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An acetonitrile based protein extraction method was developed that demonstrated high efficient and effective removal of high abundant proteins from both human and murine serum. The protein content of the extract was characterised using gel electrophoresis, the Bradford assay and liquid chromatography tandem mass spectrometry (LC-MS/MS) with database searching. Selected reaction monitoring (SRM) analysis was used to quantify the levels of high abundant serum proteins to further validate the extraction methodology. The ACN depletion method, in combination with artificial neural networks (ANNs) data mining software, was applied to a murine growth hormone (GH) gene doping study with the aim of identifying biomarker ions capable of detecting gene doping. The LC-MS and ANNs analysis approach failed to conclusively identify a biomarker to gene doping in the mouse model. However, the application of the same technique to serum from a rhGH administration study in humans, returned models capable of discriminating between rhGH treated placebo states. The ion identified as being the most discriminatory was characterised using mass spectrometry, and was derived from the protein leucine-rich a-2-glycoprotein (LRG). Multiple LRG related tryptic peptides were identified as being up-regulated upon dosing with recombinant human GH (rhGH). A high throughput LC-MS/MS and SRM approach was developed to quantify proteins in human serum. The approach was validated by comparison of LC-MS/MS derived APO A1 concentrations with those obtained using established clinical analyser technologies. The LC-MS/MS methodology was applied to a large cohort of 257 serum samples from two rhGH administration studies performed at Royal Free Hospital . The two administrations included serum samples from 15 individuals who had been dosed daily with rhGH. Serum concentrations of the established rhGH biomarker insulin-like growth factor-I (IGF-I) were quantified by LC-MS/MS and compared well with those determined using two different immunoassay-based methodologies. Serum concentrations of the LRG protein were measured simultaneously with IGF-I and appeared to increase in 14 of the 15 rhGH dosed individuals. Combining the LRG and IGF-I data further increased the separation of rhGH treated and placebo states within each individual, and the application of ANNs analysis showed that the combination of the two proteins increased the discrimination characteristics over using IGF-I alone. The murine equivalent of the LRG protein was identified and SRM transitions for a tryptically derived peptide were developed, along with transitions for monitoring a peptide from the murine IGF-I protein. These transitions were used to quantify the two proteins in the remaining aliquots from a murine GH gene doping experiment, however neither protein appeared to increase in the GH +ve plasmid samples that were analysed.

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