In-depth analysis of HeLa cell proteome

The tryptic peptide mixture from HeLa cells was fractionated using a High pH Reversed-Phase Peptide Fractionation Kit (Thermo Fisher Scientific). Each peptide fraction was subjected to LC-MS/MS in triplicate using a Q Exactive Orbitrap mass spectrometer (Thermo Fisher Scientific) equipped with an UltiMate 3000 liquid chromatograph (Thermo Fisher Scientific). LC-MS/MS data were integrated on a Progenesis QI for proteomics software (Waters), followed by sequence database search of the MS/MS data using Mascot software (Matrix Science). The search results showed identification of the total of 6151 protein groups, filtered at 1% false discovery rate (FDR) peptide threshold.