Several different fragmentation techniques produce fragment ions of peptides, such as ECD, ETD, CID, EThcD, higher-energy C-trap dissociation (HCD), UVPD, and infrared multi-photon dissociation (IRMPD).
As an example, MS/MS and ESI generate low-energy CID spectra, which are sequence-specific. The fragment ion spectra contain peaks of the fragment ions formed by the cleavage of the peptide bond and are used to determine amino acid sequences. A fragment must have at least one charge for it to be detected.
The fragment ions produced are identified according to where they are fragmented in the peptide. A, b, and c fragment ions have a charge on the N-terminal side, and x, y, and z fragment ions have a charge on the C-terminal side. Fragment ions a*, b*, and y* are ions that have lost ammonia (–17 Da), and fragment ions ao, bo, and co are ions that have lost water (–18 Da). The subscript next to the letter indicates the number of residues in the fragment ion. 1)
The following table summarizes the fragment ions used in the application.
Ions | Description |
|---|---|
a | A ion with charge on the N-terminal side |
b | B ion with charge on the N-terminal side |
c | C ion with charge on the N-terminal side |
x | X ion with charge on the C-terminal side |
y | Y ion with charge on the C-terminal side |
z | Z ion with charge on the C-terminal side |
a* | A ion that has lost ammonia (–17 Da) |
b* | B ion that has lost ammonia (–17 Da) |
y* | Y ion that has lost ammonia (–17 Da) |
ao | A ion that has lost water (–18 Da) |
bo | B ion that has lost water (–18 Da) |
co | C ion that has lost water (–18 Da) |