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-De Novo Peptide Sequencing Tutorial


Peptide Fragmentation Nomenclature

b, y and a ions



click to see the full annotation



The most common peptide fragments observed in low energy collisions are a, b and y ions, as described in the figure above.  The b ions appear to extend from the amino terminus, sometimes called the N-terminus, and y ions appear to extend from the carboxyl terminus, or C-terminus.  While readily observed and diagnostic for b ions, a ions occur at a lower frequency and abundance in relation to b ions. The a ions are often used as a diagnostic for b ions, such that a-b pairs are often observed in fragment spectra.  The a-b pairs are separated by 28u, the mass for the carbonyl, C=O.  

The fragment types listed above are the most common fragments observed with ion trap, triple quadrupole, and q-TOF mass spectrometers.  Follow the link to see the fully annotated fragmentation nomenclature as proposed by Biemann.  An important note: an earlier nomenclature was proposed by Roepstorff and Fohlman and later modified by Biemann.  The Biemann adaptation has been widely accepted.  

Proceed onto the next page to learn a little more about b and y ions.




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  1. Roepstorff P, Fohlman J. Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed Mass Spectrom. 1984 Nov;11(11):601.
  2. K. Biemann In: J.A. McCloskey, Editor, Methods in Enzymology 193, Academic, San Diego (1990), pp. 886�887.
  3. Biemann K. Contributions of mass spectrometry to peptide and protein structure. Biomed Environ Mass Spectrom. 1988 Oct;16(1-12):99-111.





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