You might try immunohistochemistry techniques if you have antibody for the desired protein otherwise try digest the embedded protein with highly purified sequence grade trypsin or other endopeptidases overnight desalt and concentrate the resulting peptides then mass specterometeric analysis LC-Ms/MS then sequence analysis using protein data base.The problem with routine extraction the induced protein protein cross linking and protein Nucleic acids cross linking. Good luck 

Thanks. Actually, we already performed IHC on paraffin-embedded tissue sections with three different antibodies against single target and none of them didn't work well. But, one of these antibody worked well for the detection of the target XXX on tumor cell lines by western blotting. We already knew that the target XXX is expressed in that tumor cell line. Now, I was wondering whether my target is expressed on human tumor tissue. We don't have fresh (or) frozen tissues but, we have formalin fixed and paraffin-embedded tissues. Therefore, we wanted to check the target expression by extracting the protein from paraffin-embedded tissues and performing western blotting with same antibody.  

HI dear friend

I hope the following articles be useful for your study.