Surface-Enhanced Laser Desorption/Ionization Mass Spectrometry for Protein and Peptide Profiling of

Recently, Ciphergen Biosystems (Fremont, CA, USA) has developed a technique called surface-enhanced laser desorption/ionization (SELDI). This technology is based on ProteinChips� with chemically or biochemically modified surfaces for the selective retention and enrichment of protein subsets from a complex protein mixture. The proteins or peptides of interest can then be identified by using mass spectrometry (SELDI-MS). This highly sensitive and high-throughput technique can detect minute differences in proteins and peptide profiles between biological samples. The versatility of this technology enables a wide variety of applications in basic research, clinical, proteomic, and drug discovery such as identification of novel biomarkers associated with certain diseases or treatments. Many disease biomarkers or biomarker patterns have been identified using SELDI-MS in various laboratories. In this chapter, we provide a general guide to the profiling of proteins or peptides as well as biomarker discovery using the most common body fluids such as serum/plasma, nipple aspiration fluid, and urine.