Protein quantification by the SELDI-TOF-MS–based ProteinChip® System

Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) represents the successful combination of retentate chromatography and mass spectrometry, and this technology is an integral part of Ciphergen's ProteinChip System, which was designed to answer biomedical questions by performing protein analyses on a single experimental platform. The quantification capability of the ProteinChip System is essential in all proteomic applications for which this technology is used. Here we describe methods and results for three short experiments mimicking realistic analytical challenges to provide practical examples of quantification.