Advances in protein complex analysis using mass spectrometry

Journal of Physiology

Volumn 563, Issue 1, 2005, Pages 11-21

  Gingras, Anne Claude ^a   Aebersold, Ruedi ^a,b   Raught, Brian ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^b ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN A; PROTEIN ANTIBODY; MULTIPROTEIN COMPLEX; RECOMBINANT PROTEIN; TRANSCRIPTION FACTOR;

CELL FUNCTION; DNA SEQUENCE; MASS SPECTROMETRY; METABOLITE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN PURIFICATION; QUANTITATIVE ANALYSIS; REVIEW; SIGNAL TRANSDUCTION; WESTERN BLOTTING; CHEMICAL LABELING; COMPLEX FORMATION; HOMOLOGOUS RECOMBINATION; HUMAN; INTRACELLULAR SIGNALING; ISOLATION PROCEDURE; ISOTOPE LABELING; LIQUID CHROMATOGRAPHY; PROTEIN DNA INTERACTION; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; PROTEOMICS; SIGNAL NOISE RATIO; TANDEM AFFINITY PURIFICATION;

ANIMALS; GENE EXPRESSION PROFILING; HUMANS; MASS SPECTROMETRY; PROTEIN INTERACTION MAPPING; PROTEINS; PROTEOMICS; SEQUENCE ANALYSIS, PROTEIN;

EID: 14844314804     PISSN: 00223751     EISSN: None     Source Type: Journal    
DOI: 10.1113/jphysiol.2004.080440     Document Type: Review

References (39)

1. Bauer A & Kuster B (2003). Affinity purification-mass spectrometry. Powerful tools for the characterization of protein complexes. Eur J Biochem 270, 570-578.
2. Bertwistle D, Sugimoto M & Sherr CJ (2004). Physical and functional interactions of the Arf tumor suppressor protein with nucleophosmin/B23. Mol Cell Biol 24, 985-996.
3. Blagoev B, Kratchmarova I, Ong SE, Nielsen M, Foster LJ & Mann M (2003). A proteomics strategy to elucidate functional protein - protein interactions applied to EGF signaling. Nat Biotechnol 21 315-318.
4. Blagoev B, Ong SE, Kratchmarova I & Mann M (2004). Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol 22, 1139-1145.
5. Bouwmeester T, Bauch A, Ruffner H, Angrand PO, Bergamini G, Croughton K et al. (2004). A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat Cell Biol 6, 97-105.
6. Brajenovic M, Joberty G, Kuster B, Bouwmeester T & Drewes G (2004). Comprehensive proteomic analysis of human Par protein complexes reveals an interconnected protein network. J Biol Chem 279, 12804-12811.
7. Brand M, Ranish JA, Kummer NT, Hamilton J, Igarashi K, Francastel C, Chi TH, Crabtree GR, Aebersold R & Groudine M (2004). Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics. Nat Struct Mol Biol 11, 73-80.
8. Dziembowski A & Seraphin B (2004). Recent developments in the analysis of protein complexes. FEBS Lett 556, 1-6.
9. Eng J, Martin D & Aebersold R (2005). Tandem mass spectrometry database searching. In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, ed. Dunn M, Jorde L, Little P, Subramaniam S, (in press). John Wiley & Sons Ltd, Chichester, UK.
10. Flory MR, Griffin TJ, Martin D & Aebersold R (2002). Advances in quantitative proteomics using stable isotope tags. Trends Biotechnol 20, S23-29.
11. Forler D, Kocher T, Rode M, Gentzel M, Izaurralde E & Wilm M (2003). An efficient protein complex purification method for functional proteomics in higher eukaryotes. Nat Biotechnol 21, 89-92.
12. Fritze CE & Anderson TR (2000). Epitope tagging: general method for tracking recombinant proteins. Meth Enzymol 327, 3-16.
13. Gagneur J, Krause R, Bouwmeester T & Casari G (2004). Modular decomposition of protein - protein interaction networks. Genome Biol 5, R57.
14. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A et al. (2002). Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147.
15. Giglia-Mari G, Coin F, Ranish JA, Hoogstraten D, Theil A, Wijgers N et al. (2004). A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A. Nat Genet 36, 714-719.
16. Goshe MB & Smith RD (2003). Stable isotope-coded proteomic mass spectrometry. Curr Opin Biotechnol 14, 101-109.
17. Gould KL, Ren L, Feoktistova AS, Jennings JL & Link AJ (2004). Tandem affinity purification and identification of protein complex components. Methods 33, 239-244.
18. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH & Aebersold R (1999). Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17, 994-999.
19. Harlow E & Lane D (1999). Using Antibodies: a Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
20. Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A et al. (2004). The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data. Nat Biotechnol 22, 177-183.
21. Himeda CL, Ranish JA, Angello JC, Maire P, Aebersold R & Hauschka SD (2004). Quantitative proteomic identification of six4 as the trex-binding factor in the muscle creatine kinase enhancer. Mol Cell Biol 24, 2132-2143.
22. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL et al. (2002). Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183.
23. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M & Sakaki Y (2001). A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 98, 4569-4574.
24. Jarvik JW & Telmer CA (1998). Epitope tagging. Annu Rev Genet 32, 601-618.
25. Jeronimo C, Langelier MF, Zeghouf M, Cojocaru M, Bergeron D, Baali D et al. (2004). RPAP1, a novel human RNA polymerase II-associated protein affinity purified with recombinant wild-type and mutated polymerase subunits. Mol Cell Biol 24, 7043-7058.
26. Knuesel M, Wan Y, Xiao Z, Holinger E, Lowe N, Wang W & Liu X (2003). Identification of novel protein - protein interactions using a versatile mammalian tandem affinity purification expression system. Mol Cell Proteomics 2, 1225-1233.
27. Nesvizhskii AI & Aebersold R (2004). Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS. Drug Discov Today 9, 173-181.
28. Oda Y, Owa T, Sato T, Boucher B, Daniels S, Yamanaka H et al. (2003). Quantitative chemical proteomics for identifying candidate drug targets. Anal Chem 75, 2159-2165.
29. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A & Mann M (2002). Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1, 376-386.
30. Ong SE, Foster LJ & Mann M (2003). Mass spectrometric-based approaches in quantitative proteomics. Methods 29, 124-130.
31. Ranish JA, Hahn S, Lu Y, Yi EC, Li XJ, Eng J & Aebersold R (2004). Identification of TFB5, a new component of general transcription and DNA repair factor IIH. Nat Genet 36, 707-713.
32. Ranish JA, Yi EC, Leslie DM, Purvine SO, Goodlett DR, Eng J & Aebersold R (2003). The study of macromolecular complexes by quantitative proteomics. Nat Genet 33, 349-355.
33. Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M & Seraphin B (1999). A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 17, 1030-1032.
34. Rohila JS, Chen M, Cerny R & Fromm ME (2004). Improved tandem affinity purification tag and methods for isolation of protein heterocomplexes from plants. Plant J 38, 172-181.
35. Ross PL, Huang YN, Marchese J, Williamson B, Parker K, Hattan S et al. (2004). Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3, 1154-1169.
36. Sechi S & Oda Y (2003). Quantitative proteomics using mass spectrometry. Curr Opin Chem Biol 7, 70-77.
37. Steen H & Mann M (2004). The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol 5, 699-711.
38. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR et al. (2000). A comprehensive analysis of protein - protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627.
39. Zhou D, Ren JX, Ryan TM, Higgins NP & Townes TM (2004). Rapid tagging of endogenous mouse genes by recombineering and ES cell complementation of tetraploid blastocysts. Nucleic Acids Res 32 e128.