Model-based assessment of the effects of liver disease on drug pharmacokinetics requires quantification of changes in enzymes and transporters responsible for drug metabolism and disposition. Different proteomic methods are currently used for protein quantification in tissues and in vitro systems, each with specific procedures and requirements. The outcome of quantitative proteomic assays from four different methods (one targeted and three label-free), applied to the same sample set, were compared in this study. Three pooled cirrhotic liver microsomal samples, corresponding to cirrhosis with non-alcoholic fatty liver disease, biliary disease or cancer, and a control microsomal pool, were analyzed using QconCAT-based targeted proteomics, the total protein approach (TPA), high three (Hi3) ion intensity approach, and intensity-based absolute quantification (iBAQ), to determine the absolute and relative abundance in disease compared with control. The relative abundance data provided a ‘disease perturbation factor’ (DPF) for each target protein. Absolute and relative abundances generated by standard-based label-free methods (iBAQ and Hi3) showed good agreement with targeted proteomics (limited bias and scatter) but TPA (standard-free method) over-estimated absolute abundances by approximately 2 fold. DPF was consistent between different proteomic methods but varied between enzymes and transporters, indicating discordance of effects of cirrhosis on various ADME proteins. DPF ranged from no change (e.g. for UGT1A6 in NAFLD group) to less than 0.3 (e.g. CES1 in cirrhosis of biliary origin).