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Electrospray mass spectrometry (ESI-MS), tandem massspectrometry and on-line RP-HPLC-ESI-MS were used toevaluate the composition and purity of three differentaryl ether mixtures consisting of 10 and 45 arylethers synthesized on solid support by Williamsonetherification. The libraries feature two potentialpharmacophores connected with three different spacersand serve as models for a detailed component analysis.Individual members of the library and by-products wereidentified rapidly and conveniently by product ionscans. Compound collections obtained by two differentsynthetic methods, the split/combine approach and thepremix method, showed different mass distributions inthe ESI-MS spectra. Some components were not detectedin direct ESI-MS measurements, but were found by MS/MSexperiments. Precursor ion and constant neutral lossscans allowed the identification of components withcommon structural features.