Introduction: The quantification of drug-metabolizing cytochrome P450 (P450) and uridine 5ꞌ-diphospho-glucuronosyltransferase (UGT) 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 (AQUA) 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 (QconCAT) 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.