A photodissociation spectrometer, containing a spray ionization source and a temperature-variable multipole ion trap, has been constructed to examine the structure and reactivity of gas phase biological molecular ions at various temperatures. Ultraviolet (UV) and infrared (IR) photodissociation spectra of protonated alanyltryptophan (Ala-TrpH(+)) and tryptophanylglycine (Trp-GlyH(+)) have been measured. In UV spectra, the S-1-S-0 band origin of Ala-TrpH(+) exhibits a significant red shift with respect to those of protonated tryptophan (TrpH(+)) and Trp-GlyH(+). This red shift is ascribed to the stabilization of the excited state due to the strong interaction between the NH3+ group and indole ring. We also discuss the temperature effect on the structure and reactivity for these peptides. In addition to the UV photodissociation spectra of the dipeptides, IR spectra of the complex of Ala-TrpH(+) with methanol are measured. IR photodissociation spectra of solvated ions show that Ala-TrpH(+)-methanol has the closed structure, which is consistent with the large spectral shift in UV spectrum of bare dipeptide.