For proteomic analysis, we initially reversed the cross-linking by boiling the beads in a final concentration of 1× NuPAGE LDS Sample Buffer (Thermo Fisher Scientific) at 95°C for 30 min on a thermomixer (at 750 rpm). After boiling, the samples were loaded on precast NuPAGE 4 to 12% Bis-Tris Protein Gels (Thermo Fisher Scientific) and separated for 20 min at constant voltage (200 V). The gels were stained overnight with Coomassie G250, and for each lane, five to six pieces were cut. In-gel digestion was performed overnight using trypsin. Samples were dried, and peptides were resuspended in 5% acetonitrile and 0.05% trifluoroacetic acid. Samples were further processed for liquid chromatography–MS in an online UltiMate 3000 RSLCnano high-performance liquid chromatography system (Thermo Fisher Scientific) coupled online to an Orbitrap Fusion Tribrid MS instrument (Thermo Fisher Scientific). Peptides were desalted on a reversed-phase C18 precolumn (3 cm long; inner diameter, 100 μm; outer diameter, 360 μm) for 3 min. After 3 min, the precolumn was switched online with the analytical column (~30 cm long; inner diameter, 75 μm) prepared in-house using ReproSil-Pur C18 AQ 1.9-μm reversed-phase resin. The peptides were separated with a linear gradient of 5 to 50% buffer B (80% acetonitrile and 0.1% formic acid) at a flow rate of 10 nl/min over 58-min gradient time. The temperature of the precolumn and the column was set to 50°C during chromatography. The MS data were acquired by scanning the precursors in a mass range from 380 to 1500 Da at a resolution of 120 K at a mass/charge ratio of 200. The acquired RAW data were analyzed using MaxQuant software on the basis of the Andromeda search engine. The updated rat UniProt database was used for identifying proteins (visit the PRIDE dataset identifier PXD013434 for details).

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