C-terminal peptide sequencing using acetylated peptides with MSn in a quadrupole ion trap.

MS/MS has been used to sequence peptides and small proteins for a number of years. This method allows one to isolate the peptide of interest, which makes it possible to analyze impure samples and unseparated mixtures, such as protein digests. Collision-induced dissociation (CID) of the selected peptide ion generates the product ions that provide sequence information. However, often the MS/MS spectrum does not provide adequate information for complete sequence determination. The quadrupole ion trap has the capability to do multiple stages of mass spectrometry, MSn, which can increase the information available to determine the peptide sequence. A regular and predictable dissociation pattern for peptides further simplifies this analysis. By forming predominantly one type of ion, ambiguity is removed as to whether the ion is N- or C-terminal. This pattern can also be advantageous in that ion intensity remains concentrated for the next stage of MS/MS. In this work, a method to take advantage of the MSn capabilities of the quadrupole ion trap by controlling the dissociation pathways is explored. Dissociation is altered by acetylating the N-terminus of the peptide. MSn of a variety of acetylated peptides is used to determine the effects of the identity of the C-terminal residue and the length of the peptide on the dissociation pathways observed.