http://icim.marseille.inserm.fr/proteomics

qcDIGE: quality control tools for DIGE

● Sample and gel preparation● Image acquisition

http://icim.marseille.inserm.fr/proteomics

DIGE normalisation benefits

● Standard in each gel insures right interpretation● Cy dyes are linear over 4 or 5 log

http://icim.marseille.inserm.fr/proteomics

GelBrowser module (Gel)

● All the channels of a gel at once

● Dynamical range can be checked

● Dye swap is available for technical reproducibility

http://icim.marseille.inserm.fr/proteomics

GelBrowser module (Cy2)

● All the standards at once

● Overall quality of the experiment can be estimated

http://icim.marseille.inserm.fr/proteomics

Detection, quantitation and export

● GE Decyder● NonLinear

● XML export convert to text file imported in R by a Bioconductor library

● MeV available

http://icim.marseille.inserm.fr/proteomics

GelPlot (Gel, Cy2)

● Quantitation reports

● Quality control plots

● Dye swap

http://icim.marseille.inserm.fr/proteomics

Data analysis: Spot selection

● Open, validated, statistical methods

● Alternative to commercial solutions

http://icim.marseille.inserm.fr/proteomics

SpotReview

● Final review of selected spots with all its useful characteristics

● Before MS identification

http://icim.marseille.inserm.fr/proteomics

Protein annotation

● Automated cross-databases annotation● Customisable template report with external links● Ease gene interactions interpretation

http://icim.marseille.inserm.fr/proteomics

Conclusions

● Set of tools at each important step of a DIGE experiment

● Ease DIGE analysis● Quality indicators:

dynamic, dye swap, standards...

● HTML report for ease● Perl, R, ImageJ● LIMS integration...

● Plateforme protéomiqueICIM, IFR 137

● Matthieu HainautFabrice LabisteMatthieu Pophillat

● See you at SMAP 2007 in Pau

http://icim.marseille.inserm.fr/proteomics