Native protein mass spectrometry (MS), the measurement of proteins and protein complexes from non-denaturing solutions, with electrospray ionization (ESI) has utility in the biological sciences. Protein complexes exceeding 1 MDa have been measured by MS and ion mobility spectrometry (IMS), and the data yields information not only regarding size, but structural details can be revealed also. ESI-IMS allows the relative stability of protein–ligand binding to be measured. Top-down MS, the direct dissociation of the intact gas phase biomolecule, can generate sequence and identity information for monomeric (denatured) proteins, and topology information for noncovalent protein complexes. For protein complexes with small molecule ligands, i.e., drugs, cofactors, metals, etc., top-down MS with electron capture dissociation can be used to elucidate the site(s) of ligand binding. Increasing protein ESI charging, e.g., supercharging, enhances the efficiency for dissociation of protein complexes.