Could anyone please advice is there any difference ordering antibodies which immunogen mapped to either C-, N-terminus, or mid-region? Which region is preferable?
That entirely depends on your immunogen and on your application. For the detection of full-length denatured protein, it should not make a difference. If you have proteolytic degradation, the different antibodies would detect different subpopulations of proteolytic fragments. If you want to detect cell surface antigen on intact cells, you would of course want to target an epitope that is accessible, often the N-terminus. If you go for functional assays, the main criterium is that your antibody does not interfere with function, and your epitope is not hidden by protein-protein interactions, folding or post-translational modification.
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