Recent innovations in speed, accuracy and sensitivity have established mass spectrometry (MS) based methods as a key technology for the mapping and analysis of small molecules, lipids, peptides, protein, DNA and DNA-protein complexes in biological systems. In particular, Ion Mobility Spectrometry – Mass Spectrometry provides a powerful tool for the identification of structural motifs, and when complemented with theoretical calculations, it permits a better understanding of the main motifs that drive the dynamics across the free energy landscape. We have recently introduced a Trapped Ion Mobility Spectrometry coupled to Mass Spectrometry (TIMS-MS) as a high-throughput technique for the study of conformational states of biomolecules, as well as the kinetic intermediates involved during their folding as a function of the molecular environment (e.g., pH, organic and salt content). While this description holds true for most contemporary IMS analyzers, the higher resolving power (e.g., R= 150-250, 3x larger than traditional IMS systems) and the unique ability to hold and interrogate molecular ions for kinetic studies (e.g., millisecond-second time scale) provides TIMS-MS with unique capabilities for the study and interrogation as a function of the time after desolvation. Recently combined with hydrogen-deuterium exchange, HDX-TIMS-MS, a more detailed description of the accessible surface area and the folding can be achieved over time. That is, HDX-TIMS-MS has a significant advantage in the flexibility to interrogate, at the single molecule level, the molecular interactions that define the conformational space. In the present talk, recent results that reveal the kinetic intermediates and the main folding pathways for small molecules, peptides, proteins, DNA and DNA-protein complexes will be discussed as well as some novel chemical mapping strategies at the single cell level.