Methods for analyzing the terminal sequences of proteins have been refined over the previous decade; however, few studies have evaluated the quality of the data that have been produced from those methodologies. While performing global N-terminal labelling on bacteria, we observed that the labelling was not complete and investigated whether this was a common occurrence. We assessed the completeness of labelling in a selection of existing, publicly available N-terminomics datasets and empirically determined that amine-based labelling chemistry does not achieve complete labelling and potentially has issues with labelling amine groups at sequence-specific residues. This finding led us to conduct a thorough review of the historical literature that showed that this is not an unexpected finding, with numerous publications reporting incomplete labelling. These findings have implications for the quantitation of N-terminal peptides and the biological interpretations of these data.

The blood-brain barrier (BBB) is a tightly and actively regulated vascular barrier. Answering fundamental biological and translational questions about the BBB with currently available approaches is hampered by a trade-off between accessibility and biological validity. We report an approach combining micropipette-based local perfusion of capillaries in acute brain slices with multiphoton microscopy. Micro-perfusion offers control over the luminal solution and allows application of molecules and drug delivery systems, whereas the bath solution defines the extracellular milieu in the brain parenchyma. Here we show, that this combination allows monitoring of BBB transport at the cellular level, visualization of BBB permeation of cells and molecules in real-time and resolves subcellular details of the neurovascular unit. In combination with electrophysiology, it permits comparison of drug effects on neuronal activity following luminal versus parenchymal application. We further apply micro-perfusion to the human and mouse BBB of epileptic hippocampi highlighting its utility for translational research and analysis of therapeutic strategies.

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