Proteome of CBR1 transgenic SK-OV-3 and OVCAR-2 cells

Cell lysis samples containing 20 μg total protein determined by BCA method were precipitated with acetone. The precipitates were denatured with 50% trifluoroethanol. Disulfide bonds in proteins were reduced with DTT and alkylated with iodoacetamide followed by trypsin digestion. After desalting and purification of the resulting peptides, the samples were subjected to LC-MS/MS using a nanoLC system (Eksigent 400, AB Sciex) coupled online to a mass spectrometer (TripleTOF6600, AB Sciex). Database searching for acquired spectra was performed using a ProteinPilot 5.0.1 software (AB Sciex). Positive identification threshold was set at a false discovery rate of 1% or less. The resulting library file and SWATH (data independent acquisition) files were processed by PeakView (ver. 2.2.0, AB Sciex), and exported to MarkerView (ver. 1.3.0.1; AB Sciex). Peak areas of individual proteins were normalized relative to the sum of the peak areas of all detected proteins.