Positive and Negative Ion Electrospray Tandem Mass Spectrometry (ESI MS/MS) of Boc-Protected Peptides Containing Repeats of L-Ala-γ4Caa/γ4Caa-L-Ala: Differentiation of Some Positional Isomeric Peptides

High-resolution electrospray ionization (ESI) quadrupole time-of-flight and ion trap tandem mass spectrometry has been used to distinguish the positional isomers of a new class of N-blocked hybrid peptides containing repeats of the amino acids, L-Ala-γ4Caa (l)/γ4Caa(l)-L-Ala [Caa(l) = Carbo (lyxose) amino acid, derived from D-mannose]. Both MS/MS and MS3 of protonated isomeric peptides produce characteristic fragmentation involving the peptide backbone, Boc-group, and the side-chain. It is interesting to observe that the abundant yn+ ions are formed when the corresponding amide −NH does not participate in the helical structures in solution phase and relatively low abundance yn+ ions resulted when the amide −NH involves in the H-bonding. Thus, it was possible to identify the amide −NH hydrogens that participate in the helical structures through H-bonding in solution phase. Further, negative ion ESI MS/MS has also been found to be useful for differentiating these isomeric peptide acids.