Purified Δ6-TNFR1-Fc protein and transfected cell supernatants were solubilized and digested with chymotrypsin (Roche). The digested protein mixture was separated with a 140 min gradient from 5 to 60 % acetonitrile (uHPLC, Proxeon) and loaded onto a LTQ-Orbitrap or a Q-Exactive mass spectrometer (Thermo Fisher). The instrument was operated in a data-dependent top10 acquisition modus. Raw data were searched using the MaxQuant software suite (version 1.2.2.0) against the complete IPI human database (v3.68, 87061 entries) with an additional entry for the Δ6-TNFR1 isoform. The fragmentation spectra were plotted and annotated by the Viewer interface of MaxQuant.
