Flagella (aka cilia) are protrusions of the cell surface that are made by most eukaryotic cell types. The cell uses them as 'antennae' to sense stimuli or for propulsion. The transition zone is a compartment of the flagellum that helps to build the flagellar axoneme by controlling its composition, acting as a bidirectional 'gate'. Mutations in transition zone proteins cause many diseases of the cilia that are collectively termed 'ciliopathies'. I have used a new proteomics technique to find the composition of the trypanosome transition zone. Trypanosomes have unsurpassed molecular tools that allow us to discover some really interesting biology. We leveraged this transition zone proteome to investigate the dynamics and stability of transition zone proteins and how they sub-compartmentalise within the transition zone. This will help us to determine how the transition zone performs its gate function.