iqconcat: quantitative proteomics from instrument to browser
TRANSCRIPT
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QConCAT: quantitative proteomics from instrument to browser
Neil Swainston, Daniel JamesonManchester Centre for Integrative Systems Biology
7 April 2010
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QconCAT…
Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Pratt JM, et al. Nature Protocols 1, 1029-1043 (2006)
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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, within “correct” mass
range).
Preferably…• Be unmodified.
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PepSelecta
• Takes protein accession numbers as input, or SBML file (and other parameters)
• Provides list of potential QconCAT peptides• Downloads sequence• Performs BLAST against UniProt (tests uniqueness)• Filters peptides “appropriately”• Ranks peptides by “flyability” using PeptideSieve
• Future development: Use digestibility predictor?
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PRIDE Converter
• PRIDE Converter (EBI) used to extract meta-data• Who ran the sample, what was the sample,
instrument used? etc.
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QconCAT PrideWizard
• Takes raw MS data• Searches Mascot• Finds QconCAT pairs• Extracts mass chromatograms• Finds appropriate peak start / end positions• Generates ratios (and therefore concentrations)
• A Jameson / Swainston production
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QconCAT PrideWizard
• Integrate identifications, quantitations and meta-data to generate standard data format (PRIDE XML)
• Upload to database
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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
• Demo…
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Future work
• Compare with results from MaxQuant
• Peptide quantitations to protein quantitations• Weighted by Mascot score?
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QConCAT: quantitative proteomics from instrument to browser
Neil Swainston, Daniel JamesonManchester Centre for Integrative Systems Biology
7 April 2010