qcdige: quality control tools for dige
TRANSCRIPT
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http://icim.marseille.inserm.fr/proteomics
qcDIGE: quality control tools for DIGE
● Sample and gel preparation● Image acquisition
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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
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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
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http://icim.marseille.inserm.fr/proteomics
GelBrowser module (Cy2)
● All the standards at once
● Overall quality of the experiment can be estimated
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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
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http://icim.marseille.inserm.fr/proteomics
GelPlot (Gel, Cy2)
● Quantitation reports
● Quality control plots
● Dye swap
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http://icim.marseille.inserm.fr/proteomics
Data analysis: Spot selection
● Open, validated, statistical methods
● Alternative to commercial solutions
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http://icim.marseille.inserm.fr/proteomics
SpotReview
● Final review of selected spots with all its useful characteristics
● Before MS identification
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http://icim.marseille.inserm.fr/proteomics
Protein annotation
● Automated cross-databases annotation● Customisable template report with external links● Ease gene interactions interpretation
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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