IM analysis of product ions clearly shows outliers from the doubly charged ion trendline in the mobility-mass plots. This deviation is independent of precursor ion charge state as well cysteine modification and is a result of the secondary structure of the peptide. Mapping product ion identity and onset of deviation allows for identification of the start of the helix/extended coil structure. Ion type, i.e. charge retention site, influences conformational preference of product ion. Charge retention at the c-terminus helps stabilize the macro-dipole of the helix/extended coil. Other peptides with similar secondary structure demonstrate similar phenomena.
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