mass spectrometry (HPLC–MS). The use of hydrophobicseparation combined with selective mass spectrometricdetection makes this a versatile analytical tool. Electrosprayis currently the most widely used ionization source. Theelectrospray interface produces singly or multiply chargeions directly from an aqueous–organic solvent system bycreating a fine spray of highly charged droplets in thepresence of a strong electric field, with the assistance of heator pneumatics. The successful formation of ions usingelectrospray ionization requires two steps: the transfer of thecompound of interest into the gas phase and the addition ofa charge to the analyte if it is not already in a charged state[1–4].HPLC–MS systems using an electrospray ion sourcecoupled with tandem mass analyzers (HPLC–ESI–MS/MS)have been applied to a wide variety of studies inpharmaceutical analysis and life sciences. With HPLC–ESI–MS/MS now considered the benchmark for measurementof drugs and their metabolites in biological matrices[5], the high selectivity of tandem mass spectrometry, withsuccessive mass filtrations, leads to little or no observedinterference even though there may be relatively highconcentrations of coextracted and coeluted matrix componentspresent. These characteristics have led to a growingtrend of high-throughput analysis that incorporates little orno sample preparation and minimal chromatographicretention [6–8].With HPLC–ESI–MS/MS having these characteristics ofhigh selectivity, sensitivity, and throughput, it is notsurprising that this technology is being increasingly usedin the clinical laboratory. A recent review by Dooley [9]reported an exponential growth from 1991 to 2001 inclinical chemistry papers that mention tandem massspectrometry. It is now accepted that HPLC–ESI–MS/MSis the method of choice for screening for inherited metabolicdisorders [10], but it can be expected that many moreapplications will follow. While many biochemical markerssuch as steroids, fatty acids, amino acids, catecholamines,and thyroxine have been measured by this analyticaltechnique [11–15]. Specific examples of clinical laboratoriesapplying HPLC–ESI–MS/MS to drug quantification arefor the therapeutic drug monitoring of immunosuppressantdrugs [16] and protease inhibitors [17], and toxicologicalinvestigations [18,19].While HPLC–ESI–MS/MS offers much promise forclinical laboratories, one issue that must be addressed inmethod development, validation, and routine use is matrixeffects. Matrix effects are the alteration of ionizationefficiency by the presence of coeluting substances. A recentpaper by Annesley [20] highlighted the importance ofunderstanding matrix effects in clinical mass spectrometryapplications, and although critical to the success of anHPLC–ESI–MS/MS analytical method, few publishedmethods adequately address this problem [21]. The aim ofthis report is to provide an overview of matrix effects andfrom a clinical laboratory perspective show how this issue