be unique across organism.• Be detectable (digestible, flyable).
Preferably…• Be unmodified.
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QconCAT Selection Wizard
• Takes protein accession numbers as input (and other parameters)
• Provides list of potential QconCAT peptides
• Downloads sequence• Performs BLAST against UniProt (tests uniqueness)• Filters peptides “appropriately”
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QconCAT Selection Wizard
• Limitations and future work
• Currently binary• Peptides are either ‘good’ or ‘bad’
• Apply score to peptide• Use PeptideSieve? (predict flyability)• Use digestibility predictor (Jenny Siepen, Craig
Lawless)?
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QconCAT data analysis
• Work in progress
• Daniel Jameson has implemented a tool that…• Takes raw MS data• Searches Mascot• Finds QconCAT pairs• Extracts mass chromatograms• Integrates chromatogram peak areas• Generates ratios (and therefore concentrations)
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QconCAT data analysis
• Integrate identifications, quantitations and meta-data to generate standard data format (PRIDE XML)
• Pride Converter (EBI) used to extract meta-data• Who ran the sample, what was the sample,
instrument used? etc.• http://code.google.com/p/pride-converter/
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MCISB Proteome Database
• Searchable repository of quantitative proteomics data
• Geeky bit…• eXist native XML database holding PRIDE XML• JSP front end• Querying extensible through XQuery
• Web and web-service interface• Both human and computer-queryable• Web service useful for automatically parameterising
systems biology models
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MCISB Proteome Database
• Future work
• Currently only displays identifications• Quantitations coming v. soon• Overlaid mass chromatograms for heavy and light at
RT of interest
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To do list and future work
• Peptide quantitations to protein quantitations• Weighted by Mascot score?• Dealing with replicates
• Different quantitation algorithms?• SILAC Analyzer• MaxQuant
• SILAC implementation?• Tweak the web interface – solution already exists for
relative quantitation (iTRAQ)
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QConCAT: from instrument to browser
Neil Swainston, Daniel JamesonManchester Centre for Integrative Systems Biology
14 September 2009