In vivo analysis of proteomes and interactomes using Parallel Affinity Capture (iPAC) coupled to mass spectrometry

Molecular and Cellular Proteomics

Volumn 10, Issue 6, 2011, Pages

  Rees, Johanna S ^a,b,c   Lowe, Nick ^a,b   Armean, Irina M ^a,c   Roote, John ^a   Johnson, Glynnis ^a   Drummond, Emma ^a   Spriggs, Helen ^a   Ryder, Edward ^a   Russell, Steven ^a,c   St Johnston, Daniel ^a,b   Lilley, Kathryn S ^a,c  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

FAS LIGAND; NOTCH RECEPTOR; PHOSPHOPROTEIN PHOSPHATASE; PROTEOME; YELLOW FLUORESCENT PROTEIN; DROSOPHILA PROTEIN; HYBRID PROTEIN; PHOSPHOPROTEIN PHOSPHATASE 1;

ANALYTIC METHOD; ANALYTICAL EQUIPMENT; ARTICLE; BINDING AFFINITY; CELLULAR DISTRIBUTION; DROSOPHILA MELANOGASTER; EMBRYO; IMMUNOPRECIPITATION; IN VIVO STUDY; MASS SPECTROMETRY; NONHUMAN; PARALLEL AFFINITY CAPTURE; PRIORITY JOURNAL; REPRODUCIBILITY; AFFINITY CHROMATOGRAPHY; ANIMAL; CHEMISTRY; ISOLATION AND PURIFICATION; LARVA; METABOLISM; PROTEIN ANALYSIS; PROTEIN BINDING; TANDEM MASS SPECTROMETRY;

DROSOPHILA MELANOGASTER;

ANIMALS; CHROMATOGRAPHY, AFFINITY; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; LARVA; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEIN PHOSPHATASE 1; PROTEOME; RECOMBINANT FUSION PROTEINS; REPRODUCIBILITY OF RESULTS; TANDEM MASS SPECTROMETRY;

EID: 79958007632     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M110.002386     Document Type: Article

References (30)

1. Giot, L., Bader, J. S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y. L., Ooi, C. E., Godwin, B., Vitols, E., Vijayadamodar, G., Pochart, P., Machineni, H., Welsh, M., Kong, Y., Zerhusen, B., Malcolm, R., Varrone, Z., Collis, A., Minto, M., Burgess, S., McDaniel, L., Stimpson, E., Spriggs, F., Williams, J., Neurath, K., Ioime, N., Agee, M., Voss, E., Furtak, K., Renzulli, R., Aanensen, N., Carrolla, S., Bickelhaupt, E., Lazovatsky, Y., DaSilva, A., Zhong, J., Stanyon, C. A., Finley, R. L., Jr., White, K. P., Braverman, M., Jarvie, T., Gold, S., Leach, M., Knight, J., Shimkets, R. A., McKenna, M. P., Chant, J., and Rothberg, J. M. (2003) A protein interaction map of Drosophila melanogaster. Science 302, 1727-1736
2. Parrish, J. R., Gulyas, K. D., and Finley, R. L., Jr. (2006) Yeast two-hybrid contributions to interactome mapping. Curr. Opin. Biotechnol. 17, 387-393
3. Yu, H., Braun, P., Yildirim, M. A., Lemmens, I., Venkatesan, K., Sahalie, J., Hirozane-Kishikawa, T., Gebreab, F., Li, N., Simonis, N., Hao, T., Rual, J. F., Dricot, A., Vazquez, A., Murray, R. R., Simon, C., Tardivo, L., Tam, S., Svrzikapa, N., Fan, C., de Smet, A. S., Motyl, A., Hudson, M. E., Park, J., Xin, X., Cusick, M. E., Moore, T., Boone, C., Snyder, M., Roth, F. P., Barabasi, A. L., Tavernier, J., Hill, D. E., and Vidal, M. (2008) High-quality binary protein interaction map of the yeast interactome network. Science 322(5898): 104-110
4. Bork, P., Jensen, L. J., von Mering, C., Ramani, A. K., Lee, I., and Marcotte, E. M. (2004) Protein interaction networks from yeast to human. Curr. Opin. Struct. Biol. 14, 292-299
5. Vidalain, P. O., Boxem, M., Ge, H., Li, S., and Vidal, M. (2004) Increasing specificity in high-throughput yeast two-hybrid experiments. Methods 32, 363-370 (Pubitemid 38299327)
6. von Mering, C., Jensen, L. J., Kuhn, M., Chaffron, S., Doerks, T., Krüger, B., Snel, B., and Bork, P. (2007) STRING 7-recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 35, D358-362
7. Chang, I. F. (2006) Mass spectrometry-based proteomic analysis of the epitope-tag affinity purified protein complexes in eukaryotes. Proteomics 6, 6158-6166
8. Brizzard, B. L., Chubet, R. G., and Vizard, D. L. (1994) Immunoaffinity purification of FLAG epitope-tagged bacterial alkaline phosphatase using a novel monoclonal antibody and peptide elution. BioTechniques 16, 730-735
9. Gavin, A. C., Bösche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A. M., Cruciat, C. M., Remor, M., Höfert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M. A., Copley, R. R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G., and Superti-Furga, G. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147 (Pubitemid 34059510)
10. Rigaut, G., Shevchenko, A., Rutz, B., Wilm, M., Mann, M., and Séraphin, B. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17, 1030-1032
11. Bader, G. D., and Hogue, C. W. (2002) Analyzing yeast protein-protein interaction data obtained from different sources. Nat. Biotechnol. 20, 991-997
12. Braun, P., Tasan, M., Dreze, M., Barrios-Rodiles, M., Lemmens, I., Yu, H., Sahalie, J. M., Murray, R. R., Roncari, L., de Smet, A. S., Venkatesan, K., Rual, J. F., Vandenhaute, J., Cusick, M. E., Pawson, T., Hill, D. E., Tavernier, J., Wrana, J. L., Roth, F. P., and Vidal, M. (2009) An experimentally derived confidence score for binary protein-protein interactions. Nat. Methods 6, 91-97
13. Formstecher, E., Aresta, S., Collura, V., Hamburger, A., Meil, A., Trehin, A., Reverdy, C., Betin, V., Maire, S., Brun, C., Jacq, B., Arpin, M., Bellaiche, Y., Bellusci, S., Benaroch, P., Bornens, M., Chanet, R., Chavrier, P., Delattre, O., Doye, V., Fehon, R., Faye, G., Galli, T., Girault, J. A., Goud, B., de Gunzburg, J., Johannes, L., Junier, M. P., Mirouse, V., Mukherjee, A., Papadopoulo, D., Perez, F., Plessis, A., Rossé, C., Saule, S., Stoppa- Lyonnet, D., Vincent, A., White, M., Legrain, P., Wojcik, J., Camonis, J., and Daviet, L. (2005) Protein interaction mapping: a Drosophila case study. Genome Res. 15, 376-384 (Pubitemid 40467779)
14. Morin, X., Daneman, R., Zavortink, M., and Chia, W. (2001) A protein trap strategy to detect GFP-tagged proteins expressed from their endogenous loci in Drosophila. Proc. Natl. Acad. Sci. U.S.A. 98, 15050-15055
15. Buszczak, M., Paterno, S., Lighthouse, D., Bachman, J., Planck, J., Owen, S., Skora, A. D., Nystul, T. G., Ohlstein, B., Allen, A., Wilhelm, J. E., Murphy, T. D., Levis, R. W., Matunis, E., Srivali, N., Hoskins, R. A., and Spradling, A. C. (2007) The carnegie protein trap library: a versatile tool for Drosophila developmental studies. Genetics 175, 1505-1531
16. Spradling, A. C., Stern, D., Beaton, A., Rhem, E. J., Laverty, T., Mozden, N., Misra, S., and Rubin, G. M. (1999) The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital drosophila genes. Genetics 153, 135-177
17. Cary, L. C., Goebel, M., Corsaro, B. G., Wang, H. G., Rosen, E., and Fraser, M. J. (1989) Transposon mutagenesis of baculoviruses: analysis of Trichoplusia ni transposon IFP2 insertions within the FP-locus of nuclear polyhedrosis viruses. Virology 172, 156-169 (Pubitemid 19221445)
18. Horn, C., Offen, N., Nystedt, S., Häcker, U., and Wimmer, E. A. (2003) piggyBac-based insertional mutagenesis and enhancer detection as a tool for functional insect genomics. Genetics 163, 647-661
19. Missirlis, F., Holmberg, S., Georgieva, T., Dunkov, B. C., Rouault, T. A., and Law, J. H. (2006) Characterization of mitochondrial ferritin in Drosophila. Proc. Natl. Acad. Sci. U.S.A. 103, 5893-5898
20. Wilhelm, J. E., Buszczak, M., and Sayles, S. (2005) Efficient protein trafficking requires trailer hitch, a component of a ribonucleoprotein complex localized to the ER in Drosophila. Dev Cell 9, 675-685 (Pubitemid 41555149)
21. Veraksa, A., Bauer, A., and Artavanis-Tsakonas, S. (2005) Analyzing protein complexes in Drosophila with tandem affinity purification-mass spectrometry. Developmental Dynamics 232, 827-834 (Pubitemid 40315300)
22. Lyne, R., Smith, R., Rutherford, K., Wakeling, M., Varley, A., Guillier, F., Janssens, H., Ji, W. Y., Mclaren, P., North, P., Rana, D., Riley, T., Sullivan, J., Watkins, X., Woodbridge, M., Lilley, K., Russell, S., Ashburner, M., Mizuguchi, K., and Micklem, G. (2007) FlyMine: an integrated database for Drosophila and Anopheles genomics. Genome Biol. 2007; 8(7):R129.
23. Lichty, J. J., Malecki, J. L., Agnew, H. D., Michelson-Horowitz, D. J., and Tan, S. (2005) Comparison of affinity tags for protein purification. Protein Expression and Purification 41, 98-105 (Pubitemid 40406368)
24. Knuesel, M., Wan, Y., Xiao, Z., Holinger, E., Lowe, N., Wang, W., and Liu, X. (2003) Identification of novel protein-protein interactions using a versatile mammalian tandem affinity purification expression system. Mol. Cell Proteomics 2, 1225-1233
25. Przewloka, M. R., Zhang, W., Costa, P., Archambault, V., D'Avino, P. P., Lilley, K. S., Laue, E. D., McAinsh, A. D., and Glover, D. M. (2007) Molecular analysis of core kinetochore composition and assembly in Drosophila melanogaster. PLoS One 2, e478
26. Brunner, E., Ahrens, C. H., Mohanty, S., Baetschmann, H., Loevenich, S., Potthast, F., Deutsch, E. W., Panse, C., de Lichtenberg, U., Rinner, O., Lee, H., Pedrioli, P. G., Malmstrom, J., Koehler, K., Schrimpf, S., Krijgsveld, J., Kregenow, F., Heck, A. J., Hafen, E., Schlapbach, R., and Aebersold, R. (2007) A high-quality catalog of the Drosophila melanogaster proteome. Nat. Biotechnol. 25, 576-583
27. Trinkle-Mulcahy, L., Boulon, S., Lam, Y. W., Urcia, R., Boisvert, F. M., Vandermoere, F., Morrice, N. A., Swift, S., Rothbauer, U., Leonhardt, H., and Lamond, A. (2008) Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes. J. Cell Biol. 183, 223-239
28. Desiere, F., Deutsch, E. W., King, N. L., Nesvizhskii, A. I., Mallick, P., Eng, J., Chen, S., Eddes, J., Loevenich, S. N., and Aebersold, R. (2006) The PeptideAtlas project. Nucleic Acids Res. 34, D655-658
29. Vereshchagina, N., Bennett, D., Szöor, B., Kirchner, J., Gross, S., Vissi, E., White-Cooper, H., and Alphey, L. (2004) The essential role of PP1 beta in Drosophila is to regulate nonmuscle myosin. Mol. Biol. Cell 15, 4395-4405
30. Aleksic, J., Lazic, R., Müller, I., Russell, S. R., and Adryan, B. (2009) Biases in Drosophila melanogaster protein trap screens. BMC Genomics 10, 249