Tandem mass spectrometry is currently the gold standard in biomolecular analysis. The combination of robust and sensitive ionization techniques such as electrospray ionization with efficient fragmentation techniques and subsequent detection with high mass resolution enables the rapid identification of hundreds of proteins within hours. Likewise, highly complex maps of lipids and small molecule metabolites can be identified reliably from complex biological samples. However, differentiating isomeric species remains challenging through conventional mass spectrometry. In metabolomics, multiple structural candidates often exist for a given m/z, complicating precise identification. Similarly, in glycomics, isomeric glycan structures differing only in regio- or stereochemistry of a single glycosidic bond often coexist, presenting a significant analytical challenge. Recently, advances in commercially available ion mobility–mass spectrometers, gas-phase ion spectroscopy, and computational chemistry have opened new avenues to solve the isomer problem in mass spectrometry.1 Here we illustrate examples how small isomeric molecules such as metabolites and glycans can be unambiguously identified using ion mobility mass spectrometry and cryogenic gas-phase spectroscopy.