The influence of a C-terminal basic residue on peptide fragmentation pathways

A typical ‘bottom up’ proteomic workflow uses tandem mass spectrometric data to infer product ion sequence and hence identity of the protein from which they derive. Such analysis is typically performed following proteolysis with the endoproteases trypsin or Lys-C; peptides produced therefore terminate in the basic residues arginine or lysine. Removal of these C-terminal basic residues using the exopeptidase, carboxypeptidase B, generates peptides whose analysis by tandem MS yields evidence of substantially different fragmentation properties. The decompositions of peptide ions both prior to and following treatment with carboxypeptidase B have been examined using collision-induced dissociation and electron transfer dissociation. Changes in properties following secondary enzyme treatment are attributed primarily to removal of a strongly basic site, with a consequent effect both on the propensity to retain charge and the stability of the fragment ions. The data suggest a complementary value in proteome analyses for MS/MS of tryptic/Lys-C peptides with and without subsequent carboxypeptidase B treatment.

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► Removal of a C-terminal basic residue generates peptides with substantially different fragmentation properties by MS/MS.
► Changes in fragmentation properties are attributed to a consequent effect upon the propensity to retain charge and stability of fragment ions.
► The observed dominant ion series from both CID and ETD is at least in part determined by the site of highest gas phase basicity.
► The data suggest a complementary value in proteome analyses for MS/MS of tryptic/Lys-C peptides with and without carboxypeptidase B treatment.