“…QMI measures Proteins in Shared ComplexES (PiSCES), so to maximize protein complex detection, so we added several of the most connected nodes in Fig 1E to our previously-described QMI panel, which was built to measure the amount of co-association among critical TCR signalosome members 14,21 : CAR (anti-2A scar, IP only), TRAF1, TRAF2 and BIRC3. We also included three proteins that did not reach statistical significance in the mass spec experiments, but are known to be important to the TRAF and NFκB signalosome in lymphocytes: TAK1 (MAP3K7, FC=597, t=−1.09 NS), which is recruited by TAB1/2 and signals to IKKb 18 and was recently shown to be critical to IFNγ production in CD8+ T cells in a large CRISPR screen 33 ; TNIK (found in only 1 co-IP experiment) which binds TRAFs, may recruit NCK to link TRAFs with TCR signaling mechanisms 13 , and is critical for CD8+ T cell memory formation 34 ; and SHARPIN (FC=13.6, T=−1.21), a component of the linear ubiquitination complex (LUBAC) that promotes activation of the IKK complex downstream of TNF family receptors 35,36 , ubiquitinates CARMA-BCL10-MALT complex 37 , and may bind directly to TRAF1 38 . As previously described 21,32,39 , we identified two antibodies that could simultaneously bind each target in its native state on flow cytometry beads, and validated target specificity using cell lysates lacking the target (Fig S2 and Table S2).…”