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Choice of LC-MS Methods for the Absolute Quantification of Drug-Metabolizing Enzymes and Transporters in Human Tissue: a Comparative Cost Analysis

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Abstract

The quantification of drug-metabolizing enzymes and transporters is important for in vitro-in vivo extrapolation (IVIVE) of xenobiotic clearance, which has become an integral part of drug development. There are different mass spectrometry-based techniques used for quantitative proteomics, and as more laboratories are opting for the use of these methods, selecting the most appropriate tool is becoming a concern. For the first time, we attempt to determine the significance of cost of different LC-MS methods of quantitative analysis of these proteins and to present a framework to objectively assess the choice of the techniques. Based on our analysis, quantification using labeled internal standards is more expensive per sample but provides higher quality data than label-free quantification. Quantification using absolute quantification synthetic peptides is the approach of choice for analyzing less than nine proteins, whereas when quantifying a defined set of proteins (10–50), such as enzymes, in a reasonably large number of samples (20–100), the quantification concatemer technique is more economical, followed by label-free quantification. When analyzing proteomes or sub-proteomes (≥500 proteins), label-free quantification is more cost-effective than the use of labeled internal standards. A cost-benefit approach is described to assess the choice of the most appropriate mass spectrometry-based approach for the quantification of proteins relevant to IVIVE.

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Abbreviations

P450:

Cytochrome P450

UGT:

Uridine 5′-diphospho-glucuronosyltransferase

QconCAT:

Quantification concatemer

AQUA:

Absolute quantification

PSAQ:

Protein standards for absolute quantification

SRM:

Selected reaction monitoring

LC-MS:

Liquid chromatography in conjunction with mass spectrometry

MSMS:

Tandem mass spectrometry

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Acknowledgments

The authors thank Manchester Pharmacy School, the University of Manchester, for financial support, Zubida Al-Majdoub for participating in the assessment of different quantitative techniques used for absolute quantification, David Knight and Stacy Warwood from the Faculty of Life Sciences at the University of Manchester for advice on instrument time cost, and Eleanor Savill for assisting in the preparation of the manuscript.

Conflicts of Interest

The authors declare no conflicts of interest.

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Authors and Affiliations

  1. Manchester Pharmacy School, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, UK

    Hajar Al Feteisi, Brahim Achour, Jill Barber & Amin Rostami-Hodjegan

  2. Simcyp Limited, a Certara Company, Blades Enterprise Centre, Sheffield, S2 4SU, UK

    Amin Rostami-Hodjegan

Authors
  1. Hajar Al Feteisi
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  2. Brahim Achour
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Correspondence to Amin Rostami-Hodjegan.

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Al Feteisi, H., Achour, B., Barber, J. et al. Choice of LC-MS Methods for the Absolute Quantification of Drug-Metabolizing Enzymes and Transporters in Human Tissue: a Comparative Cost Analysis. AAPS J 17, 438–446 (2015). https://doi.org/10.1208/s12248-014-9712-6

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