Mass spectrometric detection is gradually replacing ultraviolet (UV) as the method of choice in bioanalysis, especially in the area of early drug discovery where high sensitivity and rapid sample throughput is required and where samples are frequently pooled or "cocktailed" prior to dosing or analysis. The change from UV to MS detection requires a significant change in approach since the use of MS poses a number of unexpected problems and limitations which relate to instrument design and the ionisation process. Whilst electrospray ionisation (ESI) allows the analyst to focus on the analyte of interest it is non-selective and blind to background effects which can in certain instances alter the response of the compound of interest, leading to inaccurate data. In addition, when analysing compound mixtures, a number of precautions need to be taken since adduct formation in the MS source, the highly ESI responsive nature of formulating agents and the effect of the isotopic distribution in organic drug molecules can all lead to the production of compromised data. Whilst many of these problems can be minimised or avoided this often results in a complex and inflexible analysis system. Ultimately the analyst has to assess the degree of risk involved and take actions which reflect the use the data.