Probing cellular complexity with proteomics

Current Opinion in Molecular Therapeutics

Volumn 1, Issue 6, 1999, Pages 702-711

  Blackstock, Walter ^a   Rowley, Adele ^a  

^a GLAXOSMITHKLINE   (United Kingdom)

Author keywords

Cell map proteomics; Expression proteomics; Functional analysis; Interaction network; Mass spectrometry; Organelle; Protein complex

Indexed keywords

MESSENGER RNA;

ARTICLE; CELLULAR DISTRIBUTION; COMPUTER PROGRAM; DATA BASE; GENE SEQUENCE; GENE TECHNOLOGY; HUMAN; MASS SPECTROMETRY; NONHUMAN; PEPTIDE MAPPING; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; PROTEIN PROCESSING; RNA TRANSCRIPTION; SEQUENCE ANALYSIS;

COMPUTATIONAL BIOLOGY; DRUG DESIGN; DRUG DISCOVERY; GENE EXPRESSION PROFILING; HUMANS; MASS SPECTROMETRY; MULTIPROTEIN COMPLEXES; PROTEIN BINDING; PROTEOME; PROTEOMICS;

EID: 0033384057     PISSN: 14648431     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (55)

1. Anderson NL, Anderson NG: Proteome and proteomics: New technologies, new concepts and new words. Electrophoresis (1998) 19:1853-1861.
2. Wasinger VC, Cordwell SJ, Cerpa-Poljak A, Yan JX, Gooley AA, Wilkins MR, Duncan MW, Harris R, Williams KL, Humphery-Smith I: Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis (1995) 16:1090-1094.
3. Blackstock WP, Weir MP: Proteomics: quantitative and physical mapping of cellular proteins. Trends Biotechnol (1999) 17:121-127.
4. Bertelsen AH, Velculescu VE: High-throughput gene expression analysis using SAGE. Drug Disc Today (1998) 3:152-159.
5. Granjeaud S, Bertucci F, Jordan BR: Expression profiling: DNA arrays in many guises. Bioessays (1999) 21(9):781-790.
6. Pardee AB, McClelland M (Eds): Expression Genetics: Differential Display. Eaton Publishing (1999).
7. De Saizieu A, Certa U, Warrington J, Gray C, Keck W, Mous J: Bacterial transcript imaging by hybridization of total RNA to oligonucleotide arrays. Nature Biotechnol (1998) 16:45-48.
8. Velculescu VE, Zhang L, Zhou W, Vogelstein J, Basrai MA, Bassett DE Jr, Hieter P, Vogelstein B, Kinzler KW: Characterization of the yeast transcriptome. Cell (1997) 88:243-251.
9. DeRisi JL, Iyer VR, Brown PO: Exploring the metabolic and genetic control of gene expression on a genomic scale. Science (1997) 278:680-686.
10. Marion MJ, DeRisi JL, Bennett HA, Iyer VR, Meyer MR, Roberts CJ, Stoughton R, Burchard J, Slade D, Dai H, Bassett DE, Hartwell LH, Brown PO, Friend SH: Drug target validation and identification of secondary drug target effects using DNA microarrays. Nature Med (1998) 4:1293-1301.
11. Anderson L, Seilhamer J: A comparison of selected mRNA and protein abundances in human liver. Electrophoresis (1997) 18:533-537.
12. Kawamoto S, Matsumoto Y, Mizuno K, Okubo K, Matsubara K: Expression profiles of active genes in human and mouse livers. Gene (1996) 174:151-158.
13. Gygi SP, Rochon Y, Franza BR, Aebersold R: Correlation between protein and mRNA abundance in yeast. Mol Cell Biol (1999) 19(3):1720-1730.
14. Neubauer G, Wilm M: From genome to function: Analysis of multi-protein complexes and protein phosphorylation. Curr Opin Mol Ther (199) 1 (6):695-701
15. Sirivatanauksom Y, Drury R, Cmogorac-Jurcevic T, Sirivatanauksom V, Lemoine NR: Laser-assisted microdissection: Applications in molecular pathology. J Pathol (1999) 189:150-154.
16. VanBogelen RA, Schiller EE, Thomas JD, Neidhardt FC: Diagnosis of cellular states of microbial organisms using proteomics. Electrophoresis (1999) 20:2149-2159.
17. Nock C, Gauss C, Schalkwyk LC, Klose J, Lehrach H, Himmelbauer H: Technology development at the interface of proteome research and genomics: Mapping non-polymorphic proteins on the physical map of mouse chromosomes. Electrophoresis (1999) 20:1027-1032
18. Strohman RC: Five stages of the Human Genome Project. Nature Biotechnol (1999) 17:112.
19. Klose J, Kobalz U: Two-dimensional electrophoresis of proteins: an updated protocol and implications for a functional analysis of the genome. Electrophoresis (1995) 16:1034-1059.
20. Shevchenko A, Wilm M, Vorm O, Mann M: Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem (1996) 68:850-858.
21. Unlu M, Morgan ME, Minden JS: Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis (1997) 18:2071-2077.
22. Chevallet M, Santoni V, Poinas A, Rouquie D, Fuchs A, Kieffer S, Rossignol M, Lunardi J, Garin J, Rabilloud T: New zwitterionic detergents improve the analysis of membrane proteins by two-dimensional electrophoresis. Electrophoresis (1998) 19:1901-1909.
23. Molloy MP, Herbert BR, Walsh BJ, Tyler MI, Traini M, Sanchez JC, Hochstrasser DF, Williams KL, Gooley AA: Extraction of membrane proteins by differential solubilization for separation using two-dimensional gel electrophoresis. Electrophoresis (1998) 19:837-844.
24. Lamond AI, Mann M: Cell biology and the genome projects - a concerted strategy for characterizing multiprotein complexes by using mass spectrometry. Trends Cell Biol (1997) 7:139-142.
25. Jensen ON, Wilm M, Shevchenko A, Mann M: Sample preparation methods for mass spectrometric peptide mapping directly from 2-DE gels. In: Methods in Molecular Biology. Link A (Ed), Humana Press, New Jersey (1999):513-530.
26. Jensen ON, Podtelejnikov AV, Mann M: Identification of the components of simple protein mixtures by high-accuracy peptide mass mapping and database searching. Anal Chem (1997) 69:4741-4750.
27. Shevchenko A, Jensen ON, Podtelejnikov AV, Sagliocco F, Wilm M, Vorm O, Mortensen P, Shevchenko A, Boucherie H, Mann M: Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels. Proc Natl Acad Sci USA (1996) 93:14440-14445.
28. Wilm M, Mann M: Analytical properties of the nanoelectrospray ion source. Anal Chem (1996) 68:1-8.
29. Mann M, Wilm M: Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal Chem (1994) 66:4390-4399.
30. Jensen ON, Wilm M, Shevchenko A, Mann M: Peptide sequencing of 2DE gel-isolated proteins by nanoelectrospray tandem mass spectrometry. In: Methods in Molecular Biology. Link A (Ed), Humana Press, New Jersey (1999):571-588.
31. Yates JR, Carmack E, Hays L, Link AJ: Automated protein identification using microcolumn liquid chromatography-tandem mass spectrometry. In: Methods in Molecular Biology. Link A (Ed), Humana Press, New Jersey (1999):553-569.
32. Tong W, Link A, Eng JK, Yates JR: Identification of proteins in complexes by solid-phase microextraction/multistep elution/capillary electrophoresis/tandem mass spectrometry. Anal Chem (1999) 71:2270-2278.
33. Moore RE, Licklider L, Schumann D, Lee TD: A microscale electrospray interface incorporating a monolithic poly(styrene-divinylbenzene) support for on-line liquid chromatography/tandem mass spectrometry analysis of peptides and proteins. Anal Chem (1998) 70:4879-4884.
34. Link AJ, Eng J, Schieltz DM, Carmack E, Mize GJ, Morris DR, Garvik BM, Yates JR: Direct analysis of protein complexes using mass spectrometry. Nature Biotechnol (1999) 17:676-682.
35. Neubauer G, Mann M: Mapping of phosphorylation sites of gel-isolated proteins by nanoelectrospray tandem mass spectrometry: potentials and limitations. Anal Chem (1999) 71:235-242.
36. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R: Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnol (1999) 17:994-999.
37. Oda Y, Huang K, Cross FR, Cowburn D, Chait BT: Accurate quantitation of protein expression and site-specific phosphorylation. Proc Natl Acad Sci USA (1999) 96:6591-6596.
38. Shevchenko A, Chemushevich I, Ens W, Standing KG, Thomson B, Wilm M, Mann M: Rapid 'de novo' peptide sequencing by a combination of nanoelectrospray, isotopic labeling and a quadrupole/time-of-flight mass spectrometer. Rapid Commun Mass Spectrom (1997) 11:1015-1024.
39. Sechi S, Chait BT: Modification of cysteine residues by alkylation. A tool in peptide mapping and protein identification. Anal Chem (1998) 70:5150-5158.
40. Boguski MS: Biosequence exegesis. (1999) Science 286:453-455.
41. Rachez C, Lemon BD, Suldan Z, Bromleigh V, Gamble M, Naar AM, Erdjument-Bromage H, Tempst P, Freedman LP: Ligand-dependent transcription activation by nuclear receptors requires the DRIP complex. Nature (1999) 398:824-828.
42. Neubauer G, King A, Rappsilber J, Calvio C, Watson M, Ajuh P, Sleeman J, Lamond A, Mann M: Mass Spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex. Nature Genet (1998) 20:46-50.
43. Shou W, Seol JH, Shevchenko A, Baskerville C, Moazed D, Chen ZW, Jang J, Shevchenko A, Charbonneau H, Deshaies RJ: Exit from mitosis Is triggered by Tem1-dependent release of the protein phosphatase Cdc14 from nucleolar RENT complex. Cell (1999) 97:233-244.
44. Grant PA, Schieltz D, Pray-Grant MG, Steger DJ, Reese JC, Yates JR, Workman JL: A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation. Cell (1998) 94:45-53.
45. Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Séraphin B: A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnol (1999) 17:1030-1032.
46. Ciosk R, Zachariae W, Michaelis C, Shevchenko A, Mann M, Nasmyth K: An ESP1/PDS1 complex regulates loss of sister chromatid cohesion at the metaphase to anaphase transition in yeast. Cell (1998) 93:1067-1076.
47. Colas P, Brent R: The impact of two-hybrid and related methods on biotechnology. Trends Biotechnol (1998) 16:355-363.
48. Vidai M, Legrain P: Yeast forward and reverse 'n'-hybrid systems. Nucleic Acids Res (1999) 27:919-929.
49. Fromont-Racine M, Rain JC, Legrain P: Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nature Genet (1997) 16:277-282.
50. Neubauer G, Gottschalk A, Fabrizio P, Seraphin B, Luhrmann R, Mann M: Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry. Proc Natl Acad Sci USA (1997) 94:385-390.
51. Wigge PA, Jensen ON, Holmes S, Soues S, Mann M, Kilmartin JV: Analysis of the Saccharomyces spindle pole by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. J Cell Biol (1998) 141:967-977.
52. Santoni V, Rouquie D, Doumas P, Mansion M, Boutry M, Degand H, Dupree P, Packman L, Sherrier J, Prime T, Bauw G, Posada E, Rouze P, Dehais P, Sahnoun I, Earlier I, Rossignol M: Use of a proteome strategy for tagging proteins present at the plasma membrane. Plant J (1998) 16:633-641.
53. Shevchenko A, Keller P, Scheiffele P, Mann M, Simons K: Identification of components of trans-Golgi network-derived transport vesicles and detergent-insoluble complexes by nanoelectrospray tandem mass spectrometry. Electrophoresis (1997) 18:2591-2600.
54. Pierre P, Mellman I: Exploring the mechanisms of antigen processing by cell fractionation. Curr Opin Immunol (1998) 10:145-153.
55. Roberts RW, Szostak JW: RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc Natl Acad Sci USA (1997) 94:12297-12302.