After standardizing the technique of DIGE for a pretty long time now, am trying to find the differntial protein profile upon viral fusion with host cells. However, with my control being heat inactivated virus, when I am performing DIGE (with 2 biological replicates and a dye-swap) I am not getting any protein expression fold difference to be greater than 1.2. But on comparision with only cells (without any virus treatment at all), many spots show good fold difference (as much as 20-30 fold in some!). So, I am otherwise not really doubting the procedure!! Has anyone really come across such an instance in their DIGE experiments? Is a protein fold difference of 1.15 and the like good enough for further WB validation? Do we not tend to accumulate false positive with such less stringent conditions??