Because of the importance of helices in the secondary structure of proteins, we have undertaken a study of their spectroscopy, fragmentation patterns and conformations in the gas phase. In this work, we describe the effects of substitution at the N-terminus of polyalanine helices capped with a lysine at the C-terminus, namely Ac-Phe-(Ala)(10)-Lys-H+, Phe-(Ala)(10)-Lys-H-divided by, and H+-Phe-(Ala)(10)-Lys-H+. Acetylation of the N-terminus has very little effect on the spectroscopy and structure, but protonation of the N-terminus changes the infrared spectrum in such a way that we believe it may also change the structure of the peptide. The ultraviolet spectroscopy and fragmentation, on the other hand, are insensitive to either acetylation or protonation.