Sample preparation is a critical step in the proteomic workflow. Numerous different approaches are used, tailored to the type of sample, the aims of the experiment, analytical method, and to an extent, user preference. This has resulted in large variation in reported protein abundances. In this study, the complementarity of two different sample preparation techniques is demonstrated for the study of absorption, distribution, metabolism, and excretion (ADME) related proteins from pig liver tissue. Filter-aided sample preparation (FASP) is a well-established and widely used method, while gel-aided sample preparation (GASP) is a relatively new method optimized and simplified from previous gel-associated digestion techniques. To investigate each method, the number of peptides and proteins characterized, reproducibility of results, and their real-time application are examined. While both methods have their merits and limitations, for example, FASP is the less technical of the two methods, while GASP is time efficient, ultimately the two methods show significant differences in the peptides identified and therefore, the use of both methods should be considered when examining and quantifying ADME related proteins. Data are available via ProteomeXchange with identifier PXD011324.