You need to have the molecular weight of your entities to decide which gel filtration medium works for you. Here is the pharmacia manual 

Gel filtration may not be the right approach if the masses of the homodimer and heterodimer are similar. Ion exchange chromatography or isoelectric focusing may be better approaches.

Hi Iramis, there is quite a difference between protein aggregation and functional hetero-homo dimers, tetramers, etc, when you do gel filtration.

Aggregated proteins will coat the top of your gel filtration column, because they are a denatured mess of proteins. 

Are you dealing with inclusion bodies?

Hello, first of all, you have to run separate GF with both proteins and compare it to the GF od the mixture.

This will give you an overview of the possible formation of homo or hetero-dimers.

If it is diffucult to analyze the GF profile, you can change the gel diameter (for example from S200 to S75 of sephacryl gels) to analyse the same sample.

If you have SEC-MALS in your lab, you can adress this question and you may have your answers.

BD.

I have done such analysis with with the chaperone Hsc70, that forms monomers in the presence, but dimers in the absence of ATP. Even with a high resolution gel like Superdex (GE), you do not get baseline resolution. Nevertheless, it is possible to assess ATP binding that way (Biochem. J. 318 (1996) 923-9, see fig. 4).