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Large-scale 2-D DIGE studies - guidelines to overcome pitfalls and challenges along the experimental procedure

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Author(s): Franziska Dautel | Stefan Kalkhof | Saskia Trump | Irina Lehmann | Andreas Beyer | Martin von Bergen

Journal: Journal of Integrated OMICS
ISSN 2182-0287

Volume: 1;
Issue: 1;
Start page: 170;
Date: 2011;
Original page

Keywords: Protein expression analysis | Proteomics | Differential gel electrophoresis | 2-D-DIGE

ABSTRACT
In large 2-D DIGE proteomic studies with a large number of samples, it is essential to design the experimental setup to detect statistically significant protein changes under consideration of experimental variances. Herein are presented guidelines and general remarks on the extrac-tion of protein expression data by following protein spots on their way from first spot synchronization, detection, quantification and statistical analysis until excision and identification. Further discussion addresses common difficulties, potential pitfalls and strategies for dealing with gel-to-gel discrepancies, labeling inefficiencies, and dye- and batch effects which might not be obvious to novices and even more experienced users of DIGE technology.
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