Raw data contour plots and data processing. The individual steps of the data processing are illustrated here, showing data obtained after screening urine from one patient. The initial raw data (A) are examined for signals that fit the criteria of “real polypeptide” signals, which are collected (B) and deposited in a peak list (D, left panel). Subsequently, a charge is assigned to each of these signals, conjugated peaks are combined as indicated by the red arrows, and as a result a spectrum based on mass and normalized migration time is obtained as graphically depicted in C. This spectrum contains the information on all peaks (a partial list is shown in D, right panel), including time, mass, intensity and signal-to-noise ratio.