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Samples for mass spectrometry were prepared as follows. HEK293 cells (150 cm^2 dish) were transfected with 6 μg of each protein-coding plasmid by using TransIT (Mirus). Cell lysis and elution were performed as described above. For loading the samples onto an SDS-PAGE, glycerol was added to the eluted supernatants and PAGE was started. Immediately after samples had entered the separation gel, electrophoresis was stopped. After staining the gel with colloidal coomassie, the protein bands were excised and subjected to in-gel digestion with trypsin. Mass spectrometric analysis was performed as described using an Orbitrap Velos Pro mass spectrometer (Thermo Fisher Scientific) which was connected online with a nano C18 RP column equipped Ultimate nanoRSLC-HPLC (Rapid separation liquid chromatography-high performance liquid chromatography) system (Dionex). An aliquot of 15 µL of the tryptic digest was usually injected onto a C18 pre-concentration column and automated trapping and desalting of the sample was performed at a flowrate of 6 µL/min using water/0.05% formic acid as solvent.
Tryptic peptides were separated with water/0.045% formic acid and 80% acetonitrile/0.05% formic acid at a flow rate of 300 nL/min. The column was connected to a stainless steel nanoemitter (Proxeon, Denmark) and the eluent sprayed directly towards the heated capillary of the mass spectrometer using a potential of 2300 V. A survey scan with a resolution of 60,000 within the Orbitrap mass analyzer was combined with at least three data-dependent MS/MS scans with dynamic exclusion for 30 s either using CID (Collision-induced dissociation) with the linear ion-trap or using HCD (Higher energy collisional dissociation) and orbitrap detection at a resolution of 7,500. Data analysis was performed using Proteome Discoverer (v4.0; Thermo Fisher Scientific) with SEQUEST and MASCOT (v2.4; Matrix science) search engines using either SwissProt or NCBI databases.