Variability in Mass Spectrometry-based Quantification of Clinically Relevant Drug Transporters and Drug Metabolizing Enzymes

Many
different methods are used for mass-spectrometry-based protein
quantification in pharmacokinetics and systems pharmacology. It has
not been established to what extent the results from these various
methods are comparable. Here, we compared six different mass spectrometry-based
proteomics methods by measuring the expression of clinically relevant
drug transporters and metabolizing enzymes in human liver. Mean protein
concentrations were in general quantified to similar levels by methods
using whole tissue lysates. Methods using subcellular membrane fractionation
gave incomplete enrichment of the proteins. When the enriched proteins
were adjusted to levels in whole tissue lysates, they were on average
4-fold lower than those quantified directly in whole tissue lysates.
The differences in protein levels were propagated into differences
in predictions of hepatic clearance. In conclusion, caution is needed
when comparing and applying quantitative proteomics data obtained
with different methods, especially since membrane fractionation is
common practice for protein quantification used in drug clearance
predictions.