The design and first applications of a new tandem mass spectrometer (BerlinTrap) combining an electrospray ion source, a quadrupole mass spectrometer, a cryogenic 22-pole ion trap (4–300K), and an orthogonal reflectron time-of-flight mass spectrometer are described. The trapped ions are cooled by helium buffer gas cooling. The formation and solvation shell structure of weakly-bound HenH3O+ complexes and the electronic photodissociation spectrum of the protonated amino acid tyrosine are used to calibrate the setup for cooling, tagging, and spectroscopic capabilities. A vibrational temperature below 20K is inferred for protonated tyrosine. The electronic spectrum of isolated protonated lumichrome, the smallest protonated flavin, is recorded in the visible range and assigned to the most stable N5 isomer by comparison with quantum chemical calculations. These results demonstrate the suitability of the BerlinTrap apparatus for spectroscopy and reactivity studies of small and large (bio-)molecular ions and their clusters.