Table 1.

Peptide probe sequences, selected ions for quantification and limit of quantification in isolated brain capillaries of each protein with LC-MS/MS.

				MRM transition
Accession No.	Synonym (gene name)	Probe sequence	Peptide mass	Q1	Q3-1	Q3-2	Q3-3	Q3-4	Limit of quantification(fmol/μg)
Q3TZN9	Mrp4	APVLFFDR	963.5	482.8	796.4	697.4	584.3	437.2	0.0460
	(Abcc4)	APVL*FFDR	970.5	486.3	803.4	704.4	584.3	437.2
O88909	Oat3	YGLSDLFR	969.5	485.8	807.4	750.4	637.3	550.3	0.163
	(Slc22a8)	YGLSDL*FR	976.5	489.3	814.4	757.4	644.3	557.3
Q9EP96	Oatp1a4	EVATHGVR	867.5	434.7	640.4	569.3	468.3	331.2	0.441
	(Slco1a4)	EVATHGV*R	873.5	437.7	646.4	575.5	474.3	337.2
Q9EPT5	Pgt	IFVDYGR	869.0	435.2	756.4	609.3	510.2	395.2	0.312
	(Slco2a1)	IFV*DYGR	875.0	438.2	762.4	615.3	510.2	395.2

The selected peptides were synthesized and their purity was checked with HPLC-UV according to the previous report [26]. The MRM transitions were determined from MS/MS spectra obtained by direct infusion of 1 μM peptide solution at a flow rate of 5 μL/min with a syringe pump (Harvard) into the mass spectrometer. Doubly charged precursor ions were selected (Q1). Four transitions per peptide (Q3-1, -2, -3 and -4), corresponding to high-intensity fragment ions, were selected. The declustering potentials and collision energies were optimized to maximize signal strength. For the stable isotope-labeled peptides, precursor ions and transitions corresponding to those of the unlabeled peptides were selected, with the same declustering potentials and collision energies as for the unlabeled peptides. Bold letters with asterisks indicate amino acid residues labeled with stable isotope (¹³C and¹⁵N). The limit of quantification was defined as the protein expression level which would give a peak area count of 5000 in the chromatogram when a brain capillary sample is measured by LC-MS/MS.