Proteomic analysis protein extraction studies

High-throughput proteomic methods hold great promise for the discovery of novel protein biomarkers that can be translated into practical interventions for the diagnosis, treatment, and prevention of disease. These approaches may also facilitate the development of therapeutic agents that are targeted to specific molecular alterations in diseases such as cancer. In many cases, malignant cells yield unique protein profiles when total protein extracts from such cells are analyzed by 2-D gel electrophoresis or mass spectrometry (MS) methods. Such proteomic studies have the potential to provide an important complement to the analysis of DNA and mRNA extracts from these tissues.1... 

A study of by Palmer-Toy et al.,12 summarized in Table 19.1, provides further empirical evidence of the utility of techniques coupling heating with efficient protein extraction for the proteomic analysis of FFPE tissue. A specimen from a patient with chronic stenosing external otitis was divided in half and preserved as fresh-frozen tissue or FFPE. Ten micromolar sections of the FFPE tissue were vortexed in heptane to deparaffinize the tissue and were then co-extracted with methanol. The methanol layer was evaporated, and the protein residue was resuspended in 2% SDS/lOOmM ammonium bicarbon-ate/20mM dithiothreitol (DTT), pH 8.5 and heated at 70°C for lh. After tryptic digestion, 123 total confident proteins were identified in the FFPE tissue, compared to 94 proteins identified from the fresh-frozen tissue. Hwang et al. also reported up to a fivefold increase in protein extraction efficiency for samples extracted in a Tris-HCl/2% SDS/1% Triton X-100/1% deoxycholate solution at 94°C for 30 min versus samples extracted in 100 mM ammonium bicarbonate/30% acetonitrile at the same temperature.14... 

A number of proteomic studies on archival material have utilized Liquid Tissue (Expression Pathology, Inc., Gaithersburg, MD), a commercial protein extraction kit for FFPE tissue.4,9,25-28 This kit is also based upon HIAR techniques and shares a similar work flow to the methods already discussed. Thin, typically 5-10pM, sections are cut from paraffin tissue blocks, the paraffin is removed, and the tissue deparaffinized and rehydrated in alcohols and distilled water before microdissection. The cellular material is then suspended in Liquid Tissue buffer and heated at 95°C for 90 min. Trypsin is added, and the material is digested overnight at 37°C prior to reduction with DTT and analysis by LC-MS/MS.26... 

Mouse liver has been widely used for proteome analysis by the 2DE method. (7, 8) In this study, the extracted proteins from the mouse liver tissue are used as an example. Protein spots are evaluated using the gel analysis software ProFINDER 2D (Perk-inElmer Life And Analytical Sciences, Inc., Wellesley, MA) and PDQuest (Bio-Rad Laboratories, Hercules, CA)). 

For the investigation of expression changes due to xenobiotic/toxin exposure, proteins have to be extracted from samples of body fluids, tissues or cells. For this purpose, many protein extraction protocols have been developed and adapted to different sample types (Link 1999). All protocols follow the main objective to recover as much of the proteome as possible with as little contamination by other biomaterials as possible. Sample preparation has to be performed prior to any proteomics technology used in investigative studies, or predictive toxicology. Depending on the method used for protein expression analysis, fractionation steps have to follow or have to be implemented in the extraction procedures (Wilkins et al. 1997 Rabilloud 2000 Liebler 2002). 

One of the most crucial considerations in proteomic analysis is sample preparation because this will ultimately dictate the number and type of proteins that can be processed. The first priority is to establish the precise protein system to be studied [e.g., will this be a comprehensive and exhaustive catalogue of every expressed protein within a tissue or cellular extract, or is only a small subset of a cellular proteome (e.g., only phosphoproteins or membrane-bound proteins) sufficient for analysis ]. Whether a full or partial proteome, or even a limited number of specific proteins is required for analysis, it is crucial that the extraction technique provide maximal protein recovery while preserving the integrity of the protein complex to be examined. Furthermore, the method of preparation must be totally compatible with the separation methods to be used. This is particularly important for separation technologies that are reliant on protein-protein interactions or drug/ligand/antibody, etc. interactions. Poor recovery of proteins is clearly... 

The procedure for proteomic study of archaeological proteins follows the general principles of conventional proteomics analysis, which can be divided into four main areas sample extraction and preparation, enzymatic digestion, LC separation, or sample plate spotting for... 

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