Proteomics to study genes and genomes (original) (raw)
Wilkins, M. R., Williams, K. L., Apple, R. D. & Hochstrasser, D. F. Proteome Research: New Frontiers in Functional Genomics 1– 243 (Springer, Berlin, 1997). Book Google Scholar
Wilkins, M. R. et al. From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis. BioTechnology14, 61–65 ( 1996). ADSCASPubMed Google Scholar
Anderson, N. G. & Anderson, N. L. Twenty years of two-dimensional electrophoresis: past, present and future. Electrophoresis17, 443–453 (1996). ArticleCASPubMed Google Scholar
O'Farrell, P. H. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem.250, 4007–4021 (1975). CASPubMed Google Scholar
Burley, S. K. et al. Structural genomics: beyond the human genome project. Nature Genet.23, 151–157 (1999). ArticleCASPubMed Google Scholar
Krogh, A. in Guide to Human Genome Computing (ed. Bishop, M. J.) 261– 274 (Academic, San Diego, 1998). Book Google Scholar
Claverie, J. M. Computational methods for the identification of genes in vertebrate genomic sequences. Hum. Mol. Genet.6, 1735– 1744 (1997). ArticleCASPubMed Google Scholar
Pandey, A. & Lewitter, F. Nucleotide sequence databases: a gold mine for biologists. Trends Biochem. Sci.24 , 276–280 (1999). ArticleCASPubMed Google Scholar
Gygi, S., Rochon, Y., Franza, B. R. & Aebersold, R. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol.19, 1720–1730 ( 1999). ArticleCASPubMedPubMed Central Google Scholar
Pandey, A., Andersen, J. S., & Mann, M. Use of mass spectrometry to study signaling pathways . Science's STKE (in the press).
Henzel, W. J., Billeci, T. M., Stults, J. T. & Wong, S. C. Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl Acad. Sci. USA90, 5011–5015 (1993). ArticleADSCASPubMedPubMed Central Google Scholar
Jensen, O. N., Mortensen, P., Vorm, O. & Mann, M. Automation of matrix assisted laser desorption/ionization mass spectrometry using fuzzy logic feedback control. Anal. Chem.69, 1706– 1714 (1997). ArticleCASPubMed Google Scholar
Berndt, P., Hobohm, U. & Langen, H. Reliable automatic protein identification from matrix-assisted laser desorption/ionization mass spectrometric peptide fingerprints. Electrophoresis20, 3521–3526 (1999). ArticleCASPubMed Google Scholar
Shevchenko, A. et al. Linking genome and proteome by mass spectrometry: large scale identification of yeast proteins from two dimensional gels. Proc. Natl Acad. Sci. USA93, 14440–14445 (1996). ArticleADSCASPubMedPubMed Central Google Scholar
Shevchenko, A. et al. MALDI quadruple time-of-flight mass spectrometry: powerful tool for proteomic research. Anal. Chem.72, 2132–2141 (2000). ArticleCASPubMed Google Scholar
Zhang, B., Liu, H., Karger, B. L. & Foret, F. Microfabricated devices for capillary electrophoresis-electrospray mass spectrometry. Anal. Chem.71, 3258–3264 (1999). ArticleCASPubMed Google Scholar
Figeys, D., Gygi, S. P., McKinnon, G. & Aebersold, R. An integrated microfluidics-tandem mass spectrometry system for automated protein analysis. Anal. Chem.70, 3728– 3734 (1998). ArticleCASPubMed Google Scholar
Li, J. et al. Integration of microfabricated devices to capillary electrophoresis—electrospray mass spectrometry using a low dead volume connection: application to rapid analyses of proteolytic digests. Anal. Chem.71, 3036–3045 (1999). ArticleCASPubMed Google Scholar
Eckerkorn, C. et al. Mass spectrometric analysis of blotted proteins after gel electrophoresis separation by matrix-assisted laser desorption/ionization . Electrophoresis13, 664– 665 (1992). Article Google Scholar
Strupat, K. et al. Matrix-assisted laser desorption ionization mass spectrometry of proteins electroblotted after polyacrylamide gel electrophoresis. Anal. Chem.66, 464–470 (1994). ArticleCAS Google Scholar
Bienvenut, W. V. et al. Toward a clinical molecular scanner for proteome research: parallel protein chemical processing before and during western blot. Anal. Chem.71, 4800–4807 (1999). ArticleCASPubMed Google Scholar
Binz, P. A. et al. A molecular scanner to automate proteomic research and to display proteome images. Anal. Chem.71, 4981–4988 (1999). ArticleCASPubMed Google Scholar
Jensen, P. K. et al. Probing proteomes using capillary isoelectric focusing-electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem.71, 2076–2084 (1999). ArticleCASPubMed Google Scholar
Mørtz, E. et al. Sequence tag identification of intact proteins by matching tandem mass spectral data against sequence data bases. Proc. Natl. Acad. Sci. USA93, 8264–8267 (1996). ArticleADSPubMedPubMed Central Google Scholar
Li, W., Hendrickson, C. L., Emmett, M. R. & Marshall, A. G. Identification of intact proteins in mixtures by alternated capillary liquid chromatography electrospray ionization and LC ESI infrared multiphoton dissociation Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem.71, 4397–4402 ( 1999). ArticleCASPubMed Google Scholar
Nuwaysir, L. & Stults, J. T. ESI mass spectrometry of phosphopeptides isolated by on-line immobilized metal affinity chromatography. J. Am. Soc. Mass Spectrom.4, 662– 669 (1993). ArticleCASPubMed Google Scholar
Betts, J. C., Blackstock, W. P., Ward, M. A. & Anderton, B. H. Identification of phosphorylation sites on neurofilament proteins by nanoelectrospray mass spectrometry. J. Biol. Chem.272, 12922 –12927 (1997). ArticleCASPubMed Google Scholar
Neubauer, G. & Mann, M. Mapping of phosphorylation sites of gel-isolated proteins by nanoelectrospray tandem mass spectrometry: potentials and limitations. Anal. Chem.71, 235– 242 (1999). ArticleCASPubMed Google Scholar
Zhang, X. et al. Identification of phosphorylation sites in proteins separated by polyacrylamide gel electrophoresis. Anal. Chem.70, 2050–2059 (1998). ArticleCASPubMed Google Scholar
Cortez, D., Wang, Y., Qin, J. & Elledge, S. J. Requirement of ATM-dependent phosphorylation of brca1 in the DNA damage response to double-strand breaks. Science286, 1162– 1166 (1999). ArticleCASPubMed Google Scholar
Soskic, V. et al. Functional proteomics analysis of signal transduction pathways of the platelet-derived growth factor beta receptor. Biochemistry38, 1757–1764 ( 1999). ArticleCASPubMed Google Scholar
Pandey, A. et al. Analysis of receptor signaling pathways by mass spectrometry: identification of Vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors. Proc. Natl Acad. Sci. USA97, 179–184 (2000). ArticleADSCASPubMedPubMed Central Google Scholar
DeRisis, J., Iyer, V. R. & Brown, O. P. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science278, 680–686 (1997). ArticleADS Google Scholar
Golub, T. R. et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science286 , 531–537 (1999). ArticleCASPubMed Google Scholar
Roberts, C. J. et al. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science287, 873–880 (2000). ArticleADSCASPubMed Google Scholar
Alizadeh, A. A. et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature403, 503–511 (2000). ArticleADSCASPubMed Google Scholar
Ostergaard, M., Wolf, H., Orntoft, T. F. & Celis, J. E. Psoriasin (S100A7): a putative urinary marker for the follow-up of patients with bladder squamous cell carcinomas. Electrophoresis20, 349 –354 (1999). ArticleCASPubMed Google Scholar
Page, M. J. et al. Proteomic definition of normal human luminal and myoepithelial breast cells purified from reduction mammoplasties. Proc. Natl Acad. Sci. USA96, 12589–12594 (1999). ArticleADSCASPubMedPubMed Central Google Scholar
Gauss, C. et al. Analysis of the mouse proteome. (I) Brain proteins: separation by two-dimensional electrophoresis and identification by mass spectrometry and genetic variation. Electrophoresis20, 575–600 (1999). ArticleCASPubMed Google Scholar
Aicher, L. et al. New insights into cyclosporine A nephrotoxicity by proteome analysis. Electrophoresis19, 1998– 2003 (1998). ArticleCASPubMed Google Scholar
Breitenbach, M. et al. Biological and immunological importance of Bet v 1 isoforms . Adv. Exp. Med. Biol.409, 117– 126 (1996). ArticleCASPubMed Google Scholar
Sander, I. et al. Allergy to aspergillus-derived enzymes in the baking industry: identification of beta-xylosidase from aspergillus niger as a new allergen (Asp n 14). J. Allergy Clin. Immunol.102, 256–264 (1998). ArticleCASPubMed Google Scholar
Lueking, A., Horn, M., Eickhoff, H., Lehrach, H. & Walter, G. Protein microarrays for gene expression and antibody screening. Anal. Biochem.270, 103– 111 (1999). ArticleCASPubMed Google Scholar
Davies, H., Lomas, L. & Austen, B. Profiling of amyloid beta peptide variants using SELDI Protein Chip arrays. Biotechniques27, 1258 –1261 (1999). CASPubMed Google Scholar
Nelson, R. W. The use of bioreactive probes in protein characterization. Mass Spectrom. Rev.16, 353–376 (1997). ArticleADSCASPubMed Google Scholar
Gygi, S. P. et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnol.17, 994 –999 (1999). ArticleCAS Google Scholar
Neubauer, G. et al. Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry. Proc. Natl Acad. Sci. USA94, 385–390 ( 1997). ArticleADSCASPubMedPubMed Central Google Scholar
Lamond, A. I. & Mann, M. Cell biology and the genome projects—a concerted strategy for characterizing multi-protein complexes using mass spectrometry . Trends Cell Biol.7, 139– 142 (1997). ArticleCASPubMed Google Scholar
Link, A. J. et al. Direct analysis of protein complexes using mass spectrometry . Nature Biotechnol.17, 676– 682 (1999). ArticleCAS Google Scholar
Blackstock, W. P. & Weir, M. P. Proteomics: quantitative and physical mapping of cellular proteins. Trends Biotechnol.17, 121–127 (1999). ArticleCASPubMed Google Scholar
Strausberg, R. L., Feingold, E. A., Klausner, R. D. & Collins, F. S. The mammalian gene collection. Science286, 455–457 (1999). ArticleCASPubMed Google Scholar
Neubauer, G. et al. Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex. Nature Genet.20, 46–50 (1998). ArticleCASPubMed Google Scholar
Winter, D., Podtelejnikiov, A. V., Mann, M. & Li, R. The complex containing actin-related proteins Arp2 and Arp3 is required for the motility and integrity of yeast actin patches. Curr. Biol.7, 519–529 (1997). ArticleCASPubMed Google Scholar
Rout, M. P. et al. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J. Cell. Biol.148, 635–651 (2000). ArticleCASPubMedPubMed Central Google Scholar
Houry, W. A. et al. Identification of in vivo substrates of the chaperonin GroEL . Nature402, 147–154 (1999). ArticleADSCASPubMed Google Scholar
Witke, W. et al. In mouse brain profilin I and profilin II associate with regulators of the endocytic pathway and actin assembly. EMBO J.17, 967–976 (1998). ArticleCASPubMedPubMed Central Google Scholar
Shevchenko, A. & Mann, M. in Mass Spectrometry in Biology and Medicine (eds Burlingame, A., Carr, C. A. & Baldwin, M. A.) 237–269 (Humana, Totowa, 1999). Google Scholar
Rigaut, G. et al. A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnol.17, 1030–1032 (1999). ArticleCAS Google Scholar
Rappsilber, J., Siniossoglou, S., Hurt, E. C. & Mann, M. A generic strategy to analyze the spatial organization of multi-protein complexes by cross-linking and mass spectrometry. Anal. Chem.72, 267–275 (2000). ArticleCASPubMed Google Scholar
Rowley, A. et al. Applications of protein mass spectrometry in cell biology . Methods20, 383–397 (2000). ArticleCASPubMed Google Scholar
Peltier, J. B. et al. Proteomics of the chloroplast. Systematic identification and targeting analysis of lumenal and peripheral thylakoid proteins. Plant Cell12, 319–342 ( 2000). ArticleCASPubMedPubMed Central Google Scholar
Fields, S. & Song, O. K. A novel genetic system to detect protein–protein interactions. Nature340, 245–246 (1989). ArticleADSCASPubMed Google Scholar
Walhout, A. J. et al. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science287, 116–122 (2000). ArticleADSCASPubMed Google Scholar
Uetz, P. et al. A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae. Nature403, 623–627 (2000). ArticleADSCASPubMed Google Scholar
Ito, T. et al. Toward a protein–protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl Acad. Sci. USA97, 1143–1147 ( 2000). ArticleADSCASPubMedPubMed Central Google Scholar
Vidal, M. & Endoh, H. Prospects for drug screening using the reverse two-hybrid system. Trends Biotechnol.17 , 374–381 (1999). ArticleCASPubMed Google Scholar
Zozulya, S. et al. Mapping signal transduction pathways by phage display. Nature Biotechnol.17, 1193–1198 (1999). ArticleCAS Google Scholar
Hufton, S. E. et al. Phage display of cDNA repertoires: the pVI display system and its applications for the selection of immunogenic ligands. J. Immunol. Methods231, 39–51 (1999). ArticleCASPubMed Google Scholar
Martzen, M. R. et al. A biochemical genomics approach for identifying genes by the activity of their products. Science286, 1153–1155 (1999). ArticleCASPubMed Google Scholar
Zambrowicz, B. P. et al. Disruption and sequence identification of 2,000 genes in mouse embryonic stem cells. Nature392, 608– 611 (1998). ArticleADSCASPubMed Google Scholar
Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature391, 806–811 (1998). ArticleADSCASPubMed Google Scholar
Winzeler, E. A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science285 , 901–906 (1999). ArticleCASPubMed Google Scholar
Mattheakis, L. C., Bhatt, R. R. & Dower, W. J. An in vitro polysome display system for identifying ligands from very large peptide libraries. Proc. Natl Acad. Sci. USA91, 9022–9026 ( 1994). ArticleADSCASPubMedPubMed Central Google Scholar
Roberts, R. W. & Szostak, J. W. RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc. Natl Acad. Sci. USA94, 12297–12302 (1997). ArticleADSCASPubMedPubMed Central Google Scholar
Wilm, M. & Mann, M. Analytical properties of the nanoelectrospray ion source. Anal. Chem.68, 1– 8 (1996). ArticleCASPubMed Google Scholar
Wilm, M. et al. Femtomole sequencing of proteins from polyacrylamide gels by nano electrospray mass spectrometry. Nature379, 466–469 (1996). ArticleADSCASPubMed Google Scholar
Roepstorff, P. & Fohlman, J. Proposed nomenclature for sequence ions. Biomed. Mass Spectrom.11, 601 (1984). ArticleCASPubMed Google Scholar
Mann, M. & Wilm, M. S. Error tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem.66, 4390–4399 ( 1994). ArticleCASPubMed Google Scholar
Mann, M. A shortcut to interesting human genes: peptide sequence tags, ESTs and computers . Trends Biochem. Sci.21, 494– 495 (1996). ArticleCASPubMed Google Scholar
Eng, J. K., McCormack, A. L. & J. R. Yates, I. An approach to correlate MS/MS data to amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom.5, 976–989 ( 1994). ArticleCASPubMed Google Scholar
Yates, J. R. III Database searching using mass spectrometry data. Electrophoresis19, 893–900 (1998). ArticleCASPubMed Google Scholar