Abstract: Infrared photodissociation (IRPD) mass spectrometryspectroscopy is a powerful method for structure study of ions in the gas phase. In this study, a 70 T Fourier transform-ion cyclotron resonancemass spectrometer (FT-ICR-MS) was combined with a bench top optical parametric oscillator (OPO) IR laser system to study the IRPD spectra of complex ions of Rubidium with Histidine and Lysine, respectively. Different from other relative studies, the ions were generated by a matrix assisted laser desorption ionization (MALDI) source, instead of an electrospray ionization (ESI) source. IRPD mass spectrum of His+Rb+ complex ion showed dissociation of the parent ion. The wavenumber of IR laser was scanned from 2 700 to 3 700 cm-1 to obtain a set of IRPD mass spectra. Relative intensities of the photo fragments were calculated and constructed to be the IRPD spectra. The IRPD spectrum for His+Rb+ showed only one significant absorption at 3 500 cm-1, while that for Lys+Rb+ showed a strong peak at 2 935 cm-1, accompanied with a series of small absorption in the range of 3 0003 400 cm-1. Difference in IRPD spectra verified that this method could identify structural information of different amino acid containing metal cation in the fashion of spectral features effectively. To identify the structures present in the experiments, DFT calculations were further performed on the isomers of His+Rb+ at the B3LYP/6311++G(d,p)LANL2DZ level of theory. Optimizations and energetic calculations gave eight stable conformations which belong to two types of structure, nonzwitterionic and zwitterionic. The newly found zwitterionic isomer His+Rb01 showed the lowest electronic energy at 0 K. However, based on the comparison of obtained IRPD experimental spectra with the calculated spectra, the most possible conformation prevailed here was more likely to be His+Rb03, instead of the lowest energy isomer of His+Rb01. The experimental and theoretical results suggested that the His+Rb+ would have different structural preference under certain experimental condition rather than the most stable one calculated under 0 K in the gas phase. Based on the previous study, parent ions should be a mixer of multiple possible isomers, instead of a single conformation. Concentration of these isomers involved might be affected by both experimental temperatures and ionization conditions. The results also reflected that the MALDIIRPD method can be applied as an effective way not only to study structures of different kinds of complexes ions in the gas phase, but also to help to analyze the effects of different ionization conditions on their structures.