Separation of human urine for proteome analysis. The left panel shows a 2-D gel (courtesy of Visith Thongboonkerd). Molecular mass (in kDa) is indicated on the left. Most of the low-molecular-weight proteins remain unseparated in the front. Polypeptides in this mass range can be analyzed by CE-MS, as indicated in the right panel. Mass (in kDa) is plotted against migration time (in min), the intensity of the peaks is indicated by height and color.

Digital data compilation. Individual datasets from CE-MS analysis of human urine samples were calibrated using internal standards. The left panel displays these data in a 3-dimensional contour plot: mass (in kDa on a logarithmic scale) plotted against normalized migration time (min). The MS signal intensity is represented by the peak height as well as color. The data were digitally compiled to a group-specific polypeptide pattern, shown in the right panel.

Protein patterns of healthy volunteers (NK), and patients with diabetic nephropathy (DN) and IgA nephropathy (IgA-N), respectively. Upper panel: compiled patterns consisting of 20 to 100 single measurements, molecular mass (0.8–25 kDa, on a logarithmic scale) against normalized migration time (18–45 min), peak height and color encode the signal intensity. Three middle panels: only selected candidate disease-specific biomarkers are displayed on the same scale. An array of general biomarkers for kidney disease present in DN and IgA-N can be defined. In addition, biomarkers that are specific for DN or IgA-N can be identified, as indicated on the right-hand side. Lower panel: zoom of the upper patterns (all peptides analysed, 1.5–5 kDa, 19–35 min). As evident, several additional biomarkers (of mostly lesser statistical value) are present, which can be further exploited.