How are the so-called b ions and y ions defined in mass spectrometry of biomolecules?

b ions and y ions are two common types of fragment ions observed in the tandem mass spectrometry analysis of proteins/peptides, produced when the peptide chain undergoes collision-induced dissociation (CID) or other fragmentation methods.

b ions are formed from the amino terminus (N-terminus) of the peptide chain. When the backbone of the peptide chain (i.e., the peptide bond) breaks, and the charged part includes the N-terminus of the peptide, the resulting ion is called a b ion. The b ion series helps determine the sequence of the peptide chain as they reflect the amino acid sequence starting from the N-terminus.

y ions are formed from the carboxyl terminus (C-terminus) of the peptide chain. When a peptide bond breaks and the charged part includes the C-terminus, the resulting ion is called a y ion. The y ion series helps determine the sequence of the peptide chain from the other end of the peptide.

In actual mass spectrometry analysis, both b ion and y ion series usually appear simultaneously, providing complementary information about the peptide chain sequence. By comparing the mass differences between b and y series ions, the amino acid sequence of the peptide chain can be deduced.

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