Mass spectrometry has frequently been employed in the analysis of biologically relevant molecules; however, mass spectrometry alone may not always be sufficient for the differentiation and characterization of isomeric and isobaric ions. In this work, infrared multiple photon dissociation (IRMPD) spectroscopy and ion mobility spectrometry (IMS) were evaluated as complementary techniques for the characterization and separation of isomeric and isobaric ions of biological relevance. In the first project, analysis of experimental IRMPD spectroscopy data shows that this technique is useful in the differentiation of hydroxyproline isomers. Absorption bands allow for the differentiation of three isomeric species: 1640 cm-1 (trans-4-hydroxyproline), 1718 cm-1 (cis-4-hydroxyproline), and 1734 cm-1 (cis-3-hydroxyproline). In the second project, theoretical CCS and IR spectroscopy predictions of isobaric modified amino acids and isomeric drugs have been carried out as predictions of IMS and IRMPD spectroscopy suitability. Preliminary IMS measurements suggest that the CCS predictions are at least qualitatively useful.