Identification of non-idealities in gel electrophoresis

The molecular weight separation, which is the second dimension of two-dimensional gel electrophoresis, is studied quantitatively with the goal of improving positional predictability and reproducibility. Mathematical modeling of carrier electrolyte dynamics is used to track the progress of a stacking front as a function of coulombs passed. In all test cases, the front moves more slowly than predicted and shows both curvature and tilt. These systematic deviations from the model are found to be influenced by a variety of factors, including both design and operating features. These factors are largely explained, and suggestions are made for improvements.