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iQconCAT: quantitative proteomics from instrument to browser
 

iQconCAT: quantitative proteomics from instrument to browser

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    iQconCAT: quantitative proteomics from instrument to browser iQconCAT: quantitative proteomics from instrument to browser Presentation Transcript

    • QConCAT: quantitative proteomics from instrument to browser
      • Neil Swainston, Daniel Jameson
      • Manchester Centre for Integrative Systems Biology
      • 7 April 2010
    • QconCAT… Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Pratt JM, et al. Nature Protocols 1, 1029-1043 (2006)
    • … from instrument to browser
      • From an QconCAT informatics perspective, there are three steps …
        • Selection of QconCAT peptides
        • Analysis and submission of data
        • Browsing / querying
    • 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 .
    • 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?
    •  
    •  
    •  
    • PRIDE Converter
      • PRIDE Converter (EBI) used to extract meta-data
        • Who ran the sample, what was the sample, instrument used? etc.
    • 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
    •  
    • QconCAT PrideWizard
      • Integrate identifications , quantitations and meta-data to generate standard data format (PRIDE XML)
      • Upload to database
    • 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
    • MCISB Proteome Database
      • Demo…
    • Future work
      • Compare with results from MaxQuant
      • Peptide quantitations to protein quantitations
        • Weighted by Mascot score?
    • QConCAT: quantitative proteomics from instrument to browser
      • Neil Swainston, Daniel Jameson
      • Manchester Centre for Integrative Systems Biology
      • 7 April 2010