Transformations in pharmaceutical research and development, driven by innovations in multidimensional mass spectrometry-based technologies Steven H. Hoke II a, *, Kenneth L. Morand b , Kenneth D. Greis b , Timothy R. Baker b , Kevin L. Harbol c , Roy L.M. Dobson b, * a The Procter & Gamble Company, Health Care Research Center, P.O. Box 8006, Mason, OH 45040, USA b Procter & Gamble Pharmaceuticals, Health Care Research Center, P.O. Box 8006, Mason, OH 45040, USA c Procter & Gamble Pharmaceuticals, Woods Corners Research Facility, P.O. Box 191, Norwich, NY 13815, USA Received 7 May 2001; accepted 14 July 2001 Abstract In the pharmaceutical industry, there is a tremendous need for qualitative and quantitative analysis of target analytes such as peptides, proteins, drugs, metabolites, biomarkers, impurities, and degradation products in various mixtures including synthetic reactions, in vitro cultures, biological fluids, drug substances, finished products, and many others. To provide adequate specificity for analysis in these complex mixtures, multidimensional analytical techniques are required. Mass spectrometry plays a central role in many of these multidimensional approaches to mixture analysis because it provides an unparalleled combination of sensitivity and specificity that is useful for both molecular identification and quantitative applications. Recent innovations in mass spectrometry and industrial implementation of these advances have transformed many aspects of pharmaceutical research and development. Data that were previously unattainable, or were not collected due to exorbitant cost or time constraints, can now be obtained using mass spectrometry-based technologies. The impact of these innovations has been most dramatically felt in early stages of discovery, as more data are available to make critical decisions, such as selecting compounds for advancement to costly preclinical and clinical trials. New MS technologies have also accelerated the progression of drug candidates through development and toward regulatory approval. Here, five major categories of pharmaceutical applications of mass spectrometry are reviewed. They are new chemical entity characterization, biomacromolecule characterization, bioanalytical quantitation, metabolite identification, and impurity and degradation product identification. A brief historical perspective and evolution of technologies for each application area are presented. Those discussions are followed with a description of the current strategies for implementation of the tremendous capabilities of the state-of-the-art approaches, along with representative applications. In addition, emerging technologies for each application area are presented to indicate the future directions of instrumentation for mixture analysis in the pharmaceutical industry. (Int J Mass Spectrom 212 (2001) 135–196) © 2001 Elsevier Science B.V. Keywords: Mixture analysis; Mass spectrometry; Liquid chromatography; Gas chromatography; Pharmaceuticals 1. Introduction Early applications of mass spectrometry, such as analysis of petrochemicals in the 1950s [1], utilized the sensitivity and selectivity of the techniques avail- able during that period. It was apparent that even a single stage of mass analysis provided a great deal of * Corresponding authors. E-mail: hoke.sh@pg.com, dobson.rl@ pg.com Dedicated to R. Graham Cooks on the occasion of his sixtieth birthday. 1387-3806/01/$20.00 © 2001 Elsevier Science B.V. All rights reserved PII S1387-3806(01)00499-7 International Journal of Mass Spectrometry 212 (2001) 135–196 www.elsevier.com/locate/ijms