Van Eyk, Dunn - Proteomic and Genomic Analysis of Cardiovascular Disease - 2003 (522919), страница 63
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The method can also provide an added level ofinformation about protein localization and turnover if used appropriately. Newchemistries that allow greater flexibility in the labeling of different reactive groupsin peptides is forthcoming (e.g. phosphates, amines, carboxyl, sugars, catalytic activity) so that not only the relative abundance but also the level of their post-translantional modifications and, if applicable, their activities will be accurately determined. For example new reagents and methods have recently been developed tocapture and purify phosphopeptides from complex peptide mixtures [80, 81]. Minor modifications of these methods will make them applicable for use in differential phosphoprotein analysis on a global scale using a strategy similar to the ICATmethod [82–86].
New developments and improvements in mass spectrometersand their corresponding software will considerably speed-up the analysis of ICATlabeled proteins in the near future, a step that is critically important if proteomicanalyses are to reach widespread application. Mass spectrometers are being designed, in particular a matrix assisted laser desorption ionization (MALDI) tandem mass spectrometer that will have the capacity to perform abundance-dependent identification of ICAT reagent labeled samples (manuscript in preparation).This will cut down on the number of protein identifications and quantificationsthat are required in a particular study since the mass spectrometer will focus onthose proteins that show a significant quantitative change under the conditionstested, ignoring the proteins that do not show a change in abundance.
These andother incremental changes will increase the sample throughput of quantitativeproteomic experiments. It is expected that the widespread application of quantitative proteomics will give us a more comprehensive map of the protein networksand their function in cells and tissues in health and disease.3Fig. 13.7 ICAT method is analogous to alarge-scale quantitative western-blot. Traditional methods in molecular biology haveused northern-blots to quantify gene expression one gene at a time.
New genomic technologies, primarily cDNA microarrays, now allow for measurements in gene expressionfrom hundreds to thousands genes. Similarly,new technologies in the area of proteomics,for example the ICAT method, now allow formeasurements in protein abundance on a global scale, which is analogous to a large-scalequantitative western-blot.22923013 Differential Expression Proteomic Analysis Using Isotope Coded Affinity Tags13.7AcknowledgementsM.E.W.
was funded by an NIH Postdoctoral Genome Training Grant fellowship.This work was also supported by a grant from the Merck Genome Research Institute (MGRI) and a grant from the National Cancer Institute (1R33CA84698).13.8References123456789Schena, M., D. Shalon, et al. “Quantitative monitoring of gene expression patterns with a complementary DNA microarray.” Science 1995, 270(5235):467–470.Hughes, T. R., D. D. Shoemaker.
“DNAmicroarrays for expression profiling.”Curr Opin Chem. Biol. 2001, 5(1):21–25.Eisen, M. B., P. T. Spellman, et al.“Cluster analysis and display of genomewide expression patterns.” Proc. Natl.Acad. Sci. USA 1998, 95(25):14863–14868.Roth, F. P., J.
D. Hughes, et al. “FindingDNA regulatory motifs within unalignednoncoding sequences clustered by wholegenome mRNA quantitation.” Nat. Biotechnol. 1998, 16(10):939–945.Bammert, G. F., J. M. Fostel. “Genomewide expression patterns in Saccharomyces cerevisiae: comparison of drugtreatments and genetic alterations affecting biosynthesis of ergosterol.” Antimicrob.Agents. Chemother. 2000, 44(5):1255–1265.Hughes, T. R., M.
J. Marton, et al.“Functional discovery via a compendiumof expression profiles.” Cell. 2000,102(1):109–126.Khan, J., R. Simon, et al. “Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays.” Cancer.Res. 1998, 58(22):5009–5013.Alon, U., N. Barkai, et al. “Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays.” Proc. Natl.
Acad. Sci. USA 1999,96(12):6745–6750.Golub, T. R., D. K. Slonim, et al. “Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.” Science 1999,286(5439):531–537.10111213141516171819Perou, C. M., S. S. Jeffrey, et al. “Distinctive gene expression patterns in human mammary epithelial cells and breastcancers.” Proc.
Natl. Acad. Sci. USA 1999,96(16):9212–9217.Alizadeh, A. A., M. B. Eisen, et al. “Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling.” Nature 2000, 403(6769):503–511.Bittner, M., P. Meltzer, et al. “Molecular classification of cutaneous malignantmelanoma by gene expression profiling.”Nature 2000, 406(6795):536–540.Clark, E. A., T. R.
Golub, et al. “Genomic analysis of metastasis reveals an essential role for RhoC.” Nature 2000,406(6795):532–535.Perou, C. M., T. Sorlie, et al. “Molecularportraits of human breast tumours.” Nature 2000, 406(6797):747–752.Ross, D. T., U. Scherf, et al. “Systematicvariation in gene expression patterns inhuman cancer cell lines.” Nat.
Genet.2000, 24(3):227–235.Scherf, U., D. T. Ross, et al. “A gene expression database for the molecular pharmacology of cancer.” Nat. Genet. 2000,24(3):236–244.Aebersold, R., D. R. Goodlett. “Massspectrometry in proteomics.” Chem. Rev.2001, 101(2):269–295.Klose, J. “Protein mapping by combinedisoelectric focusing and electrophoresisof mouse tissues. A novel approach totesting for induced point mutations inmammals.” Humangenetik 1975,26(3):231–243.O’Farrell, P. H. “High resolution two-dimensional electrophoresis of proteins.” J.Biol.
Chem. 1975, 250(10):4007–4021.13.8 References20212223242526272829Scheele, G. A. “Two-dimensional gelanalysis of soluble proteins. Charaterization of guinea pig exocrine pancreaticproteins.” J. Biol. Chem. 1975,250(14):5375–5385.Iborra, F., J. M. Buhler. “Protein subunit mapping. A sensitive high resolution method.” Anal.
Biochem. 1976,74(2):503–511.Meyer, T. S., B. L. Lamberts. “Use of coomassie brilliant blue R250 for the electrophoresis of microgram quantities of parotid saliva proteins on acrylamide-gelstrips.” Biochim. Biophys. Acta. 1965,107(1):144–145.Talbot, D. N., D. A. Yphantis. “Fluorescent monitoring of SDS gel electrophoresis.” Anal. Biochem.
1971, 44(1):246–253.Kerenyi, L., F. Gallyas. “A highly sensitive method for demonstrating proteinsin electrophoretic, immunoelectrophoretic and immunodiffusion preparations.”Clin. Chim. Acta. 1972, 38(2):465–467.Ragland, W. L., J. L. Pace, et al. “Fluorometric scanning of fluorescamine-labeledproteins in polyacrylamide gels.” Anal.Biochem. 1974, 59(1):24–33.Switzer, R.
C., 3rd, C. R. Merril, et al.“A highly sensitive silver stain for detecting proteins and peptides in polyacrylamide gels.” Anal. Biochem. 1979,98(1):231–237.Vandekerckhove, J., G. Bauw, et al.“Protein-blotting on Polybrene-coatedglass-fiber sheets. A basis for acid hydrolysis and gas-phase sequencing of picomole quantities of protein previously separated on sodium dodecyl sulfate/polyacrylamide gel.” Eur. J. Biochem.
1985,152(1):9–19.Szewczyk, B., D. F. Summers. “Fluorescent staining of proteins transferred tonitrocellulose allowing for subsequentprobing with antisera.” Anal. Biochem.1987, 164(2):303–306.Jackson, P., V. E. Urwin, et al. “Rapidimaging, using a cooled charge-coupleddevice, of fluorescent two- dimensionalpolyacrylamide gels produced by labelling proteins in the first-dimensional isoelectric focusing gel with the fluorophore2- methoxy-2,4-diphenyl-3(2H)furanone.”Electrophoresis 1988, 9(7):330–339.3031323334353637383940Vera, J.
C., C. Rivas. “Fluorescent labeling of nitrocellulose-bound proteins atthe nanogram level without changes inimmunoreactivity.” Anal. Biochem. 1988,173(2):399–404.Houston, B., D. Peddie. “A method fordetecting proteins immobilized on nitrocellulose membranes by in situ derivatization with fluorescein isothiocyanate.”Anal. Biochem. 1989, 177(2):263–267.Unlu, M., M. E. Morgan, et al. “Difference gel electrophoresis: a single gelmethod for detecting changes in proteinextracts.” Electrophoresis 1997,18(11):2071–2077.Henzel, W. J., T.
M. Billeci, et al. “Identifying proteins from two-dimensionalgels by molecular mass searching of peptide fragments in protein sequence databases.” Proc. Natl. Acad. Sci. USA 1993,90(11):5011–5015.James, P., M. Quadroni, et al. “Proteinidentification by mass profile fingerprinting.” Biochem. Biophys. Res. Commun.1993, 195(1):58–64.Mann, M., P. Hojrup, et al.
“Use ofmass spectrometric molecular weight information to identify proteins in sequence databases.” Biol. Mass. Spectrom.1993, 22(6):338–345.Yates, J. R., 3rd, S. Speicher, et al.“Peptide mass maps: a highly informative approach to protein identification.”Anal. Biochem. 1993, 214(2):397–408.Garrels, J. I., C. S. McLaughlin, et al.“Proteome studies of Saccharomyces cerevisiae: identification and characterization of abundant proteins.” Electrophoresis1997, 18(8):1347–1360.Chevallet, M., V. Santoni, et al.
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