QconCat: From Instrument To Browser

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QconCat: From Instrument To Browser

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

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