Blood-brain barrier (BBB) pharmacoproteomics: A new research field opened up by quantitative targeted absolute proteomics (QTAP)

The activities of individual functional proteins, such as transporters, receptors, enzymes, and channels, show large variations, including interspecies differences, in vitro/in vivo differences, age-related differences, and normal/disease differences, and these need to be understood in order to guide rational drug discovery and development. To address this issue, we have developed an absolute quantification method of protein expression, called quantitative targeted absolute proteomics (QTAP), by means of liquid chromatography-tandem mass spectrometry (LC-MS/MS) with multiplexed selected/multiple reaction monitoring (SRM/MRM). QTAP has high sensitivity and selectivity, allowing quantification of protein expression over a wide dynamic range (0.1-1,000 fmol/μg protein). Further, its ability to quantify multiple proteins simultaneously enables us to determine the quantitative expression profile of multiple proteins in tissues and cells. In this chapter, we introduce the technical features of QTAP, discuss its advantages and limitations compared with global proteomics, mRNA quantification, and antibody-based protein quantification, and introduce its applications in blood-brain barrier (BBB) research. Species differences (human/monkey/mouse), interindividual differences, and agerelated differences in the activities of transporters at the BBB are discussed based on their protein levels, with reference to recently reported data. QTAP also allows us to reconstruct/predict in vivo activities of transporters at the BBB, as well as drug distribution in the brain, from the results of in vitro experiments with the aid of pharmacokinetic modeling. QTAP methodology is expected to open up a new research field, BBB pharmacoproteomics.