Unusual fragmentation of derivatized cysteine‐containing peptides

Rationale Modification of cysteines by aminoethylation results in side chains similar to those of lysine. Trypsin cleaves at this modified residue and this labeling method can facilitate the analysis of proteins, specifically antibodies. In this work, the ability to identify peptides containing aminoethylated cysteines is investigated through digestion, covalent labeling, and low‐energy ion fragmentation. Methods A prototype antibody was reduced, aminoethylated, and digested with either Lys‐N or Glu‐C. The resulting peptides were amidinated with SMTA and analyzed by PSD in a MALDI‐TOF/TOF mass spectrometer or by CID in an ESI ion trap/orbitrap mass spectrometer. Results PSD and CID fragmentation of peptides with an amidinated aminoethylated cysteine can produce an intense characteristic loss from this modified residue. A neutral loss of 118 Da or charged loss of 119 Da is observed when peptides have low charges. This fragment can form when the cysteine is located in any position in the peptide. The rationalization for this ion is that the amidino group can be initially neutral or protonated and initiates fragmentation. Conclusions The combination of a dual‐labeling technique and low‐energy fragmentation produces an abundant diagnostic ion for the analysis of cysteine‐containing peptides. These 118 and 119 Da losses are observed when protons are sequestered.