Deciphering Protein Complexes and Protein Interaction Networks by Tandem Affinity Purification and Mass Spectrometry
Tài liệu tham khảo
Goffeau, 1996, Live with 6000 Genes, Science., 274, 546, 10.1126/science.274.5287.546
1998, Genome sequence of the nematode C. elegans: a platform for investigating biology, Science., 282, 2012, 10.1126/science.282.5396.2012
Adams, 2000, The genome sequence of Drosophila melanogaster, Science., 287, 2185, 10.1126/science.287.5461.2185
2001, Initial sequencing and analysis of the human genome, Nature., 409, 860, 10.1038/35057062
Venter, 2001, The sequence of the human genome, Science., 291, 1304, 10.1126/science.1058040
Alberts, 1998, The cell as a collection of protein machines: preparing the next generation of molecular biologists, Cell., 92, 291, 10.1016/S0092-8674(00)80922-8
Eisenberg, 2000, Protein function in the post-genomic era, Nature., 405, 823, 10.1038/35015694
Ideker, 2001, Integrated genomic and proteomic analyses of a systematically perturbed metabolic network, Science., 292, 929, 10.1126/science.292.5518.929
Becskei, 2001, Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion, EMBO J., 20, 2528, 10.1093/emboj/20.10.2528
Marcotte, 1999, Detecting protein function and protein-protein interactions from genome sequences, Science., 285, 751, 10.1126/science.285.5428.751
Uetz, 2000, A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae., Nature., 403, 623, 10.1038/35001009
Ito, 2001, A comprehensive two-hybrid analysis to explore the yeast protein interactome, Proc. Natl. Acad. Sci. U. S. A., 98, 4569, 10.1073/pnas.061034498
Spellman, 1998, Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization, Mol. Biol. Cell., 9, 3273, 10.1091/mbc.9.12.3273
Zhu, 2001, Global analysis of protein activities using proteome chips, Science., 293, 2101, 10.1126/science.1062191
Lamond, 1997, Cell biology and the genome projects - a concerted strategy for characterizing multiprotein complexes by using mass spectrometry, Trends Cell Biol., 7, 139, 10.1016/S0962-8924(97)01031-3
Mann, 2001, Analysis of proteins and proteomes by mass spectrometry, Annu. Rev. Biochem., 70, 437, 10.1146/annurev.biochem.70.1.437
Link, 1999, Direct analysis of protein complexes using mass spectrometry, Nat. Biotechnol., 17, 676, 10.1038/10890
Washburn, 2001, Large-scale analysis of the yeast proteome by multidimensional protein identification technology, Nat. Biotechnol., 19, 242, 10.1038/85686
Knop, 1999, Epitope tagging of yeast genes using a PCR-based strategy: more tags and improved practical routines, Yeast., 15, 963, 10.1002/(SICI)1097-0061(199907)15:10B<963::AID-YEA399>3.0.CO;2-W
Rigaut, 1999, A generic protein purification method for protein complex characterization and proteome exploration, Nat. Biotechnol., 17, 1030, 10.1038/13732
Puig, 2001, The tandem affinity purification (TAP) method: a general procedure of protein complex purification, Methods., 24, 218, 10.1006/meth.2001.1183
Bouveret, 2000, A Sm-like protein complex that participates in mRNA degradation, EMBO J., 19, 1661, 10.1093/emboj/19.7.1661
Caspary, 1999, Partial purification of the yeast U2 snRNP reveals a novel yeast pre-mRNA splicing factor required for pre-spliceosome assembly, EMBO J., 18, 3463, 10.1093/emboj/18.12.3463
Shevchenko, 1999, A strategy for the characterization of protein interaction networks by mass spectrometry, Biochem. Soc. Trans., 27, 549, 10.1042/bst0270549
Seol, 2001, Skp1 forms multiple protein complexes, including RAVE, a regulator of V-ATPase assembly, Nat. Cell Biol., 3, 384, 10.1038/35070067
Soni, 1993, Parameters affecting lithium acetate-mediated transformation of Saccharomyces cerevisiae and development of a rapid and simplified procedure, Curr. Genet., 24, 455, 10.1007/BF00351857
Logie, 1999, Purification and biochemical properties of yeast SWI/SNF complex, Methods Enzymol., 304, 726, 10.1016/S0076-6879(99)04044-6
Wessel, 1984, A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids, Anal. Biochem., 138, 141, 10.1016/0003-2697(84)90782-6
Shevchenko, 1996, Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels, Anal. Chem., 68, 850, 10.1021/ac950914h
Shevchenko, 2000, De Novo peptide sequencing by nanoelectrospray tandem mass spectrometry using triple quadrupole and quadrupole/time-of flight instrument, Methods Mol. Biol., 146, 1
Shevchenko, 1996, Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels, Proc. Natl. Acad. Sci. U. S. A., 93, 14440, 10.1073/pnas.93.25.14440
Vorm, 1994, Matrix surfaces made by fast evaporation yield improved resolution and very high sensitivity in MALDI TOF, Anal. Chem., 66, 3281, 10.1021/ac00091a044
Wilm, 1996, Femtomole sequencing of proteins from polyacrylamide gels by nanoelectrospray mass spectrometry, Nature., 379, 466, 10.1038/379466a0
Perkins, 1999, Probability-based protein identification by searching sequence databases using mass spectrometry data, Electrophoresis., 20, 3551, 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2
Roguev, 2001, The S. cerevisiae Set1 complex includes an Ash2 homolog and methylates histone 3 lysine 4, EMBO J., 20, 7137, 10.1093/emboj/20.24.7137
Kurland, 1991, Codon bias and gene expression, FEBS Lett., 285, 165, 10.1016/0014-5793(91)80797-7
Gygi, 2000, Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology, Proc. Natl. Acad. Sci. U. S. A., 97, 9390, 10.1073/pnas.160270797
Costanzo, 2001, YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information, Nucleic Acids Res., 29, 75, 10.1093/nar/29.1.75
Medzihradszky, 2001, Protein identification by in-gel digestion, high-performance liquid chromatography, and mass spectrometry: peptide analysis by complementary ionization techniques, J. Am. Soc. Mass Spectrom., 12, 215, 10.1016/S1044-0305(00)00214-2
Shevchenko, 2001, Archived polyacrylamide gels as a resource for proteome characterization by mass spectrometry, Electrophoresis., 22, 1194, 10.1002/1522-2683()22:6<1194::AID-ELPS1194>3.0.CO;2-A
Shevchenko, 2000, MALDI quadrupole time-of-flight mass spectrometry: a powerful tool for proteomic research, Anal. Chem., 72, 2132, 10.1021/ac9913659
Krutchinsky, 2000, Rapidly switchable matrix-assisted laser desorption/ionization and electrospray quadrupole-time-of-flight mass spectrometry for protein identification, J. Am. Soc. Mass Spectrom., 11, 493, 10.1016/S1044-0305(00)00114-8
Medzihradszky, 2000, The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer, Anal. Chem., 72, 552, 10.1021/ac990809y
Shevchenko, 1999, 237
Pijnappel, 2001, The S. cerevisiae SET3 complex includes two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene program, Genes Dev., 15, 2991, 10.1101/gad.207401
Deshaies, 2002, Charting the protein complexome in yeast by mass spectrometry, Mol. Cell. Proteom., 1, 3, 10.1074/mcp.R100001-MCP200
Griffin, 2001, Advances in proteome analysis by mass spectrometry, J. Biol. Chem., 276, 45497, 10.1074/jbc.R100014200
Krause, 1999, The dominance of arginine-containing peptides in MALDI-derived tryptic mass fingerprints of proteins, Anal. Chem., 71, 4160, 10.1021/ac990298f
Shevchenko, 2001, Evaluation of the efficiency of in-gel digestion of proteins by peptide isotopic labeling and MALDI mass spectrometry, Anal. Biochem., 296, 279, 10.1006/abio.2001.5321
Lauber, 2001, Mass spectrometry compatibility of two-dimensional gel protein stains, Electrophoresis., 22, 906, 10.1002/1522-2683()22:5<906::AID-ELPS906>3.0.CO;2-9
Rabilloud, 2000, Detecting proteins separated by 2-D gel electrophoresis, Anal. Chem., 72, 48A, 10.1021/ac002709u
Huynen, 2000, Predicting protein function by genomic context: quantitative evaluation and qualitative inferences, Genome Res., 10, 1204, 10.1101/gr.10.8.1204