I am no expert, but I have a few things I could suggest you look into:
1) mRNA stability. The stability of specific mRNA molecules will play a role in the regulation of protein synthesis. mRNA molecules are single-stranded and have the tendency to fold into 3D structures. Some 3D structures leave mRNAs more or less susceptible to degradation by RNase, which dictate their relative expression at the protein level.
2) Differences in ribosome binding sites (RBSs). Some RBSs bind the ribosome more strongly than others, resulting in increased rates of protein synthesis. The opposite is also true.
3) Protein factors involved in translation initiation. Various protein factors are involved in the initiation of translation that increase or decrease translation rates.
These are starting points for you.
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