Using capillary electrophoresis (CE) as a separation technique has allowed analytes, previously difficult to separate by standard methods because they did not conform to requirements for GC or HPLC, to be separated with speed and great efficiency. The only requirements for CE analysis are that the sample is soluble in a liquid matrix and that analytes are present as positive or negative ions whilst in this matrix. This technique has been used here to analyse both clinical and environmental samples, some as cations and others boron-containing complexes as anions. Samples were analysed using a combination of CE alone, mass spectrometry alone and also coupled capillary electrophoresis/electrospray mass spectrometry (CE/ES). Clinically orientated analytes, dipeptides in urine and acylcamitines from blood spots were examined and peaks detected directly via uv absorbance. The environmental samples analysed included those which contained chromophoric or non-chromophoric herbicides as well as those containing diisocyanates. Analytes were either detected in their native form as with the dipeptides and chromophoric herbicides, or more typically after derivatisation to improve their absorbance characteristics. The exception was the non-chromophoric herbicides which were detected via indirect uv.\ud \ud CE was an experimental technique for the analysis of all these compounds, except for the dipeptides, all the others having originally been analysed using HPLC or GC methods. In each case an evaluation of the CE method was performed to determine the suitability of the method. By analysing standards in each case, it was possible to confirm that the technique was suitable for qualitative and quantitative analysis of each class of compound.\ud \ud CE proved to be a viable technique for the separation of all classes of compound dealt with in this thesis. However the method could not be relied upon to confirm the identity of these analytes by their migration time alone. To identify the analytes, experiments were carried out to couple CE with a mass spectrometer. Two techniques of mass spectrometry were used within this thesis, fast atom bombardment and electrospray but only electrospray ionisation mass spectrometry was used to couple to capillary electrophoresis and was the only mass spectrometric technique used to analyse clinical and environmental samples. CE instruments were successfully coupled to an electrospray mass spectrometer which then became the detector. Mass/charge ratio measurements were obtained for each analyte used and these allowed the unambiguous identification of each analyte.\ud \ud Other work involved using CE, ES and FAI3 mass spectrometry, to develop a new technique to detect diol containing compounds. This involved complexing the diol with a boron-containing acid to produce an anion which could then be detected using ES and FAB mass spectrometric methods. This work was viewed as a possible technique for the detection of diol containing lipids found within some body fluids
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