Proteomics biomarker identification

Hamler, R. L. Zhu, K. Buchanan, N. S. Kreunin, P. Kachman, M. T. Miller, F. R. Lubman, D. M. A two-dimensional liquid-phase separation method coupled with mass spectrometry for proteomic studies of breast cancer and biomarker identification. Proteomics 2004,4, 562-577. 

H. J. Issaq, T. D. Veenstra, T. P. Conrads, and D. Felschow. The SELDI-TOF MS Approach to Proteomics Protein Profiling and Biomarker Identification. Biochem. Biophys. Res. Commun., 292(2002) 587-592. 

Issaq HJ, Veenstra TD, Conrads TP, Felschow D (2002) The SELDl-TOF MS approach to proteomics protein profiling and biomarker identification. Biochem Biophys Res Commim 292 587-592... 

Issaq H, Veenstra T, Conrads T, Felschow D The SELDI-TOF approach to proteomics. protein profiling and biomarker identification. Biochem Biophys Res Commun 2002 292 587-92. 

Chadeau-Hyam, M., Ebbels, T, Brown, I., Chan, Q., Stamler, Huang, C., Daviglus, M., Ueshima, H., Zhao, L., Holmes, E., Nicholson, J., Elliott, P. lorio, M. D. (2010). Metabolic profiling and the metabolome-wide association study significance level for biomarker identification, /. Proteome Res. 9(9) 4620 627. 

Oh, J., Craft, J., Townsend, R., Deasy, J., Bradley, J. Naqa, I. E. (2011). A bioinformatics approach for biomarker identification in radiation-induced Itmg inflammation from limited proteomics data, /. Proteome Res. 10(3) 1406-1415. 

Mitchell, B.L. et al.. Evaluation of matrix-assisted laser desorption/ionization-time of flight mass spectrometry proteomic profiling Identification of alpha 2-HS glycoprotein B-chain as a biomarker of diet, Proteomics, 5, 2238, 2005. 

The capability to identify an intact protein by deducing its partial amino acid sequence (a sequence tag) in a Fourier transform ion cyclotron resonance (FTICR) MS/MS experiment and subsequent homology search in a proteome database was first demonstrated by Mortz et al. [38]. In analogy to bottom-up proteomics, unambiguous identification of one or more intact protein biomarkers by top-down proteomics allows successful microorganism identification (provided the proteome database contains both the respective protein sequences and the respective organism sources). Top-down proteomics approaches for Bacillus spore protein biomarkers and from there Bacillus species identification have been also described [27,45]. For instance, biomarker proteins from Bacillus cereus T spores have been analyzed... 

The present chapter does not consider analysis of extracted protein biomarkers but rather focuses on strategies for rapid chemotaxonomic analysis of intact microorganisms with automated sample manipulation. Rapid means less than 5 minutes. Advantages of the application of bioinformatics and proteomics strategies for rapid identification of microorganisms include the following ... 

Melle C, Ernst G, Schimmel B, et al. A technical triade for proteomic identification and characterization of cancer biomarkers. Cancer Res. 2004 64 4099-4104. 

In addition to MALDI-TOF and LC-MS/MS, SELDI-TOF-MS can also be used to determine expression profiling of various biological samples, such as serum or plasma for early detection of infection. Serum proteomic profiling assay, for instance, has been used to distinguish patients with acute SARS (severe acute respiratory syndrome) from patients with fever and influenza with 100% accuracy [16]. A major limitation of SELDI-TOF-MS, however, is that it cannot be used for direct amino acid sequence identification of the biomarker proteins, necessitating further sample fractionation and protein purification. 

Weissinger, E. M., Hertenstein, B., Mischak, H., and Ganser, A. (2005). Online coupling of capillary electrophoresis with mass spectrometry for the identification of biomarkers for clinical diagnosis. Expert Rev. Proteomics 2, 639—647. 

Proteomics have been used to develop biomarkers. This is achieved by comparative analysis of protein expression in healthy and diseased tissues to identify expressed proteins to be used as new markers, by analysis of secreted proteins in cell lines and primary cultures, and by direct serum protein profiling. MALDI seems to be a good technique for direct protein analysis in biological fluids (e.g., the identification of the small proteins-defensin 1, 2 and 3 as related to the anti-HIV-1 activity of CD8 antiviral factor). 

Consequently, proteomics is a valuable tool for identification and validation of drug targets in early phases, the investigation of the mechanism of pharmacological drug activity and toxicity, and hence, individualized drug therapy. Use of biomarkers may lead to development of nonanimal models. 

Lopez-Pedrera, C., Villalba, J.M., Siendones, E., Barbarroja N., Gomez-Diaz, C., Rodriguez-Ariza, A., Buendia, P., Torres, A., and F. Velasco, 2006, Proteomic analysis of acute myeloid leukemia Identification of potential early biomarkers and therapeutic targets. Proteomics Suppl 1 S293-9. 

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. 

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