International Journal of Mass Spectrometry 238 (2004) 85–97 SFC/MS in drug discovery at Pfizer, La Jolla Ben Bola ˜ nos ∗ , Michael Greig, Manuel Ventura, William Farrell, Christine M. Aurigemma, Haitao Li, Terri L. Quenzer, Kathleen Tivel, Jessica M.R. Bylund, Phuong Tran, Catherine Pham, Doug Phillipson Pfizer Global Research and Development, La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA Received 15 November 2003; accepted 22 November 2003 Available online 27 September 2004 Abstract We report the use of supercritical fluid chromatography/mass spectrometry (SFC/MS) for numerous applications in drug discovery at Pfizer, La Jolla. Namely, SFC/MS has been heavily relied upon for analysis and purification of a diverse set of compounds from the in-house chemical library. Supporting high-speed SFC/MS quality control of the purified compounds is made possible at high flow rate SFC along with time-of-flight mass detection. The flexibility of SFC/MS systems has been extended with the integration of an atmospheric pressure photoionization source (APPI) for use with more non-polar compounds and enhancements in signal to noise. Further SFC/MS applications of note include chiral analysis for purification and assessment of enantiomers and SFC/MS analysis of difficult to separate hydrophobic peptides. © 2004 Elsevier B.V. All rights reserved. Keywords: Supercritical fluid; Mass spectrometry; Peptide; Photoionization 1. Introduction Supercritical fluid chromatography coupled with mass spectrometry (SFC/MS) was first reported in 1978 by Ran- dall and Wahrhaftig and the first analysis of pharmaceuti- cals using packed column SFC/MS was reported in 1985 by Crowther and Henion [1,2]. Between 1985 and 1997, the science progressed at a moderate pace and is summa- rized in an excellent review by Combs [3]. Since then, packed column SFC/MS has progressed from being a unique tool for analyzing specific problems on custom systems, to a general use analytical tool in the pharmaceutical industry. A current review of SFC/MS technologies could fill this edition, so in order to limit the scope of this paper, we will discuss only applications from our labs at Pfizer in La Jolla. Within the drug discovery process, SFC/MS has made con- tributions from the analysis of crude combinatorial library ∗ Corresponding author. Tel.: +1 858 526 4861; fax: +1 858 678 8156. E-mail address: ben.bolanos@pfizer.com (B. Bola˜ nos). mixtures, including development of ultra-fast SFC/MS for post-purification analysis, to chiral analysis for medicinal chemistry. We have coupled SFC with atmospheric pressure pho- toionization (APPI) mass spectrometry as an alternative method for library analysis and analysis of difficult non-polar compounds. Application of SFC/MS/MS for use in ADME analysis has been previously reported by Hoke et al., although such work is not presented in this review [4,5]. Lastly, we have used SFC/ESI-MS for the analysis of peptides and cy- tochrome C (both the whole protein and a digest) to extend its application to separation/detection of hydrophobic com- pounds. LC/MS is used extensively in drug discovery for com- pound purification, purity assessment, compound identifica- tion, pharmacokinetic studies, and a variety of proteomics applications, to name a few. However, in such an exhaustive use of LC/MS, some of its limitations, including the speed of LC separation and its application to highly hydrophobic compounds have been noted. In pharmaceutical drug discov- ery, where large libraries of chemically diverse compounds 1387-3806/$ – see front matter © 2004 Elsevier B.V. All rights reserved. doi:10.1016/j.ijms.2003.11.021