Comparison of charged derivatives for high energy collision-induced dissociation tandem mass spectrometry

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Fixed-charge derivatives have been used to direct the fragmentation pattern of high energy collision-induced dissociation tandem mass spectra for several years. It has been noted that a fixed-charge placed at a terminus of a peptide will simplify the pattern of fragment ions that are produced in collision-induced dissociation. Trimethylammoniumacetyl, dimethyloctylammoniumacetyl, and triphenylphosphoniumethyl derivatives have been cited in the literature for this purpose and many other structures are possible. This work compares the cited derivatives as well as some new structures. The criteria used include the ease of synthesis and purification of the derivatized peptide and the effects of the derivative on the peptide sequence fragment ion yield and ionization efficiency. The trimethylammoniumacetyl derivative is concluded to be the most practical for general use, whereas the dimethyloctylammoniumacetyl derivative is found to be desirable for use with hydrophilic peptides.