GASP and FASP are complementary for LC-MS/MS proteomic analysis of drug-metabolising enzymes and transporters in pig liver

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 we demonstrate the complementarity of two different sample preparation techniques 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, whilst gel-aided sample preparation (GASP) is a relatively new method optimised and simplified from previous gel-associated digestion techniques. To investigate each method the number of peptides and proteins characterised, reproducibility of results and their real-time application were examined. Whilst both methods have their merits and limitations, for example, FASP is the less technical of the two methods, whilst 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.