Two-dimensional polyacrylamide gel electrophoresis (2DPAGE) continues to be an important protein separation
technology despite advances in other analytical methods such
as mass spectrometry. However, gel-to-gel variation remains
a major drawback. Developments such as DIGE (differential
2D fluorescence gel electrophoresis [1]) for gel-based proteome expression analysis provide amendments. In DIGE,
three matching fluorescent dyes are used to run biological
sample replicates (≥3) in parallel with an internal standard,
each sample pair (e.g. control vs.treated) on a single gel.
Although replicate experiments are favourable, multiple samples of one kind are not always available as is, for instance, the
case in patient biopsies or samples taken in field work. Therefore, CoFGE (comparative 2D fluorescence gel electrophoresis