Are you trying to 'accurately' determine the site-specific deamidation in a protein and quantify the level in a degraded (or stressed) protein? Then mass spec experiments are likely to provide an answer.
Kindly go through the attached publication from Analyst 2010; there is a discussion on 'deamidation'. For further details, the research articles cited therein can be useful. Deamidation is an important topic, especially in the case of biopharmaceuticals.
It will be a good idea if the original question can be rephrased. What are you trying to compare? Two methods or technologies? 3-D structure is not a method.
I will want to compare deamidation prediction of a protein using protein sequence and x-ray structure compared with Mass spec deamidation study - Asn and Gln residues, Asn residue is studied throughly and it is not random but Gln is very slow process when compared to Asn deamidation.
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