Magna chirp

10–20 15 cm dishes of cells were used per ChIRP-MS experiment (100million - 500million cells depending on the cell type). Cell harvesting, lysis, disruption, and ChIRP were essentially performed as previously described [20 (link)] and follow the manufacturer’s instruction (Magna ChIRP, Millipore, USA). Final protein samples were size-separated in bis-tris SDS-PAGE gels (Invitrogen) for western blots and MS. The following antibodies were used in the followed western-blotting: anti-TLR7 (ab45371, Abcam), anti-hnRNPK (ab39975, Abcam), anti-PRDX1 (ab41906, Abcam), anti-PRDX2 (ab109367, Abcam), anti-ECM1 (ab126629, Abcam) and anti-β-actin (ab8227, Abcam). See Additional file 2: Materials and Methods for details.

ChIRP assays were conducted using LITTIP-specific biotin probes as previously described (Magna ChIRP, Millipore, USA).^{45 (link)} The enzymatic hydrolysate was separated by nano-UPLC liquid phase system (EASY-nLC1200) and used for MS. The proteins precipitated by LITTIP probes were quantified based on the fold change of normalized spectral counts relative to the negative control. The ChIRP probe (LITTIP) sequences used are provided in Supplementary Table S4. The results of the ChIRP-MS assay are listed in Supplementary Table S5.