title: Peptide rearrangement during quadrupole ion trap fragmentation: added complexity to MS/MS spectra.
abstract: The emergence of proteomics has placed great interest in the understanding of the mechanisms of MS/MS fragmentation of peptides under low-energy collision-induced dissociation. In this work, we describe the presence of anomalous fragments, which correspond to neutral loss elimination of internal amino acids from ions of the b series in quadrupole ion trap MS/MS spectra from naturally occurring peptides. Internal amino acid elimination occurred preferentially with aliphatic amino acids. The phenomenon was more apparent when doubly charged precursors were fragmented and was inhibited when peptides were N-acetylated at the N-terminus. Fragmentation of isomeric peptides where some internal amino acids were relocated in N-terminal position produced MSn spectra indistinguishable from those of the original peptides, indicating that some b ions underwent a structural rearrangement process. Formation of anomalous fragments required a minimum activation time. Our data are consistent with a nucleophile attack of the N-terminal nitrogen over the electrophilic carbonyl carbon at one peptide bond, forming a cyclic b ion intermediate that, by reopening at preferential sites, exposes internal amino acids to the C-terminal side.
authors.affiliation: Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain.
authors.forename: Jesús
authors.initials: J
authors.lastname: Yagüe
authors.forename: Alberto
authors.initials: A
authors.lastname: Paradela
authors.forename: Manuel
authors.initials: M
authors.lastname: Ramos
authors.forename: Samuel
authors.initials: S
authors.lastname: Ogueta
authors.forename: Anabel
authors.initials: A
authors.lastname: Marina
authors.forename: Fernando
authors.initials: F
authors.lastname: Barahona
authors.forename: José A
authors.initials: JA
authors.lastname: López de Castro
authors.forename: Jesús
authors.initials: J
authors.lastname: Vázquez
mesh_terms: D003001:Cloning, Molecular; D003500:Cyclization; D007477:Ions; D013058:Mass Spectrometry / Q000379:methods*; D010446:Peptide Fragments / Q000737:chemistry*; D010455:Peptides / Q000032:analysis*
chemical_list: D007477:Ions; D010446:Peptide Fragments; D010455:Peptides