Secondary fragmentation of linear peptides in electron capture dissociation

Abstract

Inspection of the electron capture dissociation (ECD) spectra of doubly-protonated peptides, Leu 4-Sar-Leu 3-Lys-OH, Leu 4-Ala-Leu 3-Lys-OH, Gly 4-Sar-Gly 3-Lys-NH 2 and Gly 3-Pro-Sar-Gly 3-Lys-NH 2, reveals extensive secondary fragmentation. In addition to w ions, entire, and in some cases multiple, cleavages of amino acid side chains from backbone fragments are observed. Extensive water loss from backbone fragments is observed for the glycine-rich peptides. For Leu 4-Ala-Leu 3-Lys, the preferred fragmentation channel is cleavage of the amide bond to produce b 7 and b 8 ions. ECD of Gly 3-Pro-Sar-Gly 3-Lys-NH 2 results in amine bond (c/z) cleavage in the proline residue accompanied by CC (or secondary NC) cleavage in the proline side chain. That fragmentation channel has not been observed previously. The peptides were also subjected to “hot” electron capture dissociation (HECD) and the resulting spectra differed markedly from those obtained under standard ECD conditions. In contrast to HECD, secondary fragmentation observed under standard ECD conditions cannot be attributed to excess energy arising from the kinetic energy of the electrons prior to capture. The results suggest that the fragmentation channels available following electron capture depend somewhat on the individual peptide structure and have mechanistic implications.