We demonstrate how the recently developed methodology for the analysis of calculated vibrational spectra in terms of localized modes [J. Chem. Phys. 2009, 130, 084106] can be applied to investigate the influence of the secondary structure on infrared and Raman spectra of polypeptides. As a model system, a polypeptide consisting of 20 (S)-alanine residues in the conformation of an alpha-helix and of a 3(10)-helix is considered. Several features of the calculated spectra are analyzed in detail. First, we show for the amide II band how localized modes facilitate the decomposition of the total Raman intensities into contributions of certain groups of atoms, and how such an analysis can be used to identify the origin of differences in Raman intensity of the two helices. Second, we demonstrate how the shift of the position of the amide I band between the two considered structures can be rationalized and how the observed intensity distribution within the amide I band can be explained by considering the coupling constants between the localized modes. Third, we show how localized modes can be employed to analyze the positions of the bands found in the extended amide III region and how such an analysis makes it possible to gain a better understanding of how structural changes influence the coupling between the amide III and the C(alpha)-H bending modes in this region.