Complementary proteomics strategies identify the ataxin-1 interactome in Neuro-2a cells

To identify protein partners of ataxin-1 in neuronal cells under control or stress conditions, we use complementary proteomics strategies of proximity-dependent biotin identification (BioID) and affinity purification (via GFP-trap pulldown) in Neuro-2a cells expressing epitope-tagged forms of ataxin-1[85Q]. These approaches allowed our enrichment of proximal proteins and interacting partners, respectively, with the subsequent protein identification performed by liquid chromatography-MS/MS. Background proteins, defined by identification not dependent on the polyQ-ataxin-1 protein, were additionally identified by their endogenous biotinylation (for the BioID protocol) or by their non-specific interaction with GFP only (in the GFP-trap protocol). All datasets were generated from biological replicates.