Abstract
The low‐energy CID mass spectra of the [M − H]^−^ ions of a variety of dipeptides containing glutamic acid have been obtained using cone‐voltage collisional activation. Dipeptides with the γ‐linkage, H‐Glu(Xxx‐OH)‐OH, are readily distinguished from those with the α‐linkage, H‐Glu‐Xxx‐OH, by the much more prominent elimination of H‐Xxx‐OH from the [M − H]^−^ ions of the former isomers, resulting in formation of m/z 128, presumably deprotonated pyroglutamic acid. Dipeptides with the reverse linkage, H‐Xxx‐Glu‐OH, show distinctive fragmentation reactions of the [M − H]^−^ ions including enhanced elimination of CO~2~ and formation of deprotonated glutamic acid. Exchange of the labile hydrogens for deuterium has shown that there is considerable interchange of C‐bonded hydrogens with labile (N‐ and O‐bonded) hydrogens prior to most fragmentation reactions. All dipeptides show loss of H~2~O from [M − H]^−^. MS^3^ studies show that the [M − H − H~2~O]^−^ ion derived from H‐Glu‐Gly‐OH has the structure of deprotonated pyroglutamylglycine while the [M − H − H~2~O]^−^ ions derived from H‐Glu(Gly‐OH)‐OH and H‐Gly‐Glu‐OH show a different fragmentation behaviour indicating distinct structures for the fragment ions. Copyright © 2004 John Wiley & Sons, Ltd.