Journal of Proteomics & Bioinformatics
Open Access

Abstract

Evaluation of a Novel Automated Machine, the Auto2D, for Two-Dimensional Gel Electrophoresis

Yuki Tani, Takashi Tajima, Akira Kawai, Yutaka Unuma, Hideki Kinoshita and Tadashi Kondo

Two-dimensional gel electrophoresis (2D-PAGE) has been a commonly used technique for protein expression studies. Application of a fluorescent dye in 2D-PAGE, namely 2D-DIGE, has improved the performance of 2D-PAGE in terms of sensitivity, reproducibility and throughput. However, 2D-PAGE still requires a degree of skill, and is considerably time-consuming. Recently, a novel automated 2D-PAGE machine, the Auto2D, was developed for use in conventional protein expression studies. Here, we examined the performance of the Auto2D for 2D-DIGE from the viewpoint of proteome coverage, reproducibility, and throughput. We found that a single 2D image of osteosarcoma cells contained 521 protein spots. By running an identical sample, we found that the system reproducibility was high and the intensity of more than 409 protein spots was scattered within a 2-fold range of differences between experiments, with a correlation coefficient of at least 0.60. We also found that a single 2D-PAGE run took 140 min, and that 3 gels could be run per day. We conclude that the Auto2D can be used for conventional protein expression studies. On the other hand, as the number of observed proteins was quite limited, and only three gels can be run per day per device, the Auto2D may not be suitable for a large-scale proteomic study.