Formation of c- and z-ions due to preferential cleavage at the NC bond of Xxx-Asp/Asn residues in negative-ion CID of peptides

•We concentrate on the formation of c- and z-ions in ESI-CID experiments of peptides.•The c- and z-ions are formed in exclusively negative-ion CID experiments.•The c- and z-ions specifically originate from Xxx-Asp and Xxx-Asn residues.

In collision-induced dissociation (CID) experiments of peptides, the formation of c- and z-ions originating from NCα bond cleavage of the peptide backbone is unusual, whereas b- and y-ions are often observed in positive-ion CID spectra. Here we report that characteristic product c- and z-ions can be observed in negative-ion CID spectra of peptides with Asp and Asn residues. The negative c- and z-ions are mainly generated at the NCα bond of Xxx-Asp and Xxx-Asn residues that are classified as the flexible amino acids in protein chemistry. In the absence of any acidic amino acid residues, negative-ion CID spectra show dominant c-ion peaks originating from cleavage at the NCα bond lying in between the 3rd and 4th residues from the C-terminus of analyte peptides. It is proposed that the NCα bond cleavage leading to the formation of c- and/or z-ions is caused by the negative charge located on the amide nitrogen, which generated with an intra-molecular hydrogen abstraction from the backbone amide regions due to negative-charged acidic functional groups.

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