We explore the structure of a series of protic Ionic Liquids based on the choline cation and amino acid anions. In the series, the length and the branching of the amino acid alkyl chain varies. Ab initio molecular dynamics, X-ray diffraction measurements, and infrared spectra have been used to provide a reliable picture of the short-range structure and of the short-time dynamic process that characterize the fluids. We have put special emphasis on the peculiar and complicated network of hydrogen bonds that stem from the amphoteric nature of the anion moiety. The use of ab initio molecular dynamics allows us to calculate the "exact" charge density of the system and hence to obtain fairly accurate infrared spectra that, in turn, have been used to assign the experimental ones.