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Biochemical markers (i.e., biomarkers) are of key importance to guide clinical decisions and public health policies by enabling early detection, accurate diagnosis and/or prevention of human diseases. However, major challenges remain due to the limited clinical utility of many biomarkers and the lack of robust analytical methods for their reliable measurements in a routine clinical setting that is also suitable to large-scale epidemiological studies. This thesis includes two major research themes involving the analysis of known biomarkers that lack appropriate methods, and the discovery of new biomarkers for complex disease conditions. In particular, this thesis describes the (1) development and validation of robust analytical methods based on capillary electrophoresis (CE) with photometric detection for the measurement of inorganic anions in volume-restricted biofluids; and (2) characterization of the sweat metabolome in infants and identification of sweat biomarkers in asymptomatic cystic fibrosis (CF) infants using multisegment injection-capillary electrophoresis-mass spectrometry (MSI-CE-MS). Chapter II introduces a simple CE assay that is remarkably selective for the analysis of sulfate, sulfite and chloride, which was applied in a pilot study to investigate the role of urinary sulfate as a biomarker for kidney stone risk assessment in children. Chapter III introduces a novel CE method for assessing iodine nutrition, which is followed by an inter-method comparison with inductively coupled plasma-mass spectrometry as described in Chapter IV. This led to the development of a fully validated CE method for monitoring the prevalence of iodine deficiency on a population level as required for global health initiatives. Chapter V demonstrates that more than 64 endogenous and exogenous compounds are present in the sweat of screen-positive CF infants, including a panel of differentiating metabolites that are associated with CF status, as well as treatment responsivity to nutritional and/or drug intervention. In summary, this thesis has contributed novel analytical methods suitable for routine biomarker analysis, in addition to the first non-targeted characterization of the sweat metabolome from infants, which require further studies to evaluate their clinical utility as biomarkers that allow for improved diagnosis, prognosis and treatment monitoring of the highly variable CF disease spectrum. / Thesis / Doctor of Philosophy (PhD)