This review discusses recent trends of proteomics applications based on publications from pharmaceutical companies. In addition to protein expression profiling, applications of chemical proteomics, targeted protein quantitation, analysis of protein-protein interactions and post-translational modification have been reported from various laboratories of pharmaceutical companies, indicating that the applications of proteomics have been widespread among pharmaceutical companies since overcoming initial difficulties of proteomics applications to pharmaceutical research. Further technological progress in proteomics is desired to accelerate pharmaceutical research and development.

Recent advances in omics analysis have facilitated quantitative measurement for various molecular activity in vivo beyond large scale quantification. However, there is no guideline for how to analyze these types of omics data properly and, in general, scientists have to struggle with acquired omics data to find a clue for a novel biological findings. To overcome this challenge, we propose “trans-omics” analysis for reconstructing molecular networks by connecting multiple omic data. Trans-omics connects multiple omic layers with the support from prior knowledge of molecular networks such as publicly-available databases for reconstruction of biochemical networks and characterizes the biochemical reactions in the reconstructed network. In this review, we introduce the concept of trans-omics analysis and the ideas for integration of newly developed proteomics data into trans-omics network.

Pharmacokinetics play an important role in drug discovery and development from an early phase and contribute to clinical treatment success by reducing and predicting severe drug-drug interactions and side effects. Drug-metabolizing enzymes and drug-transporters are key regulators of the absorption, distribution, metabolism, and excretion of xenobiotics. Recent studies have demonstrated that the expression levels of proteins related to drug-metabolizing enzymes and drug-transporters in the liver, kidney, and small intestine are highly correlated with those organ’s functional activities. Thus, the quantification of protein expression of drug-metabolizing enzymes and drug-transporters in tissues is essential to clarify and predict pharmacokinetics of xenobiotics, including drugs. Multiple reaction monitoring (MRM)-based targeted proteomics is available to determine protein expression levels using stable isotope-labeled internal standard peptides. However, MRM analysis records fragments of only targeted precursor ions. Sequential window acquisition of all theoretical mass spectra (SWATH) acquisition, coupled with Quadrupole time-of-flight mass spectrometers, is a data independent approach, which is able to produce a complete and permanent record of all fragment ions of the detectable peptide precursors present in a biological sample. Thus, the quantification of any protein of interest is possible from SWATH MS datasets. To overcome the limitations of MRM-based quantitative proteomics, we applied SWATH-based comprehensive quantitative proteomics to study pharmacokinetics. In this review, we describe the advantages of SWATH-based comprehensive quantitative proteomics for the elucidation of pharmacokinetics.