It is well understood that all the samples of an experiment must be processed under identical conditions for comparision among them. If Voltage variation occurs between the samples, when isolating protein in second dimension (Gel Electrophoresis) kepping other things constant, what variation in spot position or size may occure?
Small differences in voltage should make little difference provided that the total power is similar. What will make a difference is the temperature of the gels. The higher the temperature in the gel the faster the proteins/peptides will move and there may be differences between the larger and smaller proteins. It is important to ensure that the cooling efficiency of your system is the same for each gel and also for the front and back plates ofeach gel cassette. If the cooling rate is different between the front and back then the protein/peptide ions nearer the warmer plate will move more rapidly than thos nearer the cooler plate leading to fuzzy spots or even double spotting.
Voltage variation will result in inconsistent protein spot mobility and spot density. In order to maintain the voltage stability, use chilled running buffer and maintain the electrophoresis at 8 C temperature.
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