QConCAT: from instrument to browser

Neil Swainston, Daniel JamesonManchester Centre for Integrative Systems Biology

14 September 2009

Overview

• Brief intro to the MCISB

• Data management infrastructure for quantitative proteomics (QconCAT)

Experimental data infrastructure

Enzyme kineticsQuantitativemetabolomics

Quantitativeproteomics

SBML Model

Parameters(KM, Kcat)

Variables(metabolite, proteinconcentrations)

PRIDE MeMo SABIO-RK

Web serviceWeb serviceWeb service

MeMo-RK

…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).

Preferably…• Be unmodified.

QconCAT Selection Wizard

• Takes protein accession numbers as input (and other parameters)

• Provides list of potential QconCAT peptides

• Downloads sequence• Performs BLAST against UniProt (tests uniqueness)• Filters peptides “appropriately”

QconCAT Selection Wizard

• Limitations and future work

• Currently binary• Peptides are either ‘good’ or ‘bad’

• Apply score to peptide• Use PeptideSieve? (predict flyability)• Use digestibility predictor (Jenny Siepen, Craig

Lawless)?

QconCAT data analysis

• Work in progress

• Daniel Jameson has implemented a tool that…• Takes raw MS data• Searches Mascot• Finds QconCAT pairs• Extracts mass chromatograms• Integrates chromatogram peak areas• Generates ratios (and therefore concentrations)

QconCAT data analysis

• Integrate identifications, quantitations and meta-data to generate standard data format (PRIDE XML)

• Pride Converter (EBI) used to extract meta-data• Who ran the sample, what was the sample,

instrument used? etc.• http://code.google.com/p/pride-converter/

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

• Future work

• Currently only displays identifications• Quantitations coming v. soon• Overlaid mass chromatograms for heavy and light at

RT of interest

To do list and future work

• Peptide quantitations to protein quantitations• Weighted by Mascot score?• Dealing with replicates

• Different quantitation algorithms?• SILAC Analyzer• MaxQuant

• SILAC implementation?• Tweak the web interface – solution already exists for

relative quantitation (iTRAQ)

QConCAT: from instrument to browser

Neil Swainston, Daniel JamesonManchester Centre for Integrative Systems Biology

14 September 2009