Detailed information pertaining to the mass spectrometry can be found in Tyanova et al. (2014). Briefly, samples from the crosslinked immunoprecipitations were resolved ∼2 cm into a pre-cast SDS-polyacrylamide gel, the entire lane excised and cut into six equal slices. Proteins were reduced and alkylated then digested in-gel using trypsin. The resulting peptides were analysed by LC-MSMS using a Q Exactive (Thermo Scientific) coupled to an RSLC3000nano UPLC (Thermo Scientific) with the data acquired in a data-dependent acquisition (DDA) fashion. Raw files were processed in Maxquant 1.5.2.8 using the default setting for a SILAC duplex experiment with re-quantify enabled.
