Secondary membrane transporters are found across the biological kingdom. The structural dynamics of their actions are elusive, as our understanding relies on few X-ray structures. Comparisons of the available structures show that large re-arrangements take place between two domains during transport, with what is generally described as a “rocking-bundle model”. However, dynamic motion between the transport domains remains largely inaccessible to most experimental analysis methods. Here we propose to use a novel mass spectrometric approach that allows the desolvation of intact membrane proteins directly from detergent or lipid environments in combination with ion mobility mass spectrometry to monitor conformational changes in secondary transporters. This study will initially focus on the glutamate transporter GltPh for which structures, inhibitor, mutagenesis and cysteine cross-linking studies are available. We will then apply the same approach to the less-well understood transporters harboring the NhaA-fold. The goal will be to elucidate the conformational dynamics of NhaA, NapA, and ASBT proteins during transport and monitor the effects of substrates, ions, lipids and oligomerization. In summary, this project aims to establish a novel mass spectrometry-based methodology to bridge the gap between structure and function of secondary active transporters.