Abstract
Quantitative proteomics is an emerging technique with promising applications in the field of drug metabolism to improve the translation of in vitro, preclinical, and individual data to population pharmacokinetics. For example, quantitative proteomics data can be utilized for in vitro-in vivo extrapolation (IVIVE), in vitro model validation, and determination of interindividual and species differences. Here, we describe a detailed methodology for the quantification of cytochrome P450 (CYP) in human samples. The methodology includes the preparation of human liver microsomal samples, selection of specific surrogate peptides, protein digestion, liquid chromatography (LC) separation, and mass spectrometry (MS) quantification. The focus of this chapter is limited to targeted protein quantification using a conventional LC and a triple quadruple MS instrument in selected reaction monitoring (SRM) mode. In targeted proteomics, the membrane-anchored CYP proteins are digested in-solution to peptides, and the peptide mixtures are separated by reversed-phase LC, and peptide signals are detected by a SRM-based technique (Zhang, Liu, et al. 2011). Peptide standards (light or stable isotope-labeled) are used as calibrator and internal standards, which allows absolute quantification of peptide levels. Stepwise details are provided for the efficient implementation of the quantitative proteomics technique by experts and new researchers.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Prasad B, Achour B, Artursson P, Hop CECA, Lai Y, Smith PC, Barber J, Wisniewski JR, Spellman D, Uchida Y, Zientek MA, Unadkat JD, Rostami-Hodjegan A (2019) Toward a consensus on applying quantitative liquid chromatography-tandem mass spectrometry proteomics in translational pharmacology research: a white paper. Clin Pharmacol Ther 106(3):525–543
Achour B, Russell MR, Barber J, Rostami-Hodjegan A (2014) Simultaneous quantification of the abundance of several cytochrome P450 and uridine 5’-diphospho-glucuronosyltransferase enzymes in human liver microsomes using multiplexed targeted proteomics. Drug Metab Dispos 42(4):500–510
MacLean B, Tomazela DM, Shulman N, Chambers M, Finney GL, Frewen B, Kern R, Tabb DL, Liebler DC, MacCoss MJ (2010) Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26(7):966–968
Zhang H, Liu Q, Zimmerman LJ, Ham AJ, Slebos RJ, Rahman J, Kikuchi T, Massion PP, Carbone DP, Billheimer D, Liebler DC (2011) Methods for peptide and protein quantitation by liquid chromatography-multiple reaction monitoring mass spectrometry. Mol Cell Proteomics 10(6):M110.006593
Cieslak A, Kelly I, Trottier J, Verreault M, Wunsch E, Milkiewicz P, Poirier G, Droit A, Barbier O (2016) Selective and sensitive quantification of the cytochrome P450 3A4 protein in human liver homogenates through multiple reaction monitoring mass spectrometry. Proteomics 16(21):2827–2837
Groer C, Busch D, Patrzyk M, Beyer K, Busemann A, Heidecke CD, Drozdzik M, Siegmund W, Oswald S (2014) Absolute protein quantification of clinically relevant cytochrome P450 enzymes and UDP-glucuronosyltransferases by mass spectrometry-based targeted proteomics. J Pharm Biomed Anal 100:393–401
Kamiie J, Ohtsuki S, Iwase R, Ohmine K, Katsukura Y, Yanai K, Sekine Y, Uchida Y, Ito S, Terasaki T (2008) Quantitative atlas of membrane transporter proteins: development and application of a highly sensitive simultaneous LC/MS/MS method combined with novel in-silico peptide selection criteria. Pharm Res 25(6):1469–1483
Kawakami H, Ohtsuki S, Kamiie J, Suzuki T, Abe T, Terasaki T (2011) Simultaneous absolute quantification of 11 cytochrome P450 isoforms in human liver microsomes by liquid chromatography tandem mass spectrometry with in silico target peptide selection. J Pharm Sci 100(1):341–352
Wang MZ, Wu JQ, Dennison JB, Bridges AS, Hall SD, Kornbluth S, Tidwell RR, Smith PC, Voyksner RD, Paine MF, Hall JE (2008) A gel-free MS-based quantitative proteomic approach accurately measures cytochrome P450 protein concentrations in human liver microsomes. Proteomics 8(20):4186–4196
Vrana M, Whittington D, Nautiyal V, Prasad B (2017) Database of optimized proteomic quantitative methods for human drug disposition-related proteins for applications in physiologically based pharmacokinetic modeling. CPT Pharmacometrics Syst Pharmacol 6(4):267–276
Achour B, Al-Majdoub ZM, Al Feteisi H, Elmorsi Y, Rostami- Hodjegan A, Barber J (2015) Ten years of QconCATs: application of multiplexed quantification to small medically relevant proteomes. Int J Mass Spectrom 391:93–104
Bhatt DK, Prasad B (2018) Critical issues and optimized practices in quantification of protein abundance level to determine interindividual variability in DMET proteins by LC/MS/MS proteomics. Clin Pharmacol Ther 103(4):619–630
Shirasaka Y, Chaudhry AS, McDonald M, Prasad B, Wong T, Calamia JC, Fohner A, Thornton TA, Isoherranen N, Unadkat JD, Rettie AE, Schuetz EG, Thummel KE (2016) Interindividual variability of CYP2C19-catalyzed drug metabolism due to differences in gene diplotypes and cytochrome P450 oxidoreductase content. Pharm J 16(4):375–387
Tanner JA, Prasad B, Claw KG, Stapleton P, Chaudhry A, Schuetz EG, Thummel KE, Tyndale RF (2017) Predictors of variation in CYP2A6 mRNA, protein, and enzyme activity in a human liver bank: influence of genetic and nongenetic factors. J Pharmacol Exp Ther 360(1):129–139
Drozdzik M, Busch D, Lapczuk J, Muller J, Ostrowski M, Kurzawski M, Oswald S (2019) Protein abundance of clinically relevant drug transporters in the human liver and intestine: a comparative analysis in paired tissue specimens. Clin Pharmacol Ther 105(5):1204–1212
Prasad B, Vrana M, Mehrotra A, Johnson K, Bhatt DK (2017) The promises of quantitative proteomics in precision medicine. J Pharm Sci 106(3):738–744
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Takahashi, R.H., Achour, B., Prasad, B. (2021). Quantitative Determination of Cytochrome P450 Using LC-MS/MS. In: Yan, Z., Caldwell, G.W. (eds) Cytochrome P450. Methods in Pharmacology and Toxicology. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1542-3_3
Download citation
DOI: https://doi.org/10.1007/978-1-0716-1542-3_3
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-1541-6
Online ISBN: 978-1-0716-1542-3
eBook Packages: Springer Protocols