Undesirable Protein Modifications
Many things can happen to proteins as time goes on. Most of these are favored by harsh conditions such as pH and irradiation, but even at neutral pH and in the cold things tend to happen to proteins as time progresses. The following is a short summary of chemistry which happens with time to proteins:
Aspartyl- and Asparaginyl- modification. These modifications lead to deamidated proteins (difficult to detect even by mass spectrometry), proteins which have D-amino acids in them and proteins which have the main peptide chain running through the sidechain of the Asx residue. Cleavage at the modified Asx site is also common. The effects of these modifications can be: altered enzymatic and immunological propreties, protein degradation, charge variability as seen on isoelectric focussing and unusual peptide bonds detected when determining the atomic structure of the molecule. They can be somewhat avoided by not elevating the pH and temperature and maintaining a proteins secondary structure.
Carbamylation of sidechains: Use of old urea or urea which has not been treated with mixed bed resin leads to the formation of cyanates in the solution which at various pH's can modify your protein on various amino acids. Use only fresh urea solutions or deionize before use and do not heat urea solutions. Remove your protein from urea as soon as possible.