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ACKNOWLEDGMENTS

 
We are very grateful to Elizabeth Herrick for figure making and design, and we thank Patrick Fadden, Justin MacDonald, and Timothy Wadkins for critical review of the manuscript.

FOOTNOTES

 
* Corresponding author. Mailing address: Department of Pharmacology and Cancer Biology, Duke University, Research Dr., C118 LSRC, Durham, NC 27710. Phone: (919) 613-8606. Fax: (919) 668-0977. E-mail: hayst001@mc.duke.edu .

REFERENCES

1. Abbott, A. 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. The C. elegans Sequencing Consortium. Science 282:2012-2018.[Abstract/Free Full Text]
2. Abbott, A. 1999. A post-genomic challenge: learning to read patterns of protein synthesis. Nature 402:715-720.[CrossRef]
3. Adams, M. D., S. E. Celniker, R. A. Holt, et al. 2000. The genome sequence of Drosophila melanogaster. Science 287:2185-2195.[Abstract/Free Full Text]
4. Aebersold, R., B. Rist, and S. P. Gygi. 2000. Quantitative proteome analysis: methods and applications. Ann. N. Y. Acad. Sci. 919:33-47.[Abstract/Free Full Text]
5. Aebersold, R., J. D. Watts, H. D. Morrison, and E. J. Bures. 1991. Determination of the site of tyrosine phosphorylation at the low picomole level by automated solid-phase sequence analysis. Anal. Biochem. 199:51-60.[CrossRef][Medline]
6. Aebersold, R. H., J. Leavitt, R. A. Saavedra, L. E. Hood, and S. B. Kent. 1987. Internal amino acid sequence analysis of proteins separated by one- or two-dimensional gel electrophoresis after in situ protease digestion on nitrocellulose. Proc. Natl. Acad. Sci. USA 84:6970-6974.[Abstract/Free Full Text]
7. Aebersold, R. H., G. Pipes, L. E. Hood, and S. B. Kent. 1988. N-terminal and internal sequence determination of microgram amounts of proteins separated by isoelectric focusing in immobilized pH gradients. Electrophoresis 9:520-530.[Medline]
8. Aebersold, R. H., D. B. Teplow, L. E. Hood, and S. B. Kent. 1986. Electroblotting onto activated glass. High efficiency preparation of proteins from analytical sodium dodecyl sulfate-polyacrylamide gels for direct sequence analysis. J. Biol. Chem. 261:4229-4238.[Abstract/Free Full Text]
9. Alms, G. R., P. Sanz, M. Carlson, and T. A. Haystead. 1999. Reg1p targets protein phosphatase 1 to dephosphorylate hexokinase II in Saccharomyces cerevisiae: characterizing the effects of a phosphatase subunit on the yeast proteome. EMBO J. 18:4157-4168.[CrossRef][Medline]
10. Amster, J. 1996. Fourier transform mass spectrometry. J. Mass Spectrom. 31:1325-1337.[CrossRef]
11. Andersen, J. S., and M. Mann. 2000. Functional genomics by mass spectrometry. FEBS Lett. 480:25-31.[CrossRef][Medline]
12. Anderson, L., and J. Seilhamer. 1997. A comparison of selected mRNA and protein abundances in human liver. Electrophoresis 18:533-537.[CrossRef][Medline]
13. Anderson, N. G., and N. L. Anderson. 1996. Twenty years of two-dimensional electrophoresis: past, present and future. Electrophoresis 17:443-453.[Medline]
14. Anderson, N. L., J. J. Edwards, C. S. Giometti, K. E. Willard, S. L. Tollaksen, S. L. Nance, B. J. Hickman, K. E. Taylor, B. Coulter, A. Scandora, and N. G. Anderson. 1980. Electrophoresis '79. Walter de Gruyter, New York, N.Y.
15. Appel, R. D., A. Bairoch, and D. F. Hochstrasser. 1999. 2-D databases on the World Wide Web. Methods Mol. Biol. 112:383-391.[Medline]
16. Appel, R. D., and D. F. Hochstrasser. 1999. Computer analysis of 2-D images. Methods Mol. Biol. 112:363-381.[Medline]
17. Arenkov, P., A. Kukhtin, A. Gemmell, S. Voloshchuk, V. Chupeeva, and A. Mirzabekov. 2000. Protein microchips: use for immunoassay and enzymatic reactions. Anal. Biochem. 278:123-131.[CrossRef][Medline]
18. Biemann, K. 1988. Contributions of mass spectrometry to peptide and protein structure. Biomed. Environ. Mass Spectrom. 16:99-100.[Medline]
19. Binz, P. A., M. Muller, D. Walther, W. V. Bienvenut, R. Gras, C. Hoogland, G. Bouchet, E. Gasteiger, R. Fabbretti, S. Gay, P. Palagi, M. R. Wilkins, V. Rouge, L. Tonella, S. Paesano, G. Rossellat, A. Karmime, A. Bairoch, J. C. Sanchez, R. D. Appel, and D. F. Hochstrasser. 1999. A molecular scanner to automate proteomic research and to display proteome images. Anal. Chem. 71:4981-4988.[CrossRef][Medline]
20. Bjellqvist, B., C. Pasquali, F. Ravier, J. C. Sanchez, and D. Hochstrasser. 1993. A nonlinear wide-range immobilized pH gradient for two-dimensional electrophoresis and its definition in a relevant pH scale. Electrophoresis 14:1357-1365.[Medline]
21. Blackstock, W. P., and M. P. Weir. 1999. Proteomics: quantitative and physical mapping of cellular proteins. Trends Biotechnol. 17:121-127.[CrossRef][Medline]
22. Boyle, W. J., P. van der Geer, and T. Hunter. 1991. Phosphopeptide mapping and phosphoamino acid analysis by two- dimensional separation on thin-layer cellulose plates. Methods Enzymol. 201:110-149.[Medline]
23. Broder, S., and J. C. Venter. 2000. Sequencing the entire genomes of free-living organisms: the foundation of pharmacology in the new millennium. Annu. Rev. Pharmacol. Toxicol. 40:97-132.[CrossRef][Medline]
24. Burley, S. K., S. C. Almo, J. B. Bonanno, M. Capel, M. R. Chance, T. Gaasterland, D. Lin, A. Sali, F. W. Studier, and S. Swaminathan. 1999. Structural genomics: beyond the human genome project. Nat. Genet. 23:151-157.[CrossRef][Medline]
25. Burlingame, A. L., R. K. Boyd, and S. J. Gaskell. 1998. Mass spectrometry. Anal. Chem. 70:647R-716R.
26. Campos, M., P. Fadden, G. Alms, Z. Qian, and T. A. Haystead. 1996. Identification of protein phosphatase-1-binding proteins by microcystin-biotin affinity chromatography. J. Biol. Chem. 271:28478-28484.[Abstract/Free Full Text]
27. Carr, S. A., M. J. Huddleston, and R. S. Annan. 1996. Selective detection and sequencing of phosphopeptides at the femtomole level by mass spectrometry. Anal. Biochem. 239:180-192.[CrossRef][Medline]
28. Cash, P. 2000. Proteomics in medical microbiology. Electrophoresis 21:1187-1201.[CrossRef][Medline]
29. Celis, J. E., and P. Gromov. 1999. 2D protein electrophoresis: can it be perfected? Curr. Opin. Biotechnol. 10:16-21.[CrossRef][Medline]
30. Celis, J. E., M. Ostergaard, H. H. Rasmussen, P. Gromov, I. Gromova, H. Varmark, H. Palsdottir, N. Magnusson, I. Andersen, B. Basse, J. B. Lauridsen, G. Ratz, H. Wolf, T. F. Orntoft, P. Celis, and A. Celis. 1999. A comprehensive protein resource for the study of bladder cancer: http://biobase.dk/cgi-bin/celis. Electrophoresis 20:300-309.
31. Celis, J. E., G. P. Ratz, and A. Celis. 1987. Secreted proteins from normal and SV40 transformed human MRC-5 fibroblasts: toward establishing a database of human secreted proteins. Leukemia 1:707-717.[Medline]
32. Clauser, K. R., P. Baker, and A. L. Burlingame. 1999. Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal. Chem. 71:2871-2882.[CrossRef][Medline]
33. Colledge, M., and J. D. Scott. 1999. AKAPs: from structure to function. Trends Cell Biol. 9:216-221.[CrossRef][Medline]
34. Cooks, R. G., G. L. Glish, S. A. McLuckey, and R. E. Kaiser. 1991. Ion trap mass spectrometry. Chem. Eng. Newsl. 25:26-41.
35. Cordwell, S. J., A. S. Nouwens, N. M. Verrills, D. J. Basseal, and B. J. Walsh. 2000. Subproteomics based upon protein cellular location and relative solubilities in conjunction with composite two-dimensional electrophoresis gels. Electrophoresis 21:1094-1103.[CrossRef][Medline]
36. Corthals, G. L., V. C. Wasinger, D. F. Hochstrasser, and J. C. Sanchez. 2000. The dynamic range of protein expression: a challenge for proteomic research. Electrophoresis 21:1104-1115.[CrossRef][Medline]
37. Courchesne, P. L., R. Luethy, and S. D. Patterson. 1997. Comparison of in-gel and on-membrane digestion methods at low to sub- pmol level for subsequent peptide and fragment-ion mass analysis using matrix-assisted laser-desorption/ionization mass spectrometry. Electrophoresis 18:369-381.[Medline]
38. Damer, C. K., J. Partridge, W. R. Pearson, and T. A. Haystead. 1998. Rapid identification of protein phosphatase 1-binding proteins by mixed peptide sequencing and data base searching. Characterization of a novel holoenzymic form of protein phosphatase 1. J. Biol. Chem. 273:24396-24405.
39. Davis, M. T., and T. D. Lee. 1998. Rapid protein identification using a microscale electrospray LC/MS system on an ion trap mass spectrometer. J. Am. Soc. Mass Spectrom. 9:194-201.[CrossRef][Medline]
40. de Nadal, E., R. P. Fadden, A. Ruiz, T. Haystead, and J. Arino. 2001. A role for the Ppz Ser/Thr protein phosphatases in the regulation of translation elongation factor 1B. J. Biol. Chem. 276:14829-14834.[Abstract/Free Full Text]
41. Deterding, L. J., M. A. Moseley, K. B. Tomer, and J. W. Jorgenson. 1991. Nanoscale separations combined with tandem mass spectrometry. J. Chromatogr. 554:73-82.[CrossRef][Medline]
42. Drumm, M. L., and F. S. Collins. 1993. Molecular biology of cystic fibrosis. Mol. Genet. Med. 3:33-68.[Medline]
43. Dunham, I., N. Shimizu, B. A. Roe, et al. 1999. The DNA sequence of human chromosome 22. Nature 402:489-495.[CrossRef][Medline]
44. Dunn, M. J. 2000. Studying heart disease using the proteomic approach. Drug Discov. Today 5:76-84.[CrossRef][Medline]
45. Edman, P. 1949. A method for the determination of the amino acid sequence of peptides. Arch. Biochem. Biophys. 22:475-483.
46. Eisenberg, D., E. M. Marcotte, I. Xenarios, and T. O. Yeates. 2000. Protein function in the post-genomic era. Nature 405:823-826.[CrossRef][Medline]
47. Eisenstein, E., G. L. Gilliland, O. Herzberg, J. Moult, J. Orban, R. J. Poljak, L. Banerjei, D. Richardson, and A. J. Howard. 2000. Biological function made crystal clear—annotation of hypothetical proteins via structural genomics. Curr. Opin. Biotechnol. 11:25-30.[CrossRef][Medline]
48. Ekstrom, S., P. Onnerfjord, J. Nilsson, M. Bengtsson, T. Laurell, and G. Marko-Varga. 2000. Integrated microanalytical technology enabling rapid and automated protein identification. Anal. Chem. 72:286-293.[CrossRef][Medline]
49. Eng, J. K., A. L. McCormack, and J. R. Yates. 1994. An approach to correlate tandem mass-spectral data of peptides with amino-acid-sequences in a protein database. J. Am. Soc. Mass Spectrom. 5:976-989.[CrossRef]
50. Reference deleted.
51. Fadden, P., and T. A. Haystead. 1995. Quantitative and selective fluorophore labeling of phosphoserine on peptides and proteins: characterization at the attomole level by capillary electrophoresis and laser-induced fluorescence. Anal. Biochem. 225:81-88.[CrossRef][Medline]
52. Fenn, J. B., M. Mann, C. K. Meng, S. F. Wong, and C. M. Whitehouse. 1989. Electrospray ionization for mass spectrometry of large biomolecules. Science 246:64-71.[Abstract/Free Full Text]
53. Fenyo, D. 2000. Identifying the proteome: software tools. Curr. Opin. Biotechnol 11:391-395.[CrossRef][Medline]
54. Fenyo, D., J. Qin, and B. T. Chait. 1998. Protein identification using mass spectrometric information. Electrophoresis 19:998-1005.[CrossRef][Medline]
55. Figeys, D., G. L. Corthals, B. Gallis, D. R. Goodlett, A. Ducret, M. A. Corson, and R. Aebersold. 1999. Data-dependent modulation of solid-phase extraction capillary electrophoresis for the analysis of complex peptide and phosphopeptide mixtures by tandem mass spectrometry: application to endothelial nitric oxide synthase. Anal. Chem. 71:2279-2287.[CrossRef][Medline]
56. Fleischmann, R. D., M. D. Adams, O. White, R. A. Clayton, E. F. Kirkness, A. R. Kerlavage, C. J. Bult, J. F. Tomb, B. A. Dougherty, J. M. Merrick, et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512.[Abstract/Free Full Text]
57. Garrels, J. I., B. Futcher, R. Kobayashi, G. I. Latter, B. Schwender, T. Volpe, J. R. Warner, and C. S. McLaughlin. 1994. Protein identifications for a Saccharomyces cerevisiae protein database. Electrophoresis 15:1466-1486.[Medline]
58. Goffeau, A., B. G. Barrell, H. Bussey, R. W. Davis, B. Dujon, H. Feldmann, F. Galibert, J. D. Hoheisel, C. Jacq, M. Johnston, E. J. Louis, H. W. Mewes, Y. Murakami, P. Philippsen, H. Tettelin, and S. G. Oliver. 1996. Life with 6000 genes. Science 274:546, 563-567.
59. Gorg, A., C. Obermaier, G. Boguth, A. Harder, B. Scheibe, R. Wildgruber, and W. Weiss. 2000. The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 21:1037-1053.[CrossRef][Medline]
60. Goshe, M. B., T. P. Conrads, E. A. Panisko, N. H. Angell, T. D. Veenstra, and R. D. Smith. 2001. Phosphoprotein isotope-coded affinity tag approach for isolating and quantitating phosphopeptides in proteome-wide analyses. Anal. Chem. 73:2578-2586.[CrossRef][Medline]
61. Reference deleted.
62. Green, M. K., M. V. Johnston, and B. S. Larsen. 1999. Mass accuracy and sequence requirements for protein database searching. Anal. Biochem. 275:39-46.[CrossRef][Medline]
63. Griffin, T. J., S. P. Gygi, B. Rist, R. Aebersold, A. Loboda, A. Jilkine, W. Ens, and K. G. Standing. 2001. Quantitative proteomic analysis using a MALDI quadrupole time-of-flight mass spectrometer. Anal. Chem. 73:978-986.[CrossRef][Medline]
64. Gygi, S. P., G. L. Corthals, Y. Zhang, Y. Rochon, and R. Aebersold. 2000. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl. Acad. Sci. USA 97:9390-9395.[Abstract/Free Full Text]
65. Gygi, S. P., B. Rist, and R. Aebersold. 2000. Measuring gene expression by quantitative proteome analysis. Curr. Opin. Biotechnol. 11:396-401.[CrossRef][Medline]
66. Gygi, S. P., B. Rist, S. A. Gerber, F. Turecek, M. H. Gelb, and R. Aebersold. 1999. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17:994-999.[CrossRef][Medline]
67. Gygi, S. P., Y. Rochon, B. R. Franza, and R. Aebersold. 1999. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19:1720-1730.[Abstract/Free Full Text]
68. Haynes, P. A., and J. R. Yates III. 2000. Proteome profiling—pitfalls and progress. Yeast 17:81-87.[CrossRef][Medline]
69. Heinke, M. Y., C. H. Wheeler, J. X. Yan, V. Amin, D. Chang, R. Einstein, M. J. Dunn, and C. G. dos Remedios. 1999. Changes in myocardial protein expression in pacing-induced canine heart failure. Electrophoresis 20:2086-2093.[CrossRef][Medline]
70. Henzel, W. J., T. M. Billeci, J. T. Stults, and S. C. Wong. 1993. Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. USA 90:5011-5015.[Abstract/Free Full Text]
71. Hunt, D. F., A. M. Buko, J. M. Ballard, J. Shabanowitz, and A. B. Giordani. 1981. Sequence analysis of polypeptides by collision activated dissociation on a triple quadrupole mass spectrometer. Biomed. Mass Spectrom. 8:397-408.[Medline]
72. Hunt, D. F., R. A. Henderson, J. Shabanowitz, K. Sakaguchi, H. Michel, N. Sevilir, A. L. Cox, E. Appella, and V. H. Engelhard. 1992. Characterization of peptides bound to the class I MHC molecule HLA-A2.1 by mass spectrometry. Science 255:1261-1263.[Abstract/Free Full Text]
73. Hunt, D. F., J. R. Yates, 3rd, J. Shabanowitz, S. Winston, and C. R. Hauer. 1986. Protein sequencing by tandem mass spectrometry. Proc. Natl. Acad. Sci. USA 83:6233-6237.[Abstract/Free Full Text]
74. Hunter, T. 1995. Protein kinases and phosphatases: the yin and yang of protein phosphorylation and signaling. Cell 80:225-236.[CrossRef][Medline]
75. Ideker, T., V. Thorsson, J. A. Ranish, R. Christmas, J. Buhler, J. K. Eng, R. Bumgarner, D. R. Goodlett, R. Aebersold, and L. Hood. 2001. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292:929-934.[Abstract/Free Full Text]
76. James, P. 1997. Protein identification in the post-genome era: the rapid rise of proteomics. Q. Rev. Biophys. 30:279-331.[CrossRef][Medline]
77. James, P., M. Quadroni, E. Carafoli, and G. Gonnet. 1993. Protein identification by mass profile fingerprinting. Biochem. Biophys. Res. Commun. 195:58-64.[CrossRef][Medline]
78. Jansen, M., C. H. de Moor, J. S. Sussenbach, and J. L. van den Brande. 1995. Translational control of gene expression. Pediatr. Res. 37:681-686.[Abstract]
79. Jensen, O. N., A. V. Podtelejnikov, and M. Mann. 1997. Identification of the components of simple protein mixtures by high-accuracy peptide mass mapping and database searching. Anal. Chem. 69:4741-4750.[CrossRef][Medline]
80. Joberty, G., R. R. Perlungher, P. J. Sheffield, M. Kinoshita, M. Noda, T. Haystead, and I. G. Macara. 2001. Borg proteins control septin organization and are negatively regulated by Cdc42. Nat. Cell Biol. 3:861-866.[CrossRef][Medline]
81. Jonscher, K. R., and J. R. Yates III. 1997. Matrix-assisted laser desorption ionization/quadrupole ion trap mass spectrometry of peptides. Application to the localization of phosphorylation sites on the P protein from Sendai virus. J. Biol. Chem. 272:1735-1741.[Abstract/Free Full Text]
82. Jonscher, K. R., and J. R. Yates III. 1997. The quadrupole ion trap mass spectrometer—a small solution to a big challenge. Anal. Biochem. 244:1-15.[CrossRef][Medline]
83. Jung, E., M. Heller, J. C. Sanchez, and D. F. Hochstrasser. 2000. Proteomics meets cell biology: the establishment of subcellular proteomes. Electrophoresis 21:3369-3377.[CrossRef][Medline]
84. Karas, M., and F. Hillenkamp. 1988. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. 60:2299-2301.[CrossRef][Medline]
85. Kaufmann, R., P. Chaurand, D. Kirsch, and B. Spengler. 1996. Post-source decay and delayed extraction in matrix-assisted laser desorption/ionization-reflectron time-of-flight mass spectrometry. Are there trade-offs? Rapid Commun. Mass Spectrom. 10:1199-1208.[CrossRef][Medline]
86. Kirschner, M. 1999. Intracellular proteolysis. Trends Cell Biol. 9:M42-M45.[CrossRef][Medline]
87. Klose, J. 1975. Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik 26:231-243.[Medline]
88. Krebs, E. G. 1994. The growth of research on protein phosphorylation. Trends Biochem. Sci. 19:439.[CrossRef][Medline]
89. Krishna, R. G., and F. Wold. 1993. Post-translational modification of proteins. Adv. Enzymol. Relat. Areas Mol. Biol. 67:265-298.[Medline]
90. Kristensen, D. B., K. Imamura, Y. Miyamoto, and K. Yoshizato. 2000. Mass spectrometric approaches for the characterization of proteins on a hybrid quadrupole time-of-flight (Q-TOF) mass spectrometer. Electrophoresis 21:430-439.[CrossRef][Medline]
91. Krutchinsky, A. N., W. Zhang, and B. T. Chait. 2000. Rapidly switchable matrix-assisted laser desorption/ionization and electrospray quadrupole-time-of-flight mass spectrometry for protein identification. J. Am. Soc. Mass Spectrom. 11:493-504.[CrossRef][Medline]
92. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685.[CrossRef][Medline]
93. Lander, E. S., L. M. Linton, B. Birren, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.[CrossRef][Medline]
94. Lewis, T. S., J. B. Hunt, L. D. Aveline, K. R. Jonscher, D. F. Louie, J. M. Yeh, T. S. Nahreini, K. A. Resing, and N. G. Ahn. 2000. Identification of novel MAP kinase pathway signaling targets by functional proteomics and mass spectrometry. Mol. Cell 6:1343-1354.[CrossRef][Medline]
95. Link, A. J., J. Eng, D. M. Schieltz, E. Carmack, G. J. Mize, D. R. Morris, B. M. Garvik, and J. R. Yates III. 1999. Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17:676-682.[CrossRef][Medline]
96. Link, A. J., L. G. Hays, E. B. Carmack, and J. R. Yates III. 1997. Identifying the major proteome components of Haemophilus influenzae type-strain NCTC 8143. Electrophoresis 18:1314-1334.[Medline]
97. Loboda, A. V., A. N. Krutchinsky, M. Bromirski, W. Ens, and K. G. Standing. 2000. A tandem quadrupole/time-of-flight mass spectrometer with a matrix-assisted laser desorption/ionization source: design and performance. Rapid Commun. Mass Spectrom. 14:1047-1057.[CrossRef][Medline]
98. MacBeath, G., and S. L. Schreiber. 2000. Printing proteins as microarrays for high-throughput function determination. Science 289:1760-1763.[Abstract/Free Full Text]
99. MacDonald, J. A., M. A. Borman, A. Muranyi, A. V. Somlyo, D. J. Hartshorne, and T. A. Haystead. 2001. Identification of the endogenous smooth muscle myosin phosphatase-associated kinase. Proc. Natl. Acad. Sci. USA 98:2419-2424.[Abstract/Free Full Text]
100. Reference deleted.
101. Mackey, A. J., T. A. Haystead, and W. R. Pearson. Getting more from less: algorithms for rapid protein identification with multiple short peptide sequences. Mol. Proteomics, in press.
102. Mann, M., P. Hojrup, and P. Roepstorff. 1993. Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol. Mass Spectrom. 22:338-345.[Medline]
103. Mann, M., and M. Wilm. 1994. Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 66:4390-4399.[CrossRef][Medline]
104. Marshall, A. G., C. L. Hendrickson, and G. S. Jackson. 1998. Fourier transform ion cyclotron resonance mass spectrometry: a primer. Mass Spectrom. Rev. 17:1-35.[CrossRef][Medline]
105. Matsumoto, T., J. Wu, T. Baba, Y. Katayose, K. Yamamoto, K. Sakata, M. Yano, and T. Sasaki. 2001. Rice genomics: current status of genome sequencing. Novartis Found. Symp. 236:28-38.[Medline]
106. McCormack, A. L., D. M. Schieltz, B. Goode, S. Yang, G. Barnes, D. Drubin, and J. R. Yates III. 1997. Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the low-femtomole level. Anal. Chem. 69:767-776.[CrossRef][Medline]
107. McDonald, W. H., and J. R. Yates III. 2000. Proteomic tools for cell biology. Traffic 1:747-754.[CrossRef][Medline]
108. Meyer, H. E., E. Hoffmann-Posorske, and L. M. Heilmeyer, Jr. 1991. Determination and location of phosphoserine in proteins and peptides by conversion to S-ethylcysteine. Methods Enzymol. 201:169-185.[Medline]
109. Miller, P. E., and M. B. Denton. 1986. The quadrupole mass filter: basic operating concepts. J. Chem. Ed. 63:617-622.
110. Mitchelhill, K. I., and B. E. Kemp. 1999. Phosphorylation site analysis by mass spectrometry, 2nd ed. Oxford University Press, New York, N.Y.
111. Morris, H. R., T. Paxton, A. Dell, J. Langhorne, M. Berg, R. S. Bordoli, J. Hoyes, and R. H. Bateman. 1996. High sensitivity collisionally-activated decomposition tandem mass spectrometry on a novel quadrupole/orthogonal-acceleration time-of-flight mass spectrometer. Rapid Commun. Mass Spectrom. 10:889-896.[CrossRef][Medline]
112. Morris, H. R., T. Paxton, M. Panico, R. McDowell, and A. Dell. 1997. A novel geometry mass spectrometer, the Q-TOF, for low-femtomole/attomole-range biopolymer sequencing. J. Protein Chem. 16:469-479.[Medline]
113. Myers, E. W. G. G. Sutton, A. L. Delcher, et al. 2000. A whole-genome assembly of Drosophila. Science 287:2196-2204.[Abstract/Free Full Text]
114. Nelson, P. S., N. Clegg, B. Eroglu, V. Hawkins, R. Bumgarner, T. Smith, and L. Hood. 2000. The prostate expression database (PEDB): status and enhancements in 2000. Nucleic Acids Res. 28:212-213.[Abstract/Free Full Text]
115. Neubauer, G., A. Gottschalk, P. Fabrizio, B. Seraphin, R. Luhrmann, and M. Mann. 1997. Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry. Proc. Natl. Acad. Sci. USA 94:385-390.[Abstract/Free Full Text]
116. Neubauer, G., and M. Mann. 1999. Mapping of phosphorylation sites of gel-isolated proteins by nanoelectrospray tandem mass spectrometry: potentials and limitations. Anal. Chem. 71:235-242.[CrossRef][Medline]
117. Newman, A. 1998. RNA splicing. Curr. Biol. 8:R903-R905.
118. Oda, Y., T. Nagasu, and B. T. Chait. 2001. Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat. Biotechnol. 19:379-382.
119. O'Farrell, P. H. 1975. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250:4007-4021.[Abstract/Free Full Text]
120. Opiteck, G. J., K. C. Lewis, J. W. Jorgenson, and R. J. Anderegg. 1997. Comprehensive on-line LC/LC/MS of proteins. Anal. Chem. 69:1518-1524.[CrossRef][Medline]
121. Page, M. J., B. Amess, R. R. Townsend, R. Parekh, A. Herath, L. Brusten, M. J. Zvelebil, R. C. Stein, M. D. Waterfield, S. C. Davies, and M. J. O'Hare. 1999. Proteomic definition of normal human luminal and myoepithelial breast cells purified from reduction mammoplasties. Proc. Natl. Acad. Sci. USA 96:12589-12594.[Abstract/Free Full Text]
122. Pandey, A., and F. Lewitter. 1999. Nucleotide sequence databases: a gold mine for biologists. Trends Biochem. Sci. 24:276-280.[CrossRef][Medline]
123. Pandey, A., and M. Mann. 2000. Proteomics to study genes and genomes. Nature 405:837-846.[CrossRef][Medline]
124. Pandey, A., A. V. Podtelejnikov, B. Blagoev, X. R. Bustelo, M. Mann, and H. F. Lodish. 2000. 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. USA 97:179-184.[Abstract/Free Full Text]
125. Pappin, D. D. J., P. Hojrup, and A. J. Bleasby. 1993. Rapid identification of proteins by peptide-mass finger printing. Curr. Biol. 3:327-332.[CrossRef][Medline]
126. Patton, W. F. 2000. A thousand points of light: the application of fluorescence detection technologies to two-dimensional gel electrophoresis and proteomics. Electrophoresis 21:1123-1144.[CrossRef][Medline]
127. Pawson, T., and P. Nash. 2000. Protein-protein interactions define specificity in signal transduction. Genes Dev 14:1027-1047.[Free Full Text]
128. Pennisi, E. 2001. New genomes shed light on complex cells. Science 292:1280-1281.[CrossRef]
129. Perkins, D. N., D. J. Pappin, D. M. Creasy, and J. S. Cottrell. 1999. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551-3567.[CrossRef][Medline]
130. Qin, J., and B. T. Chait. 1997. Identification and characterization of posttranslational modifications of proteins by MALDI ion trap mass spectrometry. Anal. Chem. 69:4002-4009.[CrossRef][Medline]
131. Qin, J., D. Fenyo, Y. Zhao, W. W. Hall, D. M. Chao, C. J. Wilson, R. A. Young, and B. T. Chait. 1997. A strategy for rapid, high-confidence protein identification. Anal. Chem. 69:3995-4001.[CrossRef][Medline]
132. Quadroni, M., and P. James. 1999. Proteomics and automation. Electrophoresis 20:664-677.[CrossRef][Medline]
133. Rain, J. C., L. Selig, H. De Reuse, V. Battaglia, C. Reverdy, S. Simon, G. Lenzen, F. Petel, J. Wojcik, V. Schachter, Y. Chemama, A. Labigne, and P. Legrain. 2001. The protein-protein interaction map of Helicobacter pylori. Nature 409:211-215.[CrossRef][Medline]
134. Rappsilber, J., S. Siniossoglou, E. C. Hurt, and M. Mann. 2000. A generic strategy to analyze the spatial organization of multi-protein complexes by cross-linking and mass spectrometry. Anal. Chem. 72:267-275.[CrossRef][Medline]
135. Roepstorff, P., and J. Fohlman. 1984. Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed. Mass Spectrom. 11:601.[CrossRef][Medline]
136. Rosenfeld, J., J. Capdevielle, J. C. Guillemot, and P. Ferrara. 1992. In-gel digestion of proteins for internal sequence analysis after one- or two-dimensional gel electrophoresis. Anal. Biochem. 203:173-179.[CrossRef][Medline]
137. Rout, M. P., J. D. Aitchison, A. Suprapto, K. Hjertaas, Y. Zhao, and B. T. Chait. 2000. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J. Cell Biol. 148:635-651.[Abstract/Free Full Text]
138. Rubin, G. M. M. D. Yandell, J. R. Wortman, et al. 2000. Comparative genomics of the eukaryotes. Science 287:2204-2215.[Abstract/Free Full Text]
139. Sanchez, J. C., and D. F. Hochstrasser. 1999. High-resolution, IPG-based, mini two-dimensional gel electrophoresis. Methods Mol. Biol. 112:227-233.[Medline]
140. Scheele, G. A. 1975. Two-dimensional gel analysis of soluble proteins. Characterization of guinea pig exocrine pancreatic proteins. J. Biol. Chem. 250:5375-5385.[Abstract/Free Full Text]
141. Scheler, C., X. P. Li, J. Salnikow, M. J. Dunn, and P. R. Jungblut. 1999. Comparison of two-dimensional electrophoresis patterns of heat shock protein Hsp27 species in normal and cardiomyopathic hearts. Electrophoresis 20:3623-3628.[CrossRef][Medline]
142. Schena, M., D. Shalon, R. W. Davis, and P. O. Brown. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470.[Abstract/Free Full Text]
143. Shalon, D., S. J. Smith, and P. O. Brown. 1996. A DNA microarray system for analyzing complex DNA samples using two- color fluorescent probe hybridization. Genome Res. 6:639-645.[Abstract]
144. Shaw, A. C., M. Rossel Larsen, P. Roepstorff, A. Holm, G. Christiansen, and S. Birkelund. 1999. Mapping and identification of HeLa cell proteins separated by immobilized pH-gradient two-dimensional gel electrophoresis and construction of a two-dimensional polyacrylamide gel electrophoresis database. Electrophoresis 20:977-983.[CrossRef][Medline]
145. Shevchenko, A., I. Chernushevich, W. Ens, K. G. Standing, B. Thomson, M. Wilm, and M. Mann. 1997. Rapid ‘de novo' peptide sequencing by a combination of nanoelectrospray, isotopic labeling and a quadrupole/time-of-flight mass spectrometer. Rapid Commun. Mass Spectrom. 11:1015-1024.[CrossRef][Medline]
146. Shevchenko, A., O. N. Jensen, A. V. Podtelejnikov, F. Sagliocco, M. Wilm, O. Vorm, P. Mortensen, H. Boucherie, and M. Mann. 1996. Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels. Proc. Natl. Acad. Sci. USA 93:14440-14445.[Abstract/Free Full Text]
147. Shevchenko, A., A. Loboda, W. Ens, and K. G. Standing. 2000. MALDI quadrupole time-of-flight mass spectrometry: a powerful tool for proteomic research. Anal. Chem. 72:2132-2141.[CrossRef][Medline]
148. Shevchenko, A., M. Wilm, and M. Mann. 1997. Peptide sequencing by mass spectrometry for homology searches and cloning of genes. J. Protein Chem. 16:481-490.[CrossRef][Medline]
149. Shevchenko, A., M. Wilm, O. Vorm, and M. Mann. 1996. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal. Chem. 68:850-858.[CrossRef][Medline]
150. Smith, R. D., L. Pasa-Tolic, M. S. Lipton, P. K. Jensen, G. A. Anderson, Y. Shen, T. P. Conrads, H. R. Udseth, R. Harkewicz, M. E. Belov, C. Masselon, and T. D. Veenstra. 2001. Rapid quantitative measurements of proteomes by Fourier transform ion cyclotron resonance mass spectrometry. Electrophoresis 22:1652-1668.[CrossRef][Medline]
151. Smolka, M. B., H. Zhou, S. Purkayastha, and R. Aebersold. 2001. Optimization of the isotope-coded affinity tag-labeling procedure for quantitative proteome analysis. Anal. Biochem. 297:25-31.[CrossRef][Medline]
152. Spengler, B., D. Kirsch, R. Kaufmann, and E. Jaeger. 1992. Peptide sequencing by matrix-assisted laser-desorption mass spectrometry. Rapid Commun. Mass Spectrom. 6:105-108.[CrossRef][Medline]
153. Sun, H., and N. K. Tonks. 1994. The coordinated action of protein tyrosine phosphatases and kinases in cell signaling. Trends Biochem. Sci. 19:480-485.[CrossRef][Medline]
154. Tabata, S. 2000. Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Nature 408:823-826.[CrossRef][Medline]
155. Tong, W., A. Link, J. K. Eng, and J. R. Yates III. 1999. Identification of proteins in complexes by solid-phase microextraction/multistep elution/capillary electrophoresis/tandem mass spectrometry. Anal. Chem. 71:2270-2278.[CrossRef][Medline]
156. Traini, M., A. A. Gooley, K. Ou, M. R. Wilkins, L. Tonella, J. C. Sanchez, D. F. Hochstrasser, and K. L. Williams. 1998. Towards an automated approach for protein identification in proteome projects. Electrophoresis 19:1941-1949.[CrossRef][Medline]
157. Uetz, P. L. Giot, G. Cagney, et al. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623-627.[CrossRef][Medline]
158. Unlu, M., M. E. Morgan, and J. S. Minden. 1997. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18:2071-2077.[CrossRef][Medline]
159. Vandekerckhove, J., G. Bauw, M. Puype, J. Van Damme, and M. Van Montagu. 1985. Protein-blotting on Polybrene-coated glass-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. 152:9-19.[Abstract]
160. Velculescu, V. E., L. Zhang, B. Vogelstein, and K. W. Kinzler. 1995. Serial analysis of gene expression. Science 270:484-487.[Abstract/Free Full Text]
161. Venter, J. C., M. D. Adams, E. W. Myers, et al. 2001. The sequence of the human genome. Science 291:1304-1351.[Abstract/Free Full Text]
162. Verentchikov, A. N., W. Ens, and K. G. Standing. 1994. Reflecting time-of-flight mass spectrometer with an electrospray ion source and orthogonal extraction. Anal. Chem. 66:126-133.[CrossRef][Medline]
163. Wasinger, V. C., S. J. Cordwell, A. Cerpa-Poljak, J. X. Yan, A. A. Gooley, M. R. Wilkins, M. W. Duncan, R. Harris, K. L. Williams, and I. Humphery-Smith. 1995. Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis 16:1090-1094.[CrossRef][Medline]
164. Wettenhall, R. E., R. H. Aebersold, and L. E. Hood. 1991. Solid-phase sequencing of 32P-labeled phosphopeptides at picomole and subpicomole levels. Methods Enzymol. 201:186-199.[Medline]
165. Wilkins, M. R., E. Gasteiger, A. Bairoch, J. C. Sanchez, K. L. Williams, R. D. Appel, and D. F. Hochstrasser. 1999. Protein identification and analysis tools in the ExPASy server. Methods Mol. Biol. 112:531-552.[Medline]
166. Wilkins, M. R., E. Gasteiger, A. A. Gooley, B. R. Herbert, M. P. Molloy, P. A. Binz, K. Ou, J. C. Sanchez, A. Bairoch, K. L. Williams, and D. F. Hochstrasser. 1999. High-throughput mass spectrometric discovery of protein post-translational modifications. J. Mol. Biol. 289:645-657.[CrossRef][Medline]
167. Wilkins, M. R., J. C. Sanchez, A. A. Gooley, R. D. Appel, I. Humphery-Smith, D. F. Hochstrasser, and K. L. Williams. 1995. Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol. Genet. Eng. Rev. 13:19-50.
168. Wilkins, M. R., J. C. Sanchez, K. L. Williams, and D. F. Hochstrasser. 1996. Current challenges and future applications for protein maps and post-translational vector maps in proteome projects. Electrophoresis 17:830-838.[Medline]
169. Wilm, M., and M. Mann. 1996. Analytical properties of the nanoelectrospray ion source. Anal. Chem. 68:1-8.[CrossRef][Medline]
170. Wilm, M., A. Shevchenko, T. Houthaeve, S. Breit, L. Schweigerer, T. Fotsis, and M. Mann. 1996. Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 379:466-469.[CrossRef][Medline]
171. Yan, J. X., J. C. Sanchez, L. Tonella, K. L. Williams, and D. F. Hochstrasser. 1999. Studies of quantitative analysis of protein expression in Saccharomyces cerevisiae. Electrophoresis 20:738-742.[CrossRef][Medline]
172. Yates, J. R., III. 1998. Mass spectrometry and the age of the proteome. J. Mass Spectrom. 33:1-19.[CrossRef][Medline]
173. Yates, J. R., III. 1996. Protein structure analysis by mass spectrometry. Methods Enzymol. 271:351-377.[CrossRef][Medline]
174. Yates, J. R., III, A. L. McCormack, D. Schieltz, E. Carmack, and A. Link. 1997. Direct analysis of protein mixtures by tandem mass spectrometry. J. Protein Chem. 16:495-497.[Medline]
175. Yates, J. R., III, S. Speicher, P. R. Griffin, and T. Hunkapiller. 1993. Peptide mass maps: a highly informative approach to protein identification. Anal. Biochem. 214:397-408.[CrossRef][Medline]
176. Zhang, W., and B. T. Chait. 2000. ProFound: an expert system for protein identification using mass spectrometric peptide mapping information. Anal. Chem. 72:2482-2489.[CrossRef][Medline]
177. Zhang, W., A. J. Czernik, T. Yungwirth, R. Aebersold, and B. T. Chait. 1994. Matrix-assisted laser desorption mass spectrometric peptide mapping of proteins separated by two-dimensional gel electrophoresis: determination of phosphorylation in synapsin I. Protein Sci. 3:677-686.
178. Zhang, X., C. J. Herring, P. R. Romano, J. Szczepanowska, H. Brzeska, A. G. Hinnebusch, and J. Qin. 1998. Identification of phosphorylation sites in proteins separated by polyacrylamide gel electrophoresis. Anal. Chem. 70:2050-2059.[CrossRef][Medline]
178. Zhas, S., et al. 2001. Mouse BAC ends quality assessment and sequence analyses. Genome Res. 11:1736-1745.
179. Zhou, H., J. D. Watts, and R. Aebersold. 2001. A systematic approach to the analysis of protein phosphorylation. Nat. Biotechnol. 19:375-378.[CrossRef][Medline]
180. Zhu, H., M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, N. Lan, R. Jansen, S. Bidlingmaier, T. Houfek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Snyder. 2001. Global analysis of protein activities using proteome chips. Science 293:2101-2105.[Abstract/Free Full Text]
181. Zhu, H., J. F. Klemic, S. Chang, P. Bertone, A. Casamayor, K. G. Klemic, D. Smith, M. Gerstein, M. A. Reed, and M. Snyder. 2000. Analysis of yeast protein kinases using protein chips. Nat. Genet. 26:283-289.[CrossRef][Medline]

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