Synopsis Fluorescence 2-D difference gel electrophoresis (2-D DIGE) can be used for direct differential protein expression analysis. Here, the complex secretomes of HepG2 and END2 cell lines were used to compare three commercially available DIGE analysis software packages. Green, red and blue spots represented labeled protein standard, END2 and HepG2 secretomes, respectively; therefore, the images were analyzed by using SameSpots, Dymension and DeCyder to make comparison among three software packages. The success of high-performance differential gel electrophoresis using fluorescent dyes (DIGE) depends on the quality of the digital image captured after electrophoresis, the DIGE enabled image analysis software tool chosen for highlighting the differences, and the statistical analysis. This study compares three commonly available DIGE enabled software packages for the first time: DeCyder V6.5 (GE-Healthcare), Progenesis SameSpots V3.0 (Nonlinear Dynamics), and Dymension 3 (Syngene).
DIGE gel images of cell culture media samples conditioned by HepG2 and END2 cell lines were used to evaluate the software packages both quantitatively and subjectively considering ease of use with minimal user intervention. Consistency of spot matching across the three software packages was compared, focusing on the top fifty spots ranked statistically by each package. Cubase Vst Amp Rack Itunes.
