Table 1.

DIA quantitative proteomics of DMEs and drug transporters.

Proteins of interest	Sample	Method features	Normalization method	Major findings and implications	Ref.
CYPs	HLM	Label-free; relative quantification; multiplex	Normalized to β-galactosidase tryptic peptides	The protein abundance correlated better with enzyme activity than mRNA for most CYPs.	[24]
CYPs	HLM and microsomes of HepG2, Hep3B, and Huh7 cells	Label-free; relative quantification; multiplex	Normalized to the internal standard bovine serum albumin	The results measured by DIA were highly correlated with those obtained with PRM (r2=0.87–0.90). The expression levels of most DMEs in the hepatic cell lines were lower than those in human liver tissues.	[15]
CESs, UGTs, CYPs	HLS9	Label-free; absolute quantification; multiplex	Total protein in the sample	Broader coverage than DDA-TPA; the results were comparable to those obtained from labeling and targeted methods.	[16]
DMEs, transporters	HLM, HLS9			The differences in the protein concentrations of DMEs and transporters between HLM and HLS9 were profiled.	[26]
DMEs, transporters	HLM, HIM, HKM	Labeling; absolute quantification; large-scale multiplex	Stable isotope-labeled internal standard peptides	DIA was capable of multiplex quantifying proteins with accuracy comparable to targeted methods.	[17]
Uptake transporters	Human hepatic membrane proteins extraction		Total protein in the sample	The quantification results obtained with the DIA method was consistent with the measurements from a targeted method and data from the literature.	[18]
DMEs, transporters	Mice liver and kidney fractions	Label-free and relative quantification for DIA; Labeling and absolute quantification for PRM	Stable isotope-labeled internal standard peptides for PRM	Two rounds of proteomics analysis: a DIA study for identifying proteins that differentially expressed between the control and the model groups; a PRM study for quantifying the expression changes of proteins identified by the DIA analysis.	[23]

HLM: Human liver microsomes; HIM: Human intestine microsomes; HKM: Human kidney microsomes; HLS9: Human liver S9 fractions; CYP: cytochrome P450; UGT: uridine-diphosphate glucuronosyl transferase; TPA: total protein approach; MRM: multiple reaction monitoring; SRM: selected reaction monitoring; DIA: data independent acquisition; PRM: parallel reaction monitoring.