QConCAT: quantitative proteomics from instrument to browser <ul><li>Neil Swainston, Daniel Jameson </li></ul><ul><li>Manch...
QconCAT… Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes...
… from instrument to browser <ul><li>From an  QconCAT  informatics perspective, there are  three steps … </li></ul><ul><ul...
Selection of QconCAT peptides <ul><li>Q. Given a given protein,  which peptides are suitable candidates for QconCAT peptid...
PepSelecta <ul><li>Takes  protein accession numbers  as input, or SBML file (and other parameters) </li></ul><ul><li>Provi...
 
 
 
PRIDE Converter <ul><li>PRIDE Converter  (EBI) used to extract meta-data </li></ul><ul><ul><li>Who ran the sample, what wa...
QconCAT PrideWizard <ul><li>Takes raw MS data </li></ul><ul><li>Searches  Mascot </li></ul><ul><li>Finds QconCAT pairs </l...
 
QconCAT PrideWizard <ul><li>Integrate  identifications ,  quantitations  and  meta-data  to generate standard data format ...
MCISB Proteome Database <ul><li>Searchable  repository of quantitative proteomics data </li></ul><ul><li>Geeky bit… </li><...
MCISB Proteome Database <ul><li>Demo… </li></ul>
Future work <ul><li>Compare with results from MaxQuant </li></ul><ul><li>Peptide quantitations to  protein  quantitations ...
QConCAT: quantitative proteomics from instrument to browser <ul><li>Neil Swainston, Daniel Jameson </li></ul><ul><li>Manch...
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iQconCAT: quantitative proteomics from instrument to browser

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iQconCAT: quantitative proteomics from instrument to browser

  1. 1. QConCAT: quantitative proteomics from instrument to browser <ul><li>Neil Swainston, Daniel Jameson </li></ul><ul><li>Manchester Centre for Integrative Systems Biology </li></ul><ul><li>7 April 2010 </li></ul>
  2. 2. QconCAT… Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Pratt JM, et al. Nature Protocols 1, 1029-1043 (2006)
  3. 3. … 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>
  4. 4. 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, within “correct” mass range). </li></ul><ul><li>Preferably… </li></ul><ul><li>Be unmodified . </li></ul>
  5. 5. PepSelecta <ul><li>Takes protein accession numbers as input, or SBML file (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><ul><li>Ranks peptides by “flyability” using PeptideSieve </li></ul><ul><ul><li>Future development: Use digestibility predictor? </li></ul></ul>
  6. 9. PRIDE Converter <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>
  7. 10. QconCAT PrideWizard <ul><li>Takes raw MS data </li></ul><ul><li>Searches Mascot </li></ul><ul><li>Finds QconCAT pairs </li></ul><ul><li>Extracts mass chromatograms </li></ul><ul><li>Finds appropriate peak start / end positions </li></ul><ul><li>Generates ratios (and therefore concentrations) </li></ul><ul><li>A Jameson / Swainston production </li></ul>
  8. 12. QconCAT PrideWizard <ul><li>Integrate identifications , quantitations and meta-data to generate standard data format (PRIDE XML) </li></ul><ul><li>Upload to database </li></ul>
  9. 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>
  10. 14. MCISB Proteome Database <ul><li>Demo… </li></ul>
  11. 15. Future work <ul><li>Compare with results from MaxQuant </li></ul><ul><li>Peptide quantitations to protein quantitations </li></ul><ul><ul><li>Weighted by Mascot score? </li></ul></ul>
  12. 16. QConCAT: quantitative proteomics from instrument to browser <ul><li>Neil Swainston, Daniel Jameson </li></ul><ul><li>Manchester Centre for Integrative Systems Biology </li></ul><ul><li>7 April 2010 </li></ul>
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