Electron capture by doubly charged peptide cations leads to neutral losses in addition to N–Cα bond cleavages that give c and z fragments. In this work we discuss the influence of amino acid sequence on hydrogen versus ammonia loss and the propensity for subsequent partial side-chain cleavage after ammonia loss to give w fragment ions. Experiments were done on two series of doubly protonated dipeptides, [XK+2H]2+ and [XR+2H]2+, where X is one of the twenty common amino acid residues, excluding aspartic acid (D), and K and R are lysine and arginine, respectively. While it was previously established that NH3 is lost exclusively from the N-terminal ammonium group and not from side-chain ammonium groups, we find here that ammonia can be lost from guanidinium radicals as well. The ratio between H loss and NH3 loss reveals some information on internal ionic hydrogen bonds and peptide conformation since proton sharing between the N-terminal ammonium group and a basic side chain decreases the probability for NH3 loss due to a lower recombination energy and as a result reduced capture probability. The abundance of w ions was found to correlate with the reaction energy for their formation; highest yield was found for CK and lowest for AK and HK. The survival rate of charge-reduced species was higher for XR than for XK, which is likely linked to the formation of long-lived Cα radicals in the latter case. The probability for N–Cα bond cleavage is smaller on average for XR than for XK which indicates that hydrogen transfer from the ε-ammonium radical to the amide group triggers some of the cleavages, or is a result of the different distances between the amide group and the charges in XR and XK. Finally, our data support the previous concept that charge partitioning between c and z fragments can be explained by competition between the two fragments for the proton.
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