title: Unusual fragmentation of β-linked peptides by ExD tandem mass spectrometry.
abstract: Ion-electron reaction based fragmentation methods (ExD) in tandem mass spectrometry (MS), such as electron capture dissociation (ECD) and electron transfer dissociation (ETD) represent a powerful tool for biological analysis. ExD methods have been used to differentiate the presence of the isoaspartate (isoAsp) from the aspartate (Asp) in peptides and proteins. IsoAsp is a β(3)-type amino acid that has an additional methylene group in the backbone, forming a C(α)-C(β) bond within the polypeptide chain. Cleavage of this bond provides specific fragments that allow differentiation of the isomers. The presence of a C(α)-C(β) bond within the backbone is unique to β-amino acids, suggesting a similar application of ExD toward the analysis of peptides containing other β-type amino acids. In the current study, ECD and ETD analysis of several β-amino acid containing peptides was performed. It was found that N-C(β) and C(α)-C(β) bond cleavages were rare, providing few c and z• type fragments, which was attributed to the instability of the C(β) radical. Instead, the electron capture resulted primarily in the formation of a• and y fragments, representing an alternative fragmentation pathway, likely initiated by the electron capture at a backbone amide nitrogen protonation site within the β amino acid residues.
authors.affiliation: Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA.
authors.forename: Nadezda P
authors.initials: NP
authors.lastname: Sargaeva
authors.forename: Cheng
authors.initials: C
authors.lastname: Lin
authors.forename: Peter B
authors.initials: PB
authors.lastname: O'Connor
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D026581:Isoaspartic Acid / Q000737:chemistry*; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry*; D013373:Substance P; D053719:Tandem Mass Spectrometry / Q000379:methods*; D050337:Trimethyl Ammonium Compounds
chemical_list: D000596:Amino Acids; D026581:Isoaspartic Acid; D010446:Peptide Fragments; D010455:Peptides; D050337:Trimethyl Ammonium Compounds; C522723:cholamine; D013373:Substance P