Proteome analysis

Lu B, Soreghan BA, Thomas SN, Chen T, Yang AJ. Towards global proteomic analysis in a PSl/APP mouse of Alzheimer s disease. ACS. San Diego, 2005. 

Meier, B. W. Gomez, J. D. Zhou, A. Thompson, J. A. Immunochemical and proteomic analysis of covalent adducts formed by quinone methide tumor promoters in mouse lung epithelial cell lines. Chem. Res. Toxicol. 2005, 18, 1575-1585. 

Hancock, W., Apffel, A., Chakel, J., Hahnenberger, K., Choudhary, G., Traina, J.A., and Pungor, E., Integrated genomic/proteomic analysis, Anal. Chem. News Reports, 71(21), 742A, 1999. 

Chen, M.-L. Chen, C.-H. (2005a). Comparative proteome analysis revealed up-regulation of transthyretin in rat brain under chronic clozapine treatment. /. Psychiatric Res., 41(1/2), 63-8. 

Aicher, L., Wahl, D., Arce, A., Grenet, O., and Steiner, S. (1998). New insights into cyclosporine A nephrotoxicity by proteome analysis. Electrophoresis 19, 1998-2003. 

Gygi, S. P., Corthals, G. L., Zhang, Y., Rochon, Y., and Aebersold, R. (2000). Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl. Acad. Sci. USA 97, 9390-9395. 

Soskic, V., Gorlach, M., Poznanovic, S., Boehmer, F. D., and Godovac-Zimmermann, J. (1999). Functional proteomics analysis of signal transduction pathways of the platelet-derived growth factor b receptor. Biochemistry 38, 1757-1764. 

Williams, C., and Addona, T. A. (2000). The integration of SPR biosensors with mass spectrometry possible applications for proteome analysis. Trends Biotechnol. 18, 45-48. 

Proteome Analysis Protocols. Totowa, NJ Humana Press, 1999. 

Griffin, T. J. Han, D. K. Gygi, S. R Rist, B. Lee, H. Aebersold, R. Parker, K. C. Toward a high-throughput approach to quantitative proteomic analysis Expression-dependent protein identification by mass spectrometry. J. Am. Soc. Mass. Spectrom. 2001,12,1238-1246. 

Fulda, S., S. Mikkat, F. Huang et al. (2006). Proteome analysis of salt stress response in the cyanobacterium Synechocystis sp. strain PCC 6803. Proteomics 6(9) 2733-2745. 

Crabb, JW, Miyagi, M, Gu, X, Shadrach, K, West, KA, Sakaguchi, H, Kamei, M, Hasan, A, Yan, L, Raybom, ME, Salomon, RG, and Hollyfield, JG, 2002. Drusen proteome analysis an approach to the etiology of age-related macular degeneration. Proc Natl Acad Sci USA 99, 14682-14687. 

Mann, M., Jensen, O.L. (2003). Proteomic analysis of post-translational modifications. Nature Biotech. 21, 255. 

Polymer monolithic columns with small diameter have been successfully employed for proteome analysis. Karger and coworkers reported MALDI-TOF of separated fractions spotted on a plate from a polymeric reversed-phase column that showed high peak capacity (Chen et al., 2005). Huber and coworkers reported separation and detection of about 200 peaks within 5 min by using a PSDVB column (Premstaller et al., 2001). 

Chen, H.S., Rejtar, T., Andreev, V., Moskovets, E., Karger, B.L. (2005). High-speed, high-resolution monolithic capillary LC-MALDI MS using an off-line continuous deposition interface for proteomic analysis. Anal. Chem. 77, 2323-2331. 

Schley, C., Altmeyer, M.O., Swart, R., Muller, R., Huber, C.G. (2006). Proteome analysis of Myxococcus xanthus by off-line two-dimensional chromatographic separation using monolithic poly-(styrene-divinylbenzene) columns combined with ion-trap tandem mass spectrometry. J. Proteome Res. 5, 2760-2768. 

Hoffmann, R, Ji, H., Moritz, R. L., Connolly, L. M., Frecklington, D. F., Layton, M. J., Eddes, J. S., Simpson, R. J. (2001). Continuous free-flow electrophoresis separation of cytosolic proteins from the human colon carcinoma cell line LIM 1215 a non two-dimensional gel electrophoresis-based proteome analysis strategy. Proteomics 1(7), 807. 

Proteomic analysis and identification of new hiomarkers and therapeutic targets for invasive ovarian cancer. Proteomics 2(1), 76-84. 

Adkins, J.N., Vamum, S.M., Auberry, K.J., Moore, R.J., Angell, N.H., Smith, R.D., Springer, D.L., Pounds, J.G. (2002). Toward a human blood serum proteome analysis by multidimensional separation coupled with mass spectrometry. Mol. Cell. Proteomics 1,47-955. 

Chen, J., Balgley, B.M., DeVoe, D.L., Lee, C.S. (2003a). Capillary isoelectric focusing-hased multidimensional concentration/separation platform for proteome analysis. Anal. Chem. 

Skipp, P., Robinson, J., O Connor, C.D., Clarke, I.N. (2005). Shotgun proteomic analysis of Chlamydia trachomatis. Proteomics 5, 1558-1573. 

Vollmer, M., Nagele, E., Horth, P. (2003). Differential proteome analysis two-dimensional nano-LC/MS of E. coli proteome grown on different carbon sources. J. Biomol. Tech. 14, 128-135. 

Wenner, B.R., Lovell, M.A., Lynn, B.C. (2004). Proteomic analysis of human ventricular cerebrospinal fluid from neurologically normal, elderly subjects using two-dimensional LC-MS/MS. J. Proteome Res. 3, 97-103. 

The enormous dynamic range of proteins in the sample represents an additional difficulty in proteome analysis. The best example is semm with a protein abundance ranging over eleven orders of magnitude (Anderson and Anderson, 2002). To detect the low abundant species, one has to load a sufficient amount of digest on a column to meet the limit of detection (LOD) of the MS instrument. Some reports published used up to 2.5 L of plasma with an extensive fractionation of intact proteins prior to LC-MS analysis on the peptide level (Rose et al., 2004). 

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