title: Choice of LC-MS methods for the absolute quantification of drug-metabolizing enzymes and transporters in human tissue: a comparative cost analysis.
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.
authors: Manchester Pharmacy School, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, UK.
authors: Hajar
authors: H
authors: Al Feteisi
authors: Brahim
authors: B
authors: Achour
authors: Jill
authors: J
authors: Barber
authors: Amin
authors: A
authors: Rostami-Hodjegan
mesh_terms: D002853:Chromatography, Liquid / Q000191:economics / Q000379:methods*; D003362:Cost-Benefit Analysis; D004798:Enzymes / Q000032:analysis*; D006801:Humans; D013058:Mass Spectrometry / Q000191:economics / Q000379:methods*; D026901:Membrane Transport Proteins / Q000032:analysis*; D010455:Peptides / Q000032:analysis; D011506:Proteins / Q000032:analysis; D020543:Proteome / Q000032:analysis; D040901:Proteomics / Q000379:methods
chemical_list: D004798:Enzymes; D026901:Membrane Transport Proteins; D010455:Peptides; D011506:Proteins; D020543:Proteome