All proteomics data analysis software have deamidation as variable PTM (+1Da). I normally rely on them and then, if needed, I manually double check the MS/MS spectra.

we can predict based on known crystal structure of protein

Primary sequence appears to play a role, with the residue c-terminal to the deamidating residue being important.  There are several interesting papers that discuss the propensity for asparagine side chains to deamidate - see Tyler-Cross and Schirch 1991, Xie and Schowen 1999, etc.  Of course tertiary/quaternary structure can also play a role as the residue has to be solvent-exposed to undergo the complete deamidation reaction including hydrolysis of the succinimide intermediate.

Thank you David. I agreed that protein sequence and 3D structure are playing major role in predicting deamidation asn and gln residues.

Dear Govinda, you may find a paper we authored last year interesting with regard to this topic

http://www.sciencedirect.com/science/article/pii/S1359511313002948

Dave

Dear Govinda, as David has pointed out Asn groups followed by a Gly are pariticularly prone to deamidate. But in addition this pair may also form so called isoaspartyl linkages. These will not show up by SDS gel electrophoresis but will reveal themselves by isoelectric focusing.  The deamidation may in fact lead to two isoforms  - either with an alfa-peptide linkage or a beta-peptide linkage. This is detailed in a paper we published in "Biochemisty" in 1989 ( DOI 10.1021/bi00447a055)

Dear Sture Forsen, Thank you. I read through your paper and learned about ASN residues deamidation and do you know about Gln deamidation in proteins?

Dear Govinda, further to Dr Forsen's excellent point you may be interested in learning about the PIMT system and its uses in isoaspartate detection.  There are many references describing it from Professor Aswad's group in California and the PIMT is available as a kit from PROMEGA.  Hope this is of interest.  Dave