title: Natural structural motifs that suppress peptide ion fragmentation after electron capture.
abstract: Series of doubly and triply protonated diarginated peptide molecules with different number of glutamic acid (E) and asparagine (N) residues were analyzed under ECD conditions. ECD spectra of doubly-protonated peptides show a strong dependence on the number of E and N residues. Both the backbone cleavages and hydrogen radical (H*) loss from the charge-reduced precursor ions ([M+2H](+*)) were suppressed as the number of E and N residues increases. A strong inhibition of the backbone cleavages and H* loss from [M+2H](+*) was found for peptides with 6E residues (or 4E + 2N residues). The results obtained using these model peptides were re-confirmed by analyzing N-arginated Fibrinopeptide-B (i.e., REGVNDNEEGFFSAR). In contrast to the N-arginated peptide, ECD of the doubly-protonated Fibrinopeptide-B and its analogues show extensive backbone cleavages leading to series of c- and z-ions ( approximately 80% sequence coverage). Based on these results, it is believed that peptide ions with all surplus protons sequestered in arginine-residues would show enhanced stability under ECD conditions as the number of acid-residue increases. The suppression of backbone cleavages and H* loss from [M+2H](+*) are presumably attributed to the low reactivity of the charge-reduced precursor ions. One of the possible hypothesis is that diarginated E-rich peptides may contain hydrogen bonds between carbonyl oxygen of E side chains and backbone amide hydrogen. These hydrogen bonds would provide extra stabilization for [M+2H](+*). This is the first demonstration of natural structural motifs in peptides that would inhibit the backbone fragmentation of the charge-reduced peptide ions under ECD conditions.
authors.affiliation: Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.
authors.forename: Wai Yi Kelly
authors.initials: WY
authors.lastname: Chan
authors.forename: Tak Wah Dominic
authors.initials: TW
authors.lastname: Chan
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D005345:Fibrinopeptide B / Q000737:chemistry; D007477:Ions / Q000737:chemistry*; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry*; D011522:Protons
chemical_list: D007477:Ions; D010455:Peptides; D011522:Protons; D005345:Fibrinopeptide B