Microtubule-associated protein tau is a central factor in Alzheimer’s disease and other tauopathies. However, physiological functions of tau are unclear. Here, we used proximity labelling proteomics to chart functional tau interactomes in primary neurons and mouse brain in vivo. Here, we use proximity labelling with the biotin ligase BioID2 to map interactomes of tau in neurons. Data sets relate to mass spectrometry and protein identification of biotinylated proteins in primary neurons and in mouse brain after delivery of BioID2-tau fusion protein or BioID2 control protein by adeno-associated virus (AAV). Mouse brain samples are either from P35 wild-type mice with intracranial AAV delivery at P0 or from tau knockout mice at P60 after hippocampal delivery of AAV. Details on BioID2 fusion protein expression, biotin supplementation and sample extraction can be obtained in the associated publication.

Data collection:

Peptide samples sourced from primary neurons and mouse brain were run (3 μg injected per run) and captured on a C18 cartridge (Acclaim PepMap 100, 5 μm 100 Å, Thermo Scientific Dionex, Waltham, USA) using a Q Exactive Orbitrap (ThermoFisher) before switching to a capillary column (~20 cm) containing C18 reverse phase packing (Reprosil-Pur, 1.9 μm, 200 Å, Dr Maisch GmbH, Ammerbuch-Entringen, Germany), and eluted with 40 min gradient of buffer A (H₂O:CH₃CN of 98:2 with 0.1% formic acid) to buffer B (H₂O:CH₃CN of 20:80 with 0.1% formic acid) at 200 nL/min. The mass spectrometer (QExactive, Thermo) was set to positive ion mode. Peak lists were generated using MASCOT Distiller (Matrix Science, London, UK).

Data processing:

Peak lists were searched using the MASCOT search engine (v2.6.2, Matrix Science). Peak lists were matched to amino acid sequences from the SwissProt database (downloaded 10-8-19; Mammalia taxonomy, 66946 entries) and the Peptide Prophet algorithm (Keller et al, 2002) assigned identity to peptides with FDR = 1.6% and to proteins with FDR = 0.4%. Each protein was considered identified when assigned 1 unique peptide with a peptide score >38.

RAW files require MASCOT search engine (v2.6.2, Matrix Science) or similar mass spectrometry peak list reader.

.CSV files can be opened in Microsoft Excel or text editing software.