Comparative 2D DIGE analysis of protein expression in control and SMA ES cells. Control and SMA ES cells were harvested and lysed. Equal amounts of total proteins from wild-type or SMA ES cells were trace labeled with either Cy3 or Cy5. The dyed proteins indicated by the labeled colors were mixed and separated by isoelectric focusing in 7 cm pH 3-10 linear gradient IPG strips, and further separated in a second dimension of 10% SDS-PAGE. Fluorescently labeled proteins were visualized by Typhoon Trio scanner and difference between samples analyzed by the accompanied software. Samples shown in the left and right panels were from different preparations of ES cells and labeled with opposite dyes to demonstrate the reproducibility of the assay. A few abnormally expressed corresponding proteins were marked by arrows. MW = molecular weight.