ProteinChip technology, a suite of analytical tools that includes retentate chromatography, on-chip protein characterization, and multivariate analysis, allows researchers to examine patterns of protein expression and modification. Based on the surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) approach (17), ProteinChip technology has been pioneered by researchers at Ciphergen Biosystems (Fremont, CA, USA), as well as by users of Ciphergens 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.

Mass spectrometry is increasingly being applied to sift through complex protein mixtures to find biomarker patterns that can be used for diagnosis, prognosis, or monitoring of disease. Although some studies have directly examined tumor tissue, most have targeted easily accessible fluids, including urine, nipple aspirate fluid, cerebrospinal fluid, plasma, and most commonly, serum. A few studies have been performed on high-resolution instruments using a matrix-assisted laser desorption/ ionization (MALDI) ion source and a time-of-flight (TOF) ion detector. The majority, however, have used lower resolution instruments and surface-enhanced laser desorption/ionization (SELDI), a variant of MALDI that relies on commercially prepared surfaces (ProteinChips ®), to perform protein isolation or separation.