Proteomic analysis tissue, mass spectrometry

In 2001, both Lawrie et al. and Moskaluk coupled LCM (laser capture microdissection) with 2D gel proteomics to recover proteins from laser captured micro-dissected tissue in a form that can be used in 2D gel analysis and mass spectrometry. This may provide valuable information for protein profiling and databasing of human tissues in healthy and disease states. 

When fresh or frozen tissue is used for proteomic analyses, the results cannot be related directly to the clinical course of diseases in a timely manner. Instead, researchers frequently reduce the number of interesting proteins to a manageable number and then attempt to use immunohistochemistry to understand the implications of proteomic changes in archival formalin-fixed, paraffin-embedded (FFPE) tissue for which the clinical course has been established.3 Unfortunately, immunohistochemistry is a semiquantitative pro-teomic method, and the choice of interesting proteins must occur without advance knowledge of the clinical course of the disease or the response to therapy. If routinely fixed and embedded archival tissues could be used for standard proteomic methods such as 2-D gel electrophoresis and mass spectrometry (MS), these powerful techniques could be used to both qualitatively and quantitatively analyze large numbers of tissues for which the clinical course has been established. However, analysis of archival FFPE tissues by... 

Stewart NA, Veenstra TD. Sample preparation for mass spectrometry analysis of formalin-fixed paraffin-embedded tissue proteomic analysis of formalin-fixed tissue. Methods Mol. Biol. 2008 425 131-138. 

Groseclose MR, Massion PP, Chaurand P, et al. High-throughput proteomic analysis of formalin-fixed paraffin-embedded tissue microarrays using MALDI imaging mass spectrometry. Proteomics 2008 8 3715-3724. 

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... 

However, IHC as a practical method continues to evolve with increasing demands for standardization, and for true quantification of protein analytes by weight, in the context of their cellular microenvironment. Further studies combining proteomics by mass spectrometry and IHC are likely to lead to the refinement of both methods in the analysis of FFPE tissues. The end result may be the creation of a broader field that defines and quantifies protein expression at a cellular level, incorporating the advantages of the wide spectrum of proteins demonstrable by mass spectrometry and the precise localization offered by IHC. 

Mass spectrometry has been applied mainly in proteome research, but also in discovery and quantitation of neuropeptides that are involved in pain mechanisms, such as nocistatin, substance P, or verification of, for example, the structure of endogenous morphine in the central nervous system. Some proteomics studies of pain are aimed at the search for pain markers in cerebrospinal fluid, as it may reflect changes in brain and spinal cord functioning. Another research area concerns proteome analysis in cancer pain using spinal cord tissue and animal models. 

Pierson J, Norris JL, Aerni HR, Svenningsson P, Caprioli RM, et al. 2004. Molecular profiling of experimental Parkinson s disease direct analysis of peptides and proteins on brain tissue sections by MALDI mass spectrometry. J Proteome... 

The term proteome means the total protein complement of a genome, and pro-teomics means the analysis for proteome. The combination of two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) is a proteomic method of high-throughput analysis of protein expression. By using this 2-DE and MS, proteomic studies have identified many proteins that may be involved in the pathogenic mechanism of cancers. These studies analyzed cancer cell lines, as well as cancer tissues or serum from patients. 

Ha GH, Lee SU, Kang DG et al. Proteome analysis of human stomach tissue separation of soluble proteins by two-dimensional polyaerylamide gel eleetrophoresis and identification by mass spectrometry. Electrophoresis 2002 23 2513-2524. 

Kim J, Kim SH, Lee SU et al. Proteome analysis of human liver tumor tissue by two-dimensional gel eleetrophoresis and matrix-assisted laser desorption/ionization-mass spectrometry for identification of disease-related proteins. Electrophoresis 2002 23 4142 156. 

Reyzer, M. L., and Caprioli, R. M. (2005b). MALDI mass spectrometry for direct tissue analysis A new tool for biomarker discovery. J. Proteome Res. 4 1138-1142. 

Liu N, Liu F, Xu B, Gao Y, Li X, Wei K, Zhang X, Yang S (2008) Establishment of imaging mass spectrometry for biological tissue and its application on the proteome analysis of micro-wave radiated hippocampus. Chin J Anal Chem 36(4) 421—425... 

Liang CR, Leow CK, Neo JC, Tan GS, Lo SL, Lim JW, et al. Proteome analysis of human hepatocellular carcinoma tissues by two-dimensional difference gel electrophoresis and mass spectrometry. Proteomics 2005 5(8) 2258-2271. 

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