An image processing system extracts parts or characteristics of interest from prepared biological samples One suitable use of the image processing system is to find biomarkers. But many other suitable uses are possible. Some components of the system include image preprocessing (data interpolation, retention time alignment, image noise filtering, background estimation, and formation of a composite image); image feature extraction (peaks, isotope groups, and charge groups); and computation of feature characteristics and expression statistics, differential expression, and non-differential expression. Outputs of the system include a candidate list of parts or characteristic of interest for aiding further discovery.