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The ability to visualize the full depth of the serum proteome in a high-throughput manner is a major goal of clinical proteomics. Methodologies, which combine higher throughput with the ability to observe differential protein expression levels, have been applied to this goal. An example of such a system is the coupling of robotic sample processing to matrix-assisted laser desorption time of flight mass spectrometry (MALDI-TOF-MS). Within this paradigm is a modification of MALDI-TOF termed surface-enhanced laser desorption/ionization-TOF (SELDI-TOF). Both conventional MALDI and SELDI have been used to generate protein expression profiles reflective of potential peptide changes in serum. This information can be used to identify proteins, which may enable new diagnostic and therapeutic strategies. [ABSTRACT FROM AUTHOR]

Successful collection of tissue samples for molecular analysis requires critical considerations. We describe here our procedure for tissue specimen collection for proteomic purposes with emphasis on the most important steps, including timing issues and the procedures for immediate freezing, storage, and microdissection of the cells of interest or "tissue targets" and the lysates for protein isolation for SELDI, MALDI, and 2DGE applications. The pathologist is at the cornerstone of this process and is an invaluable collaborator. In most institutions, pathologists are responsible for "tissue custody," and they closely supervise the tissue bank. In addition, they are optimally trained in histopathology in order to they assist investigators to correlate tissue morphology with molecular findings. In recent years, the advent of the laser capture microscope, a tool ideally designed for pathologists, has tremendously facilitated the efficiency of collecting tissue targets for molecular analysis. [ABSTRACT FROM AUTHOR]