Comprehensive identification of Ubiquitin-like 3 (UBL3)-interacting proteins in mouse brain

Each protein extract from the cortex of Ubl3+/+ and Ubl3Tg/+ male mice (9-10-week-old, n=3, 3) was incubated with 30 μL of NeutrAvidin Agarose (ThermoFisher, 29202) for 18 h at 4 °C and subjected to mass spectrometry using previously reported methods (Ageta et al., Nat Commun 2018, PMID: 30258067). The peptides were analyzed by liquid chromatography/mass spectrometry (LC/MS) using an Orbitrap Fusion mass spectrometer coupled to an Easy-nLC 1000 using a EASY-Spray ES900 column system (ThermoFisher, 75 μm x 150 mm, particle size 3 μm). Mass spectrometry raw files is proceeded using Proteome Discoverer version 2.4 (ThermoFisher) and a local MASCOT server (version 2.6.2; Matrix Science). MS/MS data were searched against Mus musculus (SwissProt TaxID=10090_and_subtaxonomies) (v2017-10-25).