This is a very tricky question..In my experience, sometimes, Ab raised for WB simply does not work in IHC and vice-versa...another thing you can try is SDS treatments, 1% in PBS or in tris-HCL pH 7.4. 30' in agitation...but it could disrupt the morphology.

Also you ca try to play with condition for antigen retrieval. Temperature of citrate buffer, time in proteinase K...etc...

good luck!

Thanks Celsi

I tried all the possible variations, temperature, time etc using proteinase K, Citrate buffer , HCL etc... , But none worked. 

uhm...then give it a last shot with SDS buffer...and if does not work..unfortunatly you have to change your Ab....

Unfortunately I had this kind of feeling that most probably it will not work if you have tried antigen retrievals, you should order new antibody as soon as possible. I have wasted time on this already trying different things.. My advice save your time...) Better Order a new antibody..

Best of luck-.

Some general points: Antibodies detect 3D structures of a part of a protein (epitops). 3D structures of proteins differ with their state of denaturation. So a protein structure might "look" similar in a section compared to a denaturating SDS-Page+Western Blotting. In that case your antibody might be working for both assay. But it might also "look" very different, then an antibody created for a denatured protein structure won't work for a section. You might only try to do the same denaturation steps on the sections - that's probably what Fulvio Celsi's suggestions are aiming at. But PFA and retrieval already changed your protein in a different way so the probability is quite bad for an antibody sold for WB only...

If possible for your question: Use one antibody designed and sold for WB and another designed and sold for IHC as Hasan Mohammad suggested.

I think, the chance is very high, that if an antibody selling company has found out, that the product is also usable on FFPET, they would declare it in the datasheet. Otherwise it would be a disadvantage for the product on the market. And in my opinion after 20 years of antigen retrieval history most companies are very likely to proof their products for this application. 

This is a very conceptual question and has a very conceptual answer:

In WB the proteins are lysed, e.g. linearized to their primary polypeptide chain, so you search for epitopes, which are in their primary structure.

In tissues there is a conformation of the protein, which means that certain epitopes, available in the primary structure, are masked.

Basicly the WB dedicated AB cannot access them.

Certain retrieval conditions could unmask the epitopes but it is not a secure thing. They also can destroy them.

If an epitope is available both  in lysed protein (WB) and in conformed protein (tissue), then the chance that a WB antibody can bind to it is quite high

Regards and good luck!

Ivan

Here is yet another thing to look at. Does the antigen have a lysine residue ? This is usually highly immunoreactive, meaning the antibodies will recognize this sequence, but unfortunately, the PAF will react with the lysine and your epitope is gone. In principle a fixative that does not attack primary amines might work, but those are often not very good.