In recent years, spectroscopic investigations of cold, biomolecular ions have started to provide new, detailed information about the structures of biomolecules in the gas phase. The present work comprises three major parts that describe the development of instrumentation for the preparation and manipulation of cold ions as well as its application to the spectroscopic study of a protonated amino acid dimer. The first part describes the development of a tandem quadrupole mass spectrometer with a 22-pole ion trap, designed for the spectroscopic investigation of cold, biomolecular ions. Several new features improve the performance of the instrument in comparison with the previous generation of the setup. The instrument is characterized in detail, and a vibrational temperature of the ions of about 10 K is demonstrated. In the second part, a novel multipole ion trap time-of-flight mass spectrometer is described, a hybrid instrument that uses a planar multipole trap as the extraction region of a reflectron. Its development is originally motivated in the context of the first part of the present work, as a tool to obtain a time-of-flight spectrum of the ions stored in the 22-pole. However, it may offer advantages for a range of different applications. The evolution of the mechanical design and the electronics are described, as well as the different setups that were used to test the instrument. Aided by numerical simulations, the characterization experiments shed light onto several subtleties of the principle of operation. The third and last part describes the infrared (IR) and ultraviolet (UV) spectroscopic investigation of the protonated phenylalanine/serine dimer, using the instrument detailed in the first part. The isomer-specific IR spectra demonstrate that this small and apparently simple system is more complex than could have been anticipated from previous investigations of related systems. In particular, isotopic labeling experiments provide evidence for different protonation sites in different isomers. Using a UV-pump/IR-probe scheme, it is demonstrated how the lifetimes and the IR spectra of several excited state species can be obtained.