Influence of image-analysis software on quantitation of two-dimensional gel electrophoresis data

• Published in: Electrophoresis 2009, Vol.30 (2), p.325-328
• Main Authors: Stessl, Martina, Noe, Christian R, Lachmann, Bodo
• Format: Article
• Language: English
• Subjects: Electrophoresis, Gel, Two-Dimensional - methods; Image analysis; Image Processing, Computer-Assisted - methods; Normalization; Proteome - analysis; Reproducibility of Results; Software validation; Two-dimensional gel electrophoresis
• ISSN: 0173-0835; 1522-2683
• DOI: 10.1002/elps.200800213

Image analysis of two-dimensional gels is a crucial step in a proteomic workflow and has a direct impact on obtained qualitative and quantitative data. Since the analysis is a complex process and creates large data amounts, the use of a respective software is inevitable. There are only a few papers published addressing the issue of analysis-based variance; therefore, our aim was to highlight the discrepancy of received results when different commercially available image-tools are used for gel analysis especially in terms of comparability of the obtained outcome when the same digital image set is used. A set of six gels (three replicates per group) of real-life samples was created and examined with two different versions of PD-Quest (Bio-Rad) (version 6.1 and its update version 8.0) and with an external image-tool Delta 2D (Decodon) (version 3.6). Replicate groups were analyzed and compared with each other with regard to volume ratios of a group of significantly changed spots. The study points out significant variations among results depending on the software package used, underlining the importance of a careful investigation of post-experimental processes to receive comparable and reliable results.