Mass spectrometry is a powerful analytical technique, which has become invaluable across a wide range of scientific fields, such as "omics" sciences (e.g., proteomics), doping control and forensic sciences, drug development, environmental analysis, geologic research, etc. Originally developed over a century ago to measure elemental atomic weights and the natural abundances of isotopes, nowadays mass spectrometry is a vital tool for structural characterization of biomolecules, ranging from small metabolites to large macromolecular assemblies. This includes identifying unknown compounds, quantifying known compounds, and exploring molecular structures. However, the mass spectrometric analysis is based on measurements of the mass-to-charge ratio of ions, a quantity that is not sensitive to their three dimensional (3D) structure. Cold ion spectroscopy is another method of studying ions in the gas phase, that has demonstrated its capability to reveal their spectroscopic fingerprints, which are characteristic of the 3D structure of the ions on a fundamental level. In this thesis we present novel approaches to molecular structure identification, which are based on integration of high-resolution mass spectrometry (MS) with high-resolution ultraviolet (UV) photofragmentation spectroscopy of cold ions. The first part of this work describes the coupling of an Exactive Orbitrap-based mass spectrometer to a cold ion spectrometer and the use of this novel hybrid instrument for measuring two-dimensional (2D) UV-MS spectra of ionic species. The synergy of the two complementary techniques makes these spectra unique fingerprints of biomolecular ions. The second part presents an approach that uses mathematical analysis of these highly specific fingerprints for identification of isomeric biomolecules in mixtures. Using preliminarily recorded libraries of fingerprints, the UV-MS approach was successfully employed for quantitative identification of positional isomers of a phosphorylated peptide, diastereomers of an opioid peptide, and diastereomers of a drug molecule. We also demonstrate a library-free approach, which allows estimating the number of components present in a mixture and deriving their UV absorption and fragmentation mass spectra directly from the 2D UV-MS spectrum of the mixture. In the third part, we employ the library-free approach and the phenomenon of nonstatistical photofragmentation to identify conformers of gas-phase biomolecular ions and to recover their individual UV absorption and fragmentation mass spectra. We validate this approach with a benchmark dipeptide, Tyr-Ala, and then apply it to a decapeptide, gramicidin S, and a small drug molecule, homatropine. A careful analysis of the derived UV and mass spectra of the conformers of gramicidin S and homatropine provides some structural information that can be used for solving their 3D structures. In the last part, we demonstrate a use of 2D UV-MS spectroscopy for estimating the distances between the phenylalanine and tyrosine chromophores in four gas-phase opioid peptides. We have also calculated the 3D structures of their lowest energy conformers. We discuss these structures in the context of the estimated interchromophore distances and the pharmacological properties of the peptides.