SELDI-TOF mass spectrometry-based protein profiling of tissue samples for toxicological studies

Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) has become a popular method for protein profiling in clinical diagnosis, as well as in toxicological studies. It combines solid-phase chromatography with TOF-MS on a single platform, which enables the application of crude samples, such as plasma or tissue lysate. In this chapter, we outline two methods that enable the extraction of proteins from tissue samples for subsequent application on ProteinChip arrays. The first method is the extraction of proteins only from tissue using simply lysis buffers. The second method is helpful if proteins, as well as RNA or DNA, should be extracted from one and the same piece of tissue and is based on phenol-chloroform separation. Although initially developed for liver and kidney tissue both methods can be used for other tissue types.