ALTERNATIVE LABELING METHOD FOR PEPTIDE LADDER SEQUENCING USING MATRIX-ASSISTED LASER DESORPTION-IONIZATION FOURIER-TRANSFORM MASS-SPECTROMETRY

Following previous work, alternative terminating labels for ladder seq uencing of peptides have been investigated to make ladder sequencing m ore compatible with analysis by matrix-assisted laser desorption-ioniz ation Fourier transform mass spectrometry (MALDI-FT-MS). Although pept ide analysis by MALDI-FT-MS using existing ladder-generating chemistry was possible, the spectra were complicated by the loss of the phenyl isocyanate (PIG) terminating label in the gas phase on the time scale of the FT-MS experiment. Therefore, in the work described here, a new reagent which would produce more stable peptide derivatives was invest igated. A variety of substituted phenyl isocyanate terminating labels, using angiotensin III antipeptide (Gly-Val-Tyr-Val-His-Pro-Val) as a model peptide, were assessed for this purpose. Of the compounds invest igated, N-carboxy phthalimide is the best alternative terminating labe l compatible with the ladder-generating chemistry. Upon reaction of th e peptide with N-carboethoxy phthalimide, the peptide N-terminus is in corporated into a cyclic structure. As a consequence, the correspondin g peptide derivatives are very stable and do not fragment during FT-MS analysis. Unambiguous identification of amino acids is demonstrated w ith an average mass error of +/- 0.003 Da. (C) 1997 Elsevier Science B .V.