Proteome quantifiation is of great signifcane to study various biological processes.In our recent work,various new methods for the relative quantification of proteomes were develped,by which the accuracy,precision,and coverage was obviously improved.For MS based quantification,a hollow fiber membrane-aided fully automated sample treatment(FAST)method was proposed,by which samples treated by SILAC strategy could be denatured,reduced,desalted and digested in a few minutes via "one-stop" service.Through the on-line combination of FAST with nano-LC-ESI-MS/MS,we further established a fully integrated platform for high-throughput proteome quantification,and demonstrated its capacity to analyze sub-nanogram starting materials.For MS/MS based quantification,mass defect-based pseudo-isobaric dimethyl labeling(pIDL)method based on the subtle mass defect differences between 12C/13C and 1H/2H was introduced.Lys-C protein digests were labeled with CD2O/13CD2O and reduced with NaCNBD3/NaCNBH3 as heavy and light isotopologues,respectively.The fragment ion pairs with mass differences of 5.84 mDa were resolved by high-resolution MS/MS and used for quantification.The pIDL method described resulted in approximately 100-fold dynamic range and highly accurate results with relative error less than 2%.Moreover,this method can be extended to 6-plex proteome quantification.All the above-mentioned new methods were successfully applied to perform the comparative proteome quantification of hepatocellular carcinoma cells with high and low metastatic potential.