Quantitative Deep Proteomic Analysis of IFNAR-/- Mouse Liver

Parts of the liver from all infected IFNAR^−/− mice were crushed in 150 μL lysis buffer (10 mM Tris, 150 mM NaCl, 10% SDS, and protease inhibitor) using pestles. Then, samples were incubated at 4°C for 30 min and centrifuged at 13,000 rpm at 4°C for 20 min. Supernatant was collected, NuPAGE™ LDS sample buffer with 2-mercaptoethanol added and the samples boiled at 99°C for 10 min. Protein concentration for each sample was determined using Pierce™ 660 nm protein assay (Thermo Fisher Scientific). Tandem mass tag (TMTpro™, Thermo Fisher Scientific) based quantitative deep proteomic analysis, using nano-flow liquid chromatography hyphened to tandem mass spectrometry (LC-MS/MS), was performed in Proteomics Biomedicum, Karolinska Institute as described previously (46 (link)).