By combining ion mobility mass spectrometry (IM MS) with time-of-flight MS (Tof MS), Waters revolutionized the structural analysis of peptides, proteins, and protein complexes. Waters SYNAPT range of mass spectrometers have generated important breakthroughs in the determination of overall size, shape, and subunit architecture of protein complexes. For post-translational modification studies, the SYNAPT XS also offers a unique implementation of ETD. ETD is performed in the trap-region of the Triwave device allowing for the optional, supplemental activation of ions by CID. All told Waters Omics Discovery Platform allows for extensive characterization of the primary and tertiary structure of proteins.
For structural biology analysis, ion mobility mass spectrometry can be used to interrogate heterogeneous protein assemblies in the 10 kDa to 1 MDa range, intact in the gas phase. MS allows us to identify and quantify the relative abundances of the different stoichiometures, and obtain equilibrium constants for the underlying protein-protein and protein-ligand interactions. The concurrent IM measurements allow us to obtain information as to the physical size of the proteins. These experiments therefore provide powerful restraints in modelling the structures of protein assemblies that are difficult and time-consuming to study by means of conventional structural biology approaches.