# median normalization for proteomics

I am using the data from a proteomics study were the data was log2 transformed and then a median normalization was applied. The data was normalized by groups of conditions (normal, mutant), not for all the arrays at the same time, so the median for the normal group is slightly higher than for the mutant group. I am wondering if this is correct or should I normalized the data en general, I mean taking into account all the arrays and normalizing all at the same time so the 2 groups have the same median.

Regards