ProteinChip technology, a suite of analytical tools that includes retentate chromatography, on-chip protein characterization, and multivariate analysis, allows researchers to examine patterns ofprotein expression and modification. Based on the surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) approach, ProteinChip technology has been pioneered by researchers at Ciphergen Biosystems (Fremont, CA, USA), as well as by users of Ciphergen's commercial embodiment of this technology the ProteinChip Biomarker System. This report will begin with a background of the technology and describe its applications in clinical proteomics and will then conclude with a discussion of tools and strategies to mine the large amounts of data generated during the course of a typical clinical proteomics study.