mass is more convenient.

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.