Analysis of Mass Spectrometry Profiles of the Serum Proteome

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. To date, the technology has primarily been applied to search for cancer biomarkers, with some success. It is now clear that SELDI profiling of the proteome can successfully detect anonymous proteins that are produced at higher (or lower) concentrations in the tissues or fluids of cancer patients than in healthy individuals (1)(2)(3). There is also preliminary evidence that we may be able to discover patterns that can reliably distinguish cancer patients from healthy individuals (4)(5)(6)(7).