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The identification of biomarkers of disease and toxicity allows scientist understand the biochemical pathways effected by these disease states.Metabonomics employs an unbiased statistical approach to the analysis of spectrometric or spectroscopic data enabling the visualization of metabolic changes as a result of disease state progression or a toxic insult in a whole body system; With LC/MS, GC/MS or NMR being the predominant analytical platforms in this discipline.In this paper we discuss the benefits and drawback of employing a high pH aqueous mobile phase for the LC/MS analysis.Rat urine samples collected following the administration of hydrazine were analysed by both low and high pH LC/MS and the metabonomic profiles compared.