Suppression of peptide ion dissociation under electron capture: role of backbone amide hydrogen.
BACKGROUND
The electron capture dissociation (ECD) of proteins/peptides is affected by the nature and sequence of amino acid residues. Electron capture/transfer with no dissociation is an intriguing phenomenon that has occasionally been observed. We have previously identified that diarginated peptides enriched with glutamic acid residues were found to show suppression of backbone fragmentation. In this paper, we report the effect of geometrical parameters of a peptide, including chain length, conformation and amide hydrogen, on the suppression of ECD fragmentation using synthetic model peptides.


METHODS
Glycine containing model polypeptides were used to probe the mechanism. Molecular-mechanics was used to obtain the conformation of the precursor ions. The ECD experiments were performed on a Bruker APEX III 4.7 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer.


RESULTS
Significant decreases in the intensities of the fragment ions were observed for the 23-mer polypeptide with only one E residue. This implied that the E:R ratio was no longer the sole determining factor for the occurrence of suppression effects. Results of conformational searches showed that there was a hydrogen-bonding 'ladder' formed in the 23-mer polypeptide, which was not found in the 15-mer peptide. Substituting the normal amino acid residues by the corresponding N-methylated amino acid residues in the model peptide, the suppression effect disappeared.


CONCLUSIONS
Our results indicate that survival of the intact reduced peptide ion after electron capture depends also on the length of the peptide. The amide hydrogen was critical in forming the resonance structure that suppressed the ECD fragmentation.
Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR.
P-S Joyce
PS
Wong
Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR.|Shandong Academy of Sciences, Jinan, Shandong, P.R. China.
Xiangfeng
X
Chen
Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR.|Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Washington, USA.
Liulin
L
Deng
Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR.
Ze
Z
Wang
Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR.
Wan
W
Li
Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR.
Y L Elaine
YL
Wong
Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR.
T-W Dominic
TW
Chan
D000577:Amides / Q000737:chemistry*; D004583:Electrons; D006859:Hydrogen / Q000737:chemistry*; D007477:Ions / Q000032:analysis / Q000737:chemistry*; D013058:Mass Spectrometry; D010455:Peptides / Q000032:analysis / Q000737:chemistry*
D000577:Amides; D007477:Ions; D010455:Peptides; D006859:Hydrogen