We try in the lab a method for digestion of whole IgG subclass with pepsin to separated Fc and Fab fragments. But we have problems with desalting of fragments. this step it is very important to to deglycosilate the sample. And also we lost the sample during separation of fragments. Someone can tell me an efficient method in terms of quantities recovered for separating and subsequently desalting?
Did you try the standard Protein A or G to remove Fc than size exclusion?
No, in this case we didn't use this method because in the digestion with pepsin, we obtained peptides small than 10 kDa. and we don't know if these fragments will bind to protein A or G. Also we need develop the experiments in semi preparative conditions because of the small amount of protein used. This step will be useful?
Have you considered specific adsorbent that would bind to the light chains which have the antigen binding sites. So Fabsorbent F1P (www.prometic.com) may be worth trying and this can be scaled up provided it does what you need
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