For Tandem Mass Tag (TMT)-based quantification, the dried peptides were re-dissolved in 100mM TEAB (50 µL) and their concentration was measured using a fluorescent assay (CBQCA) (Life Technologies). 100 µg of peptides from each cell line to be compared, in 100 µL of TEAB, were labelled with a different TMT tag (20 µg ml-1 in 40 µL acetonitrile) (Thermo Scientific), for two hours at room temperature. After incubation, the labelling reaction was quenched using 8 µl of 5% hydroxylamine (Pierce) for 30 minutes and the different cell lines/tags were mixed and dried in vacuo.
