Application of DIGE and Mass Spectrometry in the Study of Type 2 Diabetes Mellitus Mouse Models - Difference Gel Electrophoresis (DIGE): Methods and Protocols - page 311

Fig. 2. Optimization strategy for the PMT settings for each of the three dye channels in ImageQuant (Cy3 only is shown here ) .
the Cy3 and Cy5 images are then aligned to their respective
Cy2 images. This is by far the most important step in the work-
fl ow. In practice, an automatic alignment can be carried out as
a fi rst step; this can then be reviewed using the transition and
checkerboard panes and any necessary modifi cation can be
made to the vectors.
10. Filter out any of the spots that you do not want to be included
in the analysis such as reference markers that are placed at the
edge of the gels.