HeLa cell proteome: Different amounts of the tryptic peptide mixtures for LC-MS/MS

The tryptic peptide mixture from HeLa cells was subjected to LC-MS/MS in triplicate each for 250 ng, 500 ng, 750 ng and 1000 ng peptides. LC-MS/MS was conducted using a Q Exactive mass spectrometer (Thermo Fisher Scientific) equipped with an Ultimate 3000 RSLCnano liquid chromatograph (Thermo Fisher Scientific) containing C18 capillary LC column (Nano HPLC capillary Column, 75 μm i.d., 150 mm length, 3 μm particle size, Nikkyo Technos, Tokyo, Japan). LC-MS/MS data were integrated on a Proteome Discoverer 2.2 software (Thermo Fisher Scientific), followed by sequence database search of the MS/MS data using Mascot software (Matrix Science). The search results showed identification of the total of 3649 protein groups, filtered at 1% false discovery rate (FDR) peptide threshold.