Since selective inhibition of the inducible form of cyclooxygenase (COX-2) might retain all the benefits of classical nonsteroidal antiinflammatory agents while avoiding the major side effects associated with inhibition of the constitutive isoform COX-1, COX-2 has become an important target for the discovery and development of new antiinflammatory drugs. To aid in the discovery and characterization of such selective inhibitors, we have applied a mass spectrometry-based screening technique, pulsed ultrafiltration mass spectrometry, using COX-2 as the target. In a blind study, 18 samples enriched with one or more inhibitors of COX-2 were evaluated. The matrixes for the test samples consisted of DMSO, r DMSO solutions of a plant extract, or a bacterial fermentation broth extract. The composition of the samples was unknown during the assays, as were the concentrations of the COX-2 inhibitors. A soluble recombinant form of human COX-2 was incubated with each sample, and then an aliquot of each mixture was injected into the stirred ultrafiltration chamber fitted with a 30000 MW cutoff ultrafiltration membrane. After the unbound and weakly bound compounds were washed away, the ligand-receptor complexes were disrupted using an acidified 10% methanol solution. The released ligands were trapped on a C18 cartridge and then identified using liquid chromatography-negative ion electrospray mass spectrometry with the trapping cartridge as the HPLC column. Neither the plant matrix nor the fermentation broth extract were found to interfere with the assay. Two or three ligands for COX-2 were identified in each sample, which included polar and nonpolar compounds and inhibitors with IC50 values ranging from 100 microM to 10 nM.