Abstract
The collision‐induced dissociation (CID) fragmentation reactions of a variety of deprotonated peptides containing proline have been studied in detail using MS^2^ and MS^3^ experiments, deuterium labelling and accurate mass measurements when necessary. The [MHCO~2~]^−^ (a~2~) ion derived from H‐Pro‐Xxx‐OH dipeptides shows an unusual fragmentation involving loss of C~2~H~4~; this fragmentation reaction is not observed for larger peptides. The primary fragmentation reactions of deprotonated tripeptides with an N‐terminal proline are formation of a~3~ and y~1~ ions. When proline is in the central position of tripeptides, a~3~, y~2~ and y~1~ ions are the primary fragmentation products of [MH]^−^, while when the proline is in the C‐terminal position, a~3~and y~1~ ions are the major primary products. In the latter case, the a~3~ ion fragments primarily to the ″b~2~ ion; further evidence is presented that the ″b~2~ ions have a deprotonated oxazolone structure. Larger deprotonated peptides having at least two amino acid residues N‐terminal to proline show a distinct preference for cleavage of the amide bond N‐terminal to proline to form, mainly, the appropriate y ion. This proline effect is compared and contrasted with the similar proline effect observed in the fragmentation of protonated peptides containing proline. Copyright © 2005 John Wiley & Sons, Ltd.