Peptide Derivatization Prior to Fragmentation

Aminopeptidase N. This enzyme works in a manner similar to carboxypeptidase Y, but cleaves amino acids from the N-terminus. It can be used in the same way as carboxypeptidase Y. 

Peptide Derivatization. The sequence information obtained from a peptide can be significantly improved by chemical modification. These approaches are discussed in more detail in the following section. 

The straightforward approach to de novo sequencing sometimes fails, for example, due to the low quality tandem mass spectra. Often it is not caused by the equipment settings or operator s capabilities, but just by unfavorable fragmentation pattern of a given peptide. Among possible approaches to solve such issues is chemical derivatization of peptides. 

There are two basic aims of chemical derivatization simplification of the fragmentation pattern by either promoting or demoting formation of a chosen ion series, and stable-isotopic labelling for simple assignment of ions to proper ion series (Fig. 6.21). Both methods may provide good results and their advantages and limitations will be discussed. 

It should be noted that the majority of the derivatization techniques modify the peptide s N-terminus. The reason is that the N-terminal amine group is easier to modify than the C-terminal carboxyl group. Also, due to differences in pKa value in the e-amino group of lysine, there are possible reaction that modify the N-terminus only, while the lysine side chains remain intact. Modifications of carboxyl groups 

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