I/L-discrimination by MS3 of dimethylated peptides

A novel mass spectrometric method for discriminating isoleucine and leucine by MS3. The dimethylation of peptide N-termini leads to intense a1 ions in CID and MS3 fragmentation of the isoleucine/leucine a1-ion leads to spectra with fragments that can discriminate between the two isomers. The method was applied to two antibodies in combination with a set of protease treatments using trypsin, thermolysin, chymotrypsin and pepsin to generate peptides exposing N-terminal I/L residues.