iQconCAT: quantitative proteomics from instrument to browser

QConCAT: quantitative proteomics from instrument to browser

Neil Swainston, Daniel JamesonManchester 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…

1. Selection of QconCAT peptides2. Analysis and submission of data3. 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 JamesonManchester Centre for Integrative Systems Biology

7 April 2010