Proteomics and Biomarker Discovery

PROTEOMICS AS A TOOL TO TEST EFFICACY OF FUNCTIONAL FOODS 

It is currently still difficult to visualize and detect differential regulation of proteins involved in inflammatory pathways, like for example, cytokines. These are often very low abundant proteins that are secreted in the ng/mL range. Mass spectrometry has not been sensitive enough to detect relevant changes with such low concentrations (Service 2008). Therefore, 2D gel electrophoresis coupled with mass spectrometry may not yet represent the most sensitive tool to reveal effects of nutritional interventions on inflammatory pathways. 

The laboratory of Baukje de Roos is funded by the Scottish Government Rural and Environment Researeh and Analysis Directorate (RERAD). 

Arbones-Mainar, J.M., Ross, K., Rucklidge, G.J., Reid, M., Duncan, G., Arthur, J.R., Horgan, G.W., Navarro, M.A., Camicer, R., Amal, C., Osada, J., and Roos, B.D. 2007. Extra Virgin Olive Oils Increase Hepatic Fat Accumulation and Hepatic Antioxidant Protein Levels in 

Bantscheff, M., Schirle, M., Sweetman, G., Rick, J., and Kuster, B. 2007. Quantitative mass spectrometry in proteomics a critical review. Anal.Bioanal.Chem i59 1017-1031. 

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McDonald WH, Yates JR 3rd. Shotgun proteomics and biomarker discovery. Dis Markers 2002 18 99-105. 

In proteomics and biomarker discovery, complex mass spectra from single protems, protein mixtures, or protein digests are obtained. Data systems exist that aid in characterization of spectral data to identify such properties as intact protein mass, amino acid subsequences, and post-translational modifications. Fragmentation information can also be compared with peptide databases to identify structural mutations that may be present. 

Radulovic D, Jelveh S, Ryu S, et al. Informatics platform for global proteomic profiling and biomarker discovery using liquid-chromatography-tandem mass spectrometry. Mol Cell Proteomics 2004 21 21. 

He QY, Chiu JF. Proteomics in biomarker discovery and drug development. J Cell Biochem 2003 89 868-886. 

Proteomic screening, biomarker discovery, and diagnostics (discovery of molecular markers for diagnosis and monitoring disease molecular... 

MASS SPECTROMETRY-BASED PROTEOMIC APPROACHES FOR DISEASE DIAGNOSIS AND BIOMARKER DISCOVERY... 

Bichsel, V.E., Liotta, L.A., and Petricoin, E.F., 3rd, (2001) Cancer proteomics from biomarker discovery to signal pathway profiling. Cancer J 7, 69-78. Chuaqui, R., Cole, K., Cuello, M., Silva, M., Quintana, M.E., and Emmert-Buck, M.R. (1999) Analysis of mRNA quality in freshly prepared and archival Papanicolaou samples. Acta Cytol 43, 831-6. 

Eang M. Tandem mass spectrometry-based proteomics, protein characterisation and biomarker discovery in microorganisms. In Shah, H., Gharbia, S., Editors. Mass Spectrometry for Microbial Proteomics , Wiley Hoboken 2010. pp. 75-6. 

Calve, K.R., Liotta, L.A. and Petricoin, E.F., Clinical proteomics from biomarker discovery and cell signaling profiles to individualized personal therapy. Biosci. Rep., 25(1-2), 107-125 (2005). 

Chang, P.L., Clinical hioinformatics (review). Chang Gang Med. /., 28(4), 201-211 (2005). Seihert, V., Ehert, M.P. and Buschmann, T., Advances in clinical cancer proteomics SELDI-ToE-mass spectrometry and biomarker discovery (review). Brief Funct. Genomic Proteomic, 4(1), 16-26 (2005). 

Characterizing the metabolome is only one component which needs to be integrated with its counterparts to realize its potential contributions to drug discovery and development. When all of the work has been done to define the universe of the transcriptome, proteome, and metabolome, and biomarker sets have been identified, 90% of the work remains in the validation and acceptance of these patterns. 

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. 

Melle, C., Ernst, G., Schimmel, B., Bleul, A, Koscielny, S., Wiesner, A., Bogumil, R., Moller, U., Osterloh, D., Halbhuber, K.J., and F. Von Eggling, 2003, Biomarker Discovery and Identification in Laser Microdissected Head and Neck Squamous Cell Carcinoma with ProteinChip(R) Technology, Two-dimensional Gel Electrophoresis, Tandem Mass Spectrometry, and Immunohistochemistry. Mol Cell Proteomics. 2(7) 443-52. 

Krieg RC, Paweletz CP, Liotta LA, Petricoin EF 3rd. Clinical proteomics for cancer biomarker discovery and therapeutic targeting. Technol Cancer Res Treat 2002 1 263-272. 

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