I want to investigate coronary atherosclerosis of the heart using 2D gel electrophoresis with formalin fixed specimen. My fear is that the cross linking of proteins by formalin might mask the charges on the proteins making the first dimension separation impossible. Can somebody explain to me how to extract the proteins and be able to retrieve the charges?
I have never done this before and have only performed a 2D gel as an undergrad in a biochemistry lab but I found a couple of papers discussing the mechanisms of antigen retrieval.
The first suggests that antigen retrieval results primarily in denatured proteins which is good news for 1 dimension of your gel.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3201144/#!po=63.0000
The abstract for the second (I don't have access beyond the paywall) suggests that buffer selection according to the pI of you protein of interest is important. This is bad for a fishing expedition style experiment I suppose.
http://www.ncbi.nlm.nih.gov/pubmed/19768463
Either way my little experience with 2D gel and antigen retrieval suggests that in theory your aims are possible but in practice it is highly unlikely that you will be able to achieve your goal of 2D protein resolution from formalin fixed staring conditions. Good luck in your experiments.
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