TO b OR NOT TO b: THE ONGOING SAGA OF PEPTIDE b IONS

Modern Soft ionization techniques readily produce protonated or multiply, protonated peptides. Collision-induced dissociation (CID) of these protonated species is often used as a method to obtain sequence information. In many cases fragmentation occurs at amide bonds. When the charge resides oil the C-terminal fragment so-called y ions are produced which are known to be protonated amino acids or truncated peptides. When the charge resides on the N-terminal fragment so-called b ions are produced. Often the sequence of y and b ions are essential for peptide sequencing. The b ions have many possible structures, a knowledge of which is useful in this sequencing. The structures of b ions are reviewed in the following with particular emphasis oil the variation of structure with the number of amino acid residues in the b ion and the effect of peptide side chain oil b ion structure. The recent discovery of full cyclization of larger b ions results in challenges ill peptide sequencing. This aspect is discussed ill detail. (C) 2009 Wiley Periodicals, Inc., Mass Spec Rev 28:640-654, 2009