A study protocol for quantitative targeted absolute proteomics (QTAP) by LC-MS/MS: application for inter-strain differences in protein expression levels of transporters, receptors, claudin-5, and marker proteins at the blood–brain barrier in ddY, FVB, and C57BL/6J mice

Table 3 An example of optimized analytical conditions for multiplexed SRM/MRM analysis in API5000 and QTRAP5500

Molecule name	AA Seq.	St/IS	Transition number	Q1 m/z	Q3 m/z	Dwell time (msec)	DP	CE
Mdr1a	NTTGALTTR	St	1	467.8	719.4	10	51	30
			2	467.8	618.4	10	51	30
			3	467.8	561.3	10	51	30
			4	467.8	377.2	10	51	30
	NTTGAL* TTR	IS	1	471.3	726.4	10	51	30
			2	471.3	625.4	10	51	30
			3	471.3	568.3	10	51	30
			4	471.3	377.2	10	51	30
Tfr1	SSVGTGLLLK	St	1	487.8	800.5	10	56	25
			2	487.8	701.5	10	56	23
			3	487.8	644.4	10	56	20
			4	487.8	543.4	10	56	21
	SSVGTGLLL*K	IS	1	491.3	807.5	10	56	25
			2	491.3	708.5	10	56	23
			3	491.3	651.4	10	56	20
			4	491.3	550.4	10	56	21
Na⁺/K⁺-ATPase	AAVPDAVGK	St	1	414.2	685.4	10	50	17
			2	414.2	586.3	10	50	17
			3	414.2	489.3	10	50	27
			4	414.2	374.2	10	50	27
	AAVPDAV* GK	IS	1	417.2	691.4	10	50	17
			2	417.2	592.3	10	50	17
			3	417.2	495.3	10	50	27
			4	417.2	380.2	10	50	27

Bold letters with asterisks indicate amino acid residues that are labeled with a stable isotope (¹³C and ¹⁵ N).
Abbreviations: AA amino acid; St standard; IS internal standard; DP declustering potential; CE collision energy.

ISSN: 2045-8118