When making antibodies that detect specific proteins, three different types of so-called antigens can be used: 
  1. Short synthetic peptides, 7-30 amino acids long
  2. Overexpressed proteins, full-length or partial
  3. Native proteins, purified from endogenous tissue/organism

Depending on which type of antigen is used, an antibody may or may not recognize various isoforms of the protein under investigation. Especially in cases where the difference between the protein isoforms is just a few amino acids in a linear protein sequence, using the same antibody to detect two different isoforms, even with antibodies made to a short synthetic peptide, will not work. There are exceptions, which we have seen over the last 30 years, and they have to be confirmed by using specific knockout mutants. 

Therefore, before using antibodies to distinguish between isoforms, one has to conduct sequence analysis or ask the antibody supplier for help, if the antigen information is not provided on the product information sheet. 

Check Agrisera Antibody Production Guide for further information.
  Antigen for antibody production