Peptide sequencing by tandem mass spectrometry. (A) Within the mass spectrometer, peptides can be fragmented by bombardment with inert gaseous ions to generate a family of product ions in which individual amino acids have been removed from one end. In this example, the carboxyl fragment of the cleaved peptide bond is ionized. (B) The product ions are detected in the second mass analyzer. The mass differences between the peaks indicate the sequence of amino acids in the precursor ion.
[Data from H. Steen and M. Mann. Nat. Rev. Mol. Cell Biol. 5:699–