The Amster research group specializes in the development and application of Fourier transform mass spectrometry for solving difficult problems in bioanalytical chemistry. We are exploring new methods for analyzing the structural features of glycosaminoglycans (GAGs), a class of carbohydrates that play a central role in a number of important biological processes, including cellular communication, cell signaling, and regulation of biochemical pathways. We explore a variety of ion activation methods, electron-based, ion-ion reactions, photochemistry, and collisionally induced approaches to tandem mass spectrometry, to maximize the structural information that can be obtained from a mas spectrum. We are investigating separation methods to resolving glycosaminoglycan mixtures, both gas-phase and condensed-phase approaches. Capillary electrophoresis is the most recent tool that we are using to examine GAG mixtures. We are developing software to provide automated interpretation of tandem MS data, necessary for deploying our structure characterization approaches to the broad biological community. We are also examining the interactions of GAGs with proteins, using ion mobility spectrometry to gain details such as changes in the three dimensional structure of proteins upon binding GAG ligands, oligomerization induced by GAG binding, and the stabilization of protein structure that results from forming a complex with a target GAG oligomer. Other recent research projects include the use of advanced computational methods for carrying out multiparticle simulations of ion motion within the FTICR mass analyzer. These simulations give detailed information about ion-ion interactions, and provide insight into the limits of mass accuracy in FTICR mass spectrometry.