Sequence-specific fragmentation of deprotonated peptides containing H or alkyl side chains

The [M - H](-) ions of a variety of di- to pentapeptides containing H or al kyl side chains have been prepared by electrospray ionization and low-energ y collision-induced dissociation (CID) of the deprotonated species carried out in the interface region between the atmospheric pressure source and the quadrupole mass analyzer. Using the nomenclature applied to the fragmentat ion of protonated peptides, deprotonated dipeptides fragment to give a(2) i ons (CO2 loss) and y(1) ions, where the yl ion has two fewer hydrogens than the y(1)" ions formed from protonated peptides. Deprotonated tri- and tetr apeptides fragment to give primarily y(1), c(1), and "b(2) ions, where the "b(2) ion has two fewer hydrogens than the b(2) ion observed for protonated peptides. More minor yields of y(2), c(2), and a(2) ions also are observed . The a ion formed by loss of CO2 from the [M - H](-) ion shows loss of the N-terminal residue for tripeptides and sequential loss of two amino acid r esidues from the N-terminus for tetrapeptides. The formation of c(n) ions a nd the sequential loss of N-terminus residues from the [M - H - CO2](-) ion serves to sequence the peptide from the N-terminus, whereas the formation of y(n) ions serves to sequence the peptide from the C-terminus. It is conc luded that low-energy CID of deprotonated peptides provides as much (or mor e) sequence information as does CID of protonated peptides,at least for tho se peptides containing H or alkyl side chains. Mechanistic aspects of the f ragmentation reactions observed are discussed. (C) 2001 American Society fo r Mass Spectrometry.