Research is growing in the use of mass spectrometric sequencing of peptides obtained from enzymatic digestion to determine the identity of proteins. It has recently been shown that some peptides can re-arrange during the dissociation process, which can lead to incorrect peptide assignments. Ala-Lys-Ala and Ala-Ala-Lys are two peptides that are observed to rearrange to Lys-Ala-Ala in the mass spectrometer under collision induced dissociation conditions. The rearrangements are proposed to go through the same tripeptide ring structure.<br/>Calculations are being done to determine if there is a particular bond in the intermediate rings that is easier to break and that gives Lys-Ala-Ala as product. Involvement of proton transfer from the lysine side chain in the ring opening process would suggest that the presence of the lysine is a key factor in the rearrangements of the smaller polypeptides. More research is being done to determine if this is an effect that can occur with only lysine or other basic amino acids as well.<br/><br/>

Why do Ala, Ala, Lys tripeptides preferentially rearrange to the Lys-Ala-Ala sequence in the gas phase?

249th National Meeting (2015)

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