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The technology platforms for proteome analysis have advanced considerably over the last few years. Due to these improvements the number of studies on the analysis of the proteome/peptidome with the aim of defining biomarkers has escalated. In this review, we will summarise the technical aspects that relate to the proteomics field targeting the discovery of biomarkers for disease diagnosis. We will describe the course from biomarker discovery or 'potential' biomarkers to those that are clinically important. We also present several examples of successful proteomic studies that have defined 'biomarker patterns' for clinical applications, focussed on urine as a material source and capillary electrophoresis coupled mass spectrometry as a technology. Finally, current challenges and considerations for future studies will be discussed.