Supplementary Information for

Natural Structural Motifs that Suppress Peptide Ion Fragmentation after Electron Capture

Wai Yi Kelly Chan and T. –W. Dominic Chan*

Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong

Manuscript submitted to the Journal of the American Society for Mass Spectrometry, December 2009.

* Address reprint requests to Dr. T.-W. Dominic Chan, Department of Chemistry,

The Chinese University of Hong Kong, Shatin. N.T., Hong Kong SAR.

Tel.: (852)2609-6260; Fax: (852)2603-5057; E-mail:


Table S1. Distribution of H-bond formed at backbone amide linkages of the lowest energy structures of RGEGEGEGEGEGEGR (contributed more than 1%) in zwitterionic form (salt bridge formed between N- and C-terminus) obtaining from conformational search.

Relative energy (kJmol-1) / Relative abundance (%) / H-bond / Distribution of H-bond formed at backbone amide linkage
R G E G E G E G E G E G E G R
1a / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12 / 13 / 14
-2737.52 / 73.3 / C=O—H (RSC or N-ter)b / -d / - / - / - / +d / + / - / + / - / - / - / + / + / +
N-H—O (ESC)c / - / - / - / - / + / + / - / - / + / + / - / - / - / -
-2732.66 / 10.3 / C=O—H (RSC or N-ter) / - / - / - / - / + / + / - / + / - / - / - / + / - / +
N-H—O (ESC) / - / - / - / - / + / + / - / - / - / - / - / - / - / -
-2731.12 / 5.5 / C=O—H (RSC or N-ter) / - / - / - / - / + / + / - / + / - / - / - / + / - / +
N-H—O (ESC) / - / - / - / - / - / + / - / - / - / - / + / - / - / -
-2729.26 / 2.6 / C=O—H (RSC or N-ter) / - / - / - / - / + / + / - / + / - / - / - / + / - / +
N-H—O (ESC) / - / + / - / - / + / + / - / - / - / - / + / - / - / -
-2729.24 / 2.6 / C=O—H (RSC or N-ter) / - / - / - / - / + / + / + / + / - / - / - / - / - / -
N-H—O (ESC) / - / - / - / - / - / + / + / - / - / - / - / - / - / -
-2729.05 / 2.4 / C=O—H (RSC or N-ter) / - / - / - / - / + / + / - / + / - / - / - / + / - / +
N-H—O (ESC) / - / - / - / - / + / + / - / - / - / - / + / - / - / -
-2728.14 / 1.7 / C=O—H (RSC or N-ter) / - / - / - / - / + / + / - / + / - / - / - / + / - / +
N-H—O (ESC) / - / - / - / - / + / + / - / - / - / - / + / + / - / -
-2728.03 / 1.6 / C=O—H (RSC or N-ter) / - / - / - / - / + / + / + / + / - / - / - / - / - / -
N-H—O (ESC) / - / + / - / + / - / + / + / - / - / - / - / - / - / -
Overall Distribution (%) / C=O—H (RSC or N-ter) / 0.0 / 0.0 / 0.0 / 0.0 / 100.0 / 100.0 / 4.2 / 100.0 / 0.0 / 0.0 / 0.0 / 95.8 / 73.3 / 95.8
N-H—O (ESC) / 0.0 / 4.2 / 0.0 / 1.6 / 90.3 / 100.0 / 4.2 / 0.0 / 73.3 / 73.3 / 12.2 / 1.7 / 0.0 / 0

a Numbers in italic represent the position of backbone amide linkages counting from N- to C- terminus.

b H-bond formed between backbone carbonyl oxygen and hydrogen of protonated R side chain or protonated N-terminus.

c H-bond formed between backbone amide hydrogen and carbonyl oxygen of E side chain.

d ‘+’ indicates the presence of H-bond and ‘-’ does not.