The development of new methods of chemical enzymatic drug targeting (c
hemical delivery systems and soft drugs) relies on specific and sensit
ive analytical techniques. High-performance liquid chromatography has
been a powerful technique that can separate complex mixtures of chemic
al species involved in the enzymatic and/or chemical transformation in
vivo and in vitro to produce the targeted drug. The successful chemic
al separation requires specificity of interaction of the chromatograph
ic column and the solute to resolve compounds with characteristic (som
etimes subtle) chemical differences. Differing lipophilicity and the i
onic or neutral nature of the species are the primary factors to be co
nsidered during method development. Improving the specificity toward t
he analyte has often been necessary to provide adequate detection limi
ts for tissue samples derived from the site of action. Chromatography
lacks, however, the power of identifying unknown species. Mass spectro
metry, both coupled with chromatography and as a technique providing d
irect specificity, may represent a viable solution. These issues, incl
uding future perspectives, are discussed in this review.