Beyond hairballs: The use of quantitative mass spectrometry data to understand protein–protein interactions
Open accessAbstract
The past 10 years have witnessed a dramatic proliferation in the availability of protein interaction data. However, for interaction mapping based on affinity purification coupled with mass spectrometry (AP‐MS), there is a wealth of information present in the datasets that often goes unrecorded in public repositories, and as such remains largely unexplored. Further, how this type of data is represented and used by bioinformaticians has not been well established. Here, we point out some common mistakes in how AP‐MS data are handled, and describe how protein complex organization and interaction dynamics can be inferred using quantitative AP‐MS approaches.
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Cites
Global quantification of mammalian gene expression control
Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566 · see citing works
A novel genetic system to detect protein–protein interactions
Fields, S., & Song, O.-K. (1989) · Nature · doi:10.1038/340245a0 · Cited by 6,152 · see citing works
Functional organization of the yeast proteome by systematic analysis of protein complexes
Gavin, A., Böesche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A., Cruciat, C., et al. (2002) · Nature · doi:10.1038/415141a · Cited by 4,729 · see citing works
A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. (2000) · Nature · doi:10.1038/35001009 · Cited by 4,706 · see citing works
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
Ho, Y., Gruhler, A., Heilbut, A. M., Bader, G. D., Moore, L., Adams, S., Millar, A., Taylor, P. P., Bennett, K. L., Boutilier, K., et al. (2002) · Nature · doi:10.1038/415180a · Cited by 3,573 · see citing works
A comprehensive two-hybrid analysis to explore the yeast protein interactome
Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., & Sakaki, Y. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.061034498 · Cited by 3,566 · see citing works
Human Protein Reference Database--2009 update
Prasad, T. S. K., Goel, R., Kandasamy, K., Keerthikumar, S., Kumar, S., Mathivanan, S., Telikicherla, D., Raju, R., Shafreen, R. B., Venugopal, A., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn892 · Cited by 3,241 · see citing works
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
Krogan, N. J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A., et al. (2006) · Nature · doi:10.1038/nature04670 · Cited by 2,915 · see citing works
Gillet, L. C., Navarro, P., Tate, S., Röst, H., Selevsek, N., Reiter, L., Bonner, R., & Aebersold, R. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o111.016717 · Cited by 2,877 · see citing works
Proteome survey reveals modularity of the yeast cell machinery
Gavin, A., Aloy, P., Grandi, P., Krause, R., Böesche, M., Marzioch, M., Rau, C., Jensen, L. J., Bastuck, S., Dümpelfeld, B., et al. (2006) · Nature · doi:10.1038/nature04532 · Cited by 2,544 · see citing works
A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome
Stelzl, U., Worm, U., Lalowski, M. M., Haenig, C., Brembeck, F. H., Goehler, H., Strödicke, M., Zenkner, M., Schoenherr, A., Koeppen, S., et al. (2005) · Cell · doi:10.1016/j.cell.2005.08.029 · Cited by 2,389 · see citing works
A Protein Interaction Map of Drosophila melanogaster
Giot, L., Bader, J. S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y. L., Ooi, C., Godwin, B., Vitols, E., et al. (2003) · Science · doi:10.1126/science.1090289 · Cited by 2,266 · see citing works
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., & Gygi, S. P. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0832254100 · Cited by 1,733 · see citing works
A Map of the Interactome Network of the Metazoan C. elegans
Li, S., Armstrong, C. M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P., Han, J.-D. J., Chesneau, A., Hao, T., et al. (2004) · Science · doi:10.1126/science.1091403 · Cited by 1,628 · see citing works
Network organization of the human autophagy system
Behrends, C., Sowa, M. E., Gygi, S. P., & Harper, J. W. (2010) · Nature · doi:10.1038/nature09204 · Cited by 1,554 · see citing works
Defining the Human Deubiquitinating Enzyme Interaction Landscape
Sowa, M. E., Bennett, E. J., Gygi, S. P., & Harper, J. W. (2009) · Cell · doi:10.1016/j.cell.2009.04.042 · Cited by 1,512 · see citing works
Selected reaction monitoring for quantitative proteomics: a tutorial
Lange, V., Picotti, P., Domon, B., & Aebersold, R. H. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.61 · Cited by 1,396 · see citing works
High-Quality Binary Protein Interaction Map of the Yeast Interactome Network
Yu, H., Braun, P., Yıldırım, M. A., Lemmens, I., Venkatesan, K., Sahalie, J., Hirozane-Kishikawa, T., Gebreab, F., Li, N., Simonis, N., et al. (2008) · Science · doi:10.1126/science.1158684 · Cited by 1,392 · see citing works
The IntAct molecular interaction database in 2012
Kerrien, S., Aranda, B., Breuza, L., Bridge, A. J., Broackes-Carter, F., Chen, C. C. L., Duesbury, M., Dumousseau, M., Feuermann, M., Hinz, U. G., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1088 · Cited by 1,151 · see citing works
Addona, T. A., Abbatiello, S. E., Schilling, B., Skates, S. J., Mani, D. R., Bunk, D. M., Spiegelman, C. H., Zimmerman, L. J., Ham, A.-J. L., Keshishian, H., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1546 · Cited by 1,037 · see citing works
Statistical Analysis of Membrane Proteome Expression Changes in Saccharomyces cerevisiae
Zybailov, B. L., Mosley, A. L., Sardiu, M. E., Coleman, M. K., Florens, L. A., & Washburn, M. P. (2006) · Journal of Proteome Research · doi:10.1021/pr060161n · Cited by 1,031 · see citing works
A physical and functional map of the human TNF-α/NF-κB signal transduction pathway
Bouwmeester, T., Bauch, A., Ruffner, H., Angrand, P., Bergamini, G., Croughton, K., Cruciat, C., Eberhard, D., Gagneur, J., Ghidelli, S., et al. (2004) · Nature Cell Biology · doi:10.1038/ncb1086 · Cited by 1,030 · see citing works
Large‐scale mapping of human protein–protein interactions by mass spectrometry
Ewing, R. M., Chu, P. C., Elisma, F., Li, H., Taylor, P. P., Climie, S. C., McBroom, L. D. B., Robinson, M. D., O'Connor, L., Li, M. M., et al. (2007) · Molecular Systems Biology · doi:10.1038/msb4100134 · Cited by 985 · see citing works
Protein production and purification
Biologiques, A. E. F. D. M., Facility, O. P. P., Initiative, R. S. G., & SPINE2-Complexes (2008) · Nature Methods · doi:10.1038/nmeth.f.202 · Cited by 919 · see citing works
Evidence for Network Evolution in an Arabidopsis Interactome Map
Dreze, M., Carvunis, A., Charloteaux, B., Galli, M., Pevzner, S. J., Tasan, M., Ahn, Y., Balumuri, P., Barabási, A.-Ĺ., Bautista, V., et al. (2011) · Science · doi:10.1126/science.1203877 · Cited by 895 · see citing works
Independently Evolved Virulence Effectors Converge onto Hubs in a Plant Immune System Network
Mukhtar, M. S., Carvunis, A., Dreze, M., Epple, P., Steinbrenner, J., Moore, J. D., Tasan, M., Galli, M., Hao, T., Nishimura, M. T., et al. (2011) · Science · doi:10.1126/science.1203659 · Cited by 873 · see citing works
The BioGRID Interaction Database: 2011 update
Stark, C., Breitkreutz, B., Chatr‐aryamontri, A., Boucher, L., Oughtred, R., Livstone, M. S., Nixon, J., Auken, K. M. V., Wang, X., Shi, X., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1116 · Cited by 853 · see citing works
Ito, T., Tashiro, K., Muta, S., Ozawa, R., Chiba, T., Nishizawa, M., Yamamoto, K., Kuhara, S., & Sakaki, Y. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.3.1143 · Cited by 814 · see citing works
SAINT: probabilistic scoring of affinity purification–mass spectrometry data
Choi, H., Larsen, B., Lin, Z.-Y., Breitkreutz, A., Mellacheruvu, D., Fermin, D., Qin, Z. S., Tyers, M., Gingras, A.-C., & Nesvizhskii, A. I. (2011) · Nature Methods · doi:10.1038/nmeth.1541 · Cited by 800 · see citing works
Self-citationGlobal landscape of HIV–human protein complexes
Jäger, S., Cimermancic, P., Gulbahce, N., Johnson, J. R., McGovern, K. E., Clarke, S. C., Shales, M., Mercenne, G., Pache, L., Li, K., et al. (2012) · Nature · doi:10.1038/nature10719 · Cited by 731 · see citing works
High-Throughput Mapping of a Dynamic Signaling Network in Mammalian Cells
Barrios‐Rodiles, M., Brown, K. R., Ozdamar, B., Bose, R., Liu, Z., Donovan, R. S., Shinjo, F., Liu, Y., Dembowy, J., Taylor, I. W., et al. (2005) · Science · doi:10.1126/science.1105776 · Cited by 726 · see citing works
Analysis of protein complexes using mass spectrometry
Gingras, A., Gstaiger, M., Raught, B., & Aebersold, R. H. (2007) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2208 · Cited by 709 · see citing works
Self-citationMoyer, S. E., Lewis, P. W., & Botchan, M. R. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0602400103 · Cited by 704 · see citing works
A Global Protein Kinase and Phosphatase Interaction Network in Yeast
Breitkreutz, A., Choi, H., Sharom, J. R., Boucher, L., Neduva, V., Larsen, B. G., Lin, Z., Breitkreutz, B., Stark, C., Liu, G., et al. (2010) · Science · doi:10.1126/science.1176495 · Cited by 686 · see citing works
Self-citationCIP2A inhibits PP2A in human malignancies
Junttila, M. R., Puustinen, P., Niemelä, M., Ahola, R., Arnold, H., Böttzauw, T., Ala-aho, R., Nielsen, C., Ivaska, J., Taya, Y., et al. (2007) · Cell · doi:10.1016/j.cell.2007.04.044 · Cited by 677 · see citing works
A Protein Complex Network of Drosophila melanogaster
Guruharsha, K. G., Rual, J.-F. M., Zhai, B., Mintseris, J., Vaidya, P., Vaidya, N., Beekman, C. N., Wong, C. S. F., Rhee, D. Y., Cenaj, O., et al. (2011) · Cell · doi:10.1016/j.cell.2011.08.047 · Cited by 654 · see citing works
Protein interaction mapping: ADrosophilacase studyPreprint
Formstecher, É., Aresta, S., Collura, V., Hamburger, A., Meil, A., Trehin, A., Reverdy, C., Betin, V. M. S., Maire, S., Brun, C., et al. (2005) · Genome Research · doi:10.1101/gr.2659105 · Cited by 581 · see citing works
A public genome-scale lentiviral expression library of human ORFs
Yang, X., Boehm, J. S., Yang, X., Salehi-Ashtiani, K., Hao, T., Shen, Y., Lubonja, R., Thomas, S. R., Alkan, O., Bhimdi, T., et al. (2011) · Nature Methods · doi:10.1038/nmeth.1638 · Cited by 570 · see citing works
Systematic Analysis of Human Protein Complexes Identifies Chromosome Segregation Proteins
Hutchins, J. R. A., Toyoda, Y., Hegemann, B., Poser, I., Hèriché, J.-K., Sykora, M. M., Augsburg, M., Hudecz, O., Buschhorn, B. A., Bulkescher, J., et al. (2010) · Science · doi:10.1126/science.1181348 · Cited by 502 · see citing works
Biochemical and genetic analysis of the yeast proteome with a movable ORF collectionPreprint
Gelperin, D. M., White, M. A., Wilkinson, M. L., Kon, Y., Kung, L. A., Wise, K. J., Lopez-Hoyo, N., Jiang, L., Piccirillo, S., Yu, H., et al. (2005) · Genes & Development · doi:10.1101/gad.1362105 · Cited by 479 · see citing works
Beynon, R. J., Doherty, M. K., Pratt, J. M., & Gaskell, S. J. (2005) · Nature Methods · doi:10.1038/nmeth774 · Cited by 472 · see citing works
Proteome organization in a genome-reduced bacterium
Kühner, S., van Noort, V., Betts, M. J., Leo-Macias, A., Batisse, C., Rode, M., Yamada, T., Maier, T., Bader, S., Beltran-Alvarez, P., et al. (2009) · Science · doi:10.1126/science.1176343 · Cited by 471 · see citing works
Defining human ERAD networks through an integrative mapping strategy
Christianson, J. C., Olzmann, J. A., Shaler, T. A., Sowa, M. E., Bennett, E. J., Richter, C. M., Tyler, R. E., Greenblatt, E. J., Harper, J. W., & Kopito, R. R. (2011) · Nature Cell Biology · doi:10.1038/ncb2383 · Cited by 470 · see citing works
Probing Native Protein Structures by Chemical Cross-linking, Mass Spectrometry, and Bioinformatics
Leitner, A., Walzthoeni, T., Kahraman, A., Herzog, F., Rinner, O., Beck, M., & Aebersold, R. H. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r000001-mcp201 · Cited by 459 · see citing works
An experimentally derived confidence score for binary protein-protein interactions
Falter‐Braun, P., Tasan, M., Dreze, M., Barrios‐Rodiles, M., Lemmens, I. H., Yu, H., Sahalie, J. M., Murray, R. R., Roncari, L., de Smet, A.-S., et al. (2008) · Nature Methods · doi:10.1038/nmeth.1281 · Cited by 444 · see citing works
Jerónimo, C., Forget, D., Bouchard, A., Li, Q., Chua, G., Poitras, C., Thérien, C., Bergeron, D., Bourassa, S., Greenblatt, J., et al. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.06.027 · Cited by 444 · see citing works
Isotope-labeled Protein Standards
Brun, V., Dupuis, A., Adrait, A., Marcellin, M., Thomas, D. Y., Court, M., Vandenesch, F., & Garin, J. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700163-mcp200 · Cited by 443 · see citing works
Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions
Hubner, N. C., Bird, A. W., Cox, J., Splettstoesser, B., Bandilla, P., Poser, I., Hyman, A., & Mann, M. (2010) · Journal of Cell Biology · doi:10.1083/jcb.200911091 · Cited by 440 · see citing works
Analysis of the Human Endogenous Coregulator Complexome
Malovannaya, A., Lanz, R. B., Jung, S. Y., Bulynko, Y., Le, N. T., Chan, D. W., Ding, C., Shi, Y., Yucer, N., Krenciute, G., et al. (2011) · Cell · doi:10.1016/j.cell.2011.05.006 · Cited by 432 · see citing works
Rappsilber, J. (2010) · Journal of Structural Biology · doi:10.1016/j.jsb.2010.10.014 · Cited by 414 · see citing works
Dual Role of Mitofilin in Mitochondrial Membrane Organization and Protein Biogenesis
von der Malsburg, K., Müller, J. M., Bohnert, M., Oeljeklaus, S., Kwiatkowska, P., Becker, T., Łoniewska-Lwowska, A., Wiese, S., Rao, S., Milenkovic, D., et al. (2011) · Developmental Cell · doi:10.1016/j.devcel.2011.08.026 · Cited by 412 · see citing works
Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis
Griffin, N. M., Yu, J., Long, F., Oh, P., Shore, S., Li, Y., Koziol, J., & Schnitzer, J. E. (2009) · Nature Biotechnology · doi:10.1038/nbt.1592 · Cited by 400 · see citing works
Functional Proteomics Identify Cornichon Proteins as Auxiliary Subunits of AMPA Receptors
Schwenk, J., Harmel, N., Zolles, G., Bildl, W., Kulik, Á., Heimrich, B., Chisaka, O., Jónás, P., Schulte, U., Fakler, B., et al. (2009) · Science · doi:10.1126/science.1167852 · Cited by 388 · see citing works
A roadmap to generate renewable protein binders to the human proteome
Renewable Protein Binder Working Group, Colwill, K., & Gräslund, S. (2011) · Nature Methods · doi:10.1038/nmeth.1607 · Cited by 378 · see citing works
Significance Analysis of Spectral Count Data in Label-free Shotgun Proteomics
Choi, H., Fermin, D., & Nesvizhskii, A. I. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800203-mcp200 · Cited by 364 · see citing works
Goudreault, M., D'Ambrosio, L. M., Kean, M. J., Mullin, M. J., Larsen, B. G., Sanchez, A., Chaudhry, S., Chen, G. I., Sicheri, F., Nesvizhskii, A. I., et al. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800266-mcp200 · Cited by 359 · see citing works
Self-citationTargeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana
Leene, J. V., Hollunder, J., Eeckhout, D., Persiau, G., Slijke, E. V. D., Stals, H., Isterdael, G. V., Verkest, A., Neirynck, S., Buffel, Y., et al. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.53 · Cited by 342 · see citing works
Li, S., Wang, L., Berman, M. A., Kong, Y., & Dorf, M. E. (2011) · Immunity · doi:10.1016/j.immuni.2011.06.014 · Cited by 334 · see citing works
Native GABAB receptors are heteromultimers with a family of auxiliary subunits
Schwenk, J., Metz, M., Zolles, G., Tureček, R., Fritzius, T., Bildl, W., Tarusawa, E., Kulik, Á., Unger, A., Ivankova, K., et al. (2010) · Nature · doi:10.1038/nature08964 · Cited by 333 · see citing works
Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network
Simonis, N., Rual, J.-F. M., Carvunis, A., Tasan, M., Lemmens, I. H., Hirozane-Kishikawa, T., Hao, T., Sahalie, J. M., Venkatesan, K., Gebreab, F., et al. (2008) · Nature Methods · doi:10.1038/nmeth.1279 · Cited by 303 · see citing works
Quantitative proteomics of the Cav2 channel nano-environments in the mammalian brain
Müller, C. S., Haupt, A., Bildl, W., Schindler, J., Knaus, H., Meissner, M., Rammner, B., Striessnig, J., Flockerzi, V., Fakler, B., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1005940107 · Cited by 299 · see citing works
Cell fate decisions are specified by the dynamic ERK interactome
von Kriegsheim, A., Baiocchi, D., Birtwistle, M. R., Sumpton, D. P., Bienvenut, W. V., Morrice, N. A., Yamada, K., Lamond, A. I., Kalna, G., Orton, R. J., et al. (2009) · Nature Cell Biology · doi:10.1038/ncb1994 · Cited by 287 · see citing works
hORFeome v3.1: A resource of human open reading frames representing over 10,000 human genes
Lamesch, P., Li, N., Milstein, S., Fan, C., Hao, T., Szabo, G., Hu, Z., Venkatesan, K., Bethel, G., Martin, P., et al. (2007) · Genomics · doi:10.1016/j.ygeno.2006.11.012 · Cited by 272 · see citing works
Nilsson, P., Paavilainen, L., Larsson, K., Ödling, J., Sundberg, M., Andersson, A., Kampf, C., Persson, A., Szigyarto, C., Ottosson, J., et al. (2005) · Proteomics · doi:10.1002/pmic.200500072 · Cited by 269 · see citing works
An integrated workflow for charting the human interaction proteome: insights into the PP2A system
Glatter, T., Wepf, A., Aebersold, R. H., & Gstaiger, M. (2009) · Molecular Systems Biology · doi:10.1038/msb.2008.75 · Cited by 259 · see citing works
Zhou, M., Sandercock, A. M., Fraser, C. S., Ridlova, G., Stephens, E., Schenauer, M. R., Yokoi-Fong, T., Barsky, D., Leary, J. A., Hershey, J. W. B., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0801313105 · Cited by 256 · see citing works
Toward an understanding of the protein interaction network of the human liver
Wang, J., Huo, K., Ma, L., Tang, L., Li, D., Huang, X., Yuan, Y., Li, C., Wang, W., Guan, W., et al. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.67 · Cited by 243 · see citing works
Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics
Sardiu, M. E., Cai, Y., Jin, J., Swanson, S. K., Conaway, R. C., Conaway, J. W., Florens, L., & Washburn, M. P. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706983105 · Cited by 226 · see citing works
Crosslinking combined with mass spectrometry for structural proteomics
Petrotchenko, E. V., & Borchers, C. H. (2010) · Mass Spectrometry Reviews · doi:10.1002/mas.20293 · Cited by 208 · see citing works
A human MAP kinase interactome
Bandyopadhyay, S., Chiang, C.-Y., Srivastava, J., Gersten, M. J., White, S. M., Bell, R. N., Kurschner, C., Martin, C., Smoot, M., Sahasrabudhe, S. R., et al. (2010) · Nature Methods · doi:10.1038/nmeth.1506 · Cited by 203 · see citing works
Alkhaja, A. K., Jans, D. C., Nikolov, M., Vukotic, M., Lytovchenko, O., Ludewig, F., Schliebs, W., Riedel, D., Urlaub, H., Jakobs, S., et al. (2011) · Molecular Biology of the Cell · doi:10.1091/mbc.e11-09-0774 · Cited by 193 · see citing works
Baker, C. L., Kettenbach, A. N., Loros, J., Gerber, S. A., & Dunlap, J. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.04.023 · Cited by 193 · see citing works
A Drosophila protein-interaction map centered on cell-cycle regulators
Stanyon, C. A., Liu, G., Mangiola, B. A., Patel, N. H., Giot, L., Kuang, B., Zhang, H., Zhong, J., & Finley, R. L. (2004) · Genome biology · doi:10.1186/gb-2004-5-12-r96 · Cited by 190 · see citing works
Identifying Dynamic Interactors of Protein Complexes by Quantitative Mass Spectrometry
Wang, X., & Huang, L. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700261-mcp200 · Cited by 187 · see citing works
A Novel, Evolutionarily Conserved Protein Phosphatase Complex Involved in Cisplatin Sensitivity
Gingras, A., Caballero, M., Zarske, M., Sanchez, A., Hazbun, T. R., Fields, S., Sonenberg, N., Hafen, E., Raught, B., & Aebersold, R. H. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500231-mcp200 · Cited by 186 · see citing works
Self-citationRinner, O., Mueller, L. N., Hubálek, M., Müller, M., Gstaiger, M., & Aebersold, R. H. (2007) · Nature Biotechnology · doi:10.1038/nbt1289 · Cited by 162 · see citing works
Lee, K. K., Sardiu, M. E., Swanson, S. K., Gilmore, J. M., Torok, M., Grant, P. A., Florens, L. A., Workman, J. L., & Washburn, M. P. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.40 · Cited by 160 · see citing works
Rivers, J., Simpson, D. M., Robertson, D. H. L., Gaskell, S. J., & Beynon, R. J. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m600456-mcp200 · Cited by 153 · see citing works
Quantitative interaction proteomics using mass spectrometry
Wepf, A., Glatter, T., Schmidt, A., Aebersold, R. H., & Gstaiger, M. (2009) · Nature Methods · doi:10.1038/nmeth.1302 · Cited by 151 · see citing works
Gebert, N., Gebert, M., Oeljeklaus, S., von der Malsburg, K., Stroud, D. A., Kulawiak, B., Wirth, C., Zahedi, R. P., Doležal, P., Wiese, S., et al. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.09.025 · Cited by 145 · see citing works
Composition and Topology of the Endoplasmic Reticulum–Mitochondria Encounter Structure
Stroud, D. A., Oeljeklaus, S., Wiese, S., Bohnert, M., Lewandrowski, U., Sickmann, A., Guiard, B., van der Laan, M., Warscheid, B., & Wiedemann, N. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.09.012 · Cited by 144 · see citing works
Protein Significance Analysis in Selected Reaction Monitoring (SRM) Measurements
Chang, C.-Y., Picotti, P., Hüttenhain, R., Heinzelmann-Schwarz, V. A., Jovanović, M., Aebersold, R. H., & Olga Vitek, A. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.014662 · Cited by 144 · see citing works
Structure-Function Analysis of Core STRIPAK Proteins
Kean, M. J., Ceccarelli, D. F. J., Goudreault, M., Sanches, M., Tate, S. A., Larsen, B. G., Gibson, L. C. D., Derry, W. B., Scott, I. C., Pelletier, L., et al. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.214486 · Cited by 142 · see citing works
Self-citationThe completion of the Mammalian Gene Collection (MGC)Preprint
The MGC Project Team, Temple, G. F., Gerhard, D. S., Rasooly, R. S., Feingold, E. A., Good, P. J., Robinson, C., Mandich, A., Derge, J. G., Lewis, J., et al. (2009) · Genome Research · doi:10.1101/gr.095976.109 · Cited by 134 · see citing works
Affinity-purification mass spectrometry (AP-MS) of serine/threonine phosphatases
Chen, G. I., & Gingras, A.-C. (2007) · Methods · doi:10.1016/j.ymeth.2007.02.018 · Cited by 114 · cited 1× · see citing works
“can help to maintain interactors that would otherwise be lost [48,89].”
BackgroundSelf-citationSinz, A. (2010) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-009-3405-5 · Cited by 111 · see citing works
A Novel Proteomics Approach for the Discovery of Chromatin-associated Protein Networks
Lambert, J., MITCHELL, L. A., Rudner, A. D., Baetz, K., & Figeys, D. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800447-mcp200 · Cited by 108 · see citing works
Integrating mass spectrometry of intact protein complexes into structural proteomics
Hyung, S., & Ruotolo, B. T. (2012) · PROTEOMICS · doi:10.1002/pmic.201100520 · Cited by 102 · see citing works
Kaake, R. M., Wang, X., & Huang, L. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r110.000265 · Cited by 101 · see citing works
Howson, R. W., Huh, W., Ghaemmaghami, S., Falvo, J. V., Bower, K., Belle, A., Dephoure, N., Wykoff, D. D., Weissman, J. S., & O’Shea, E. K. (2005) · Comparative and Functional Genomics · doi:10.1002/cfg.449 · Cited by 93 · see citing works
Friedman, A. A., Tucker, G., Singh, R., Yan, D., Vinayagam, A., Hu, Y., Binari, R. C., Hong, P., Sun, X., Porto, M., et al. (2011) · Science Signaling · doi:10.1126/scisignal.2002029 · Cited by 89 · see citing works
Elschenbroich, S., & Kislinger, T. (2010) · Molecular BioSystems · doi:10.1039/c0mb00159g · Cited by 81 · see citing works
PP4R4/KIAA1622 Forms a Novel Stable Cytosolic Complex with Phosphoprotein Phosphatase 4
Chen, G. I., Tisayakorn, S., Jørgensen, C., D'Ambrosio, L. M., Goudreault, M., & Gingras, A. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m803443200 · Cited by 80 · see citing works
Self-citationFunctional protein microarray technology
Hu, S., Xie, Z., Qian, J. X., Blackshaw, S., & Zhu, H. (2010) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.118 · Cited by 80 · see citing works
Ceccarelli, D. F. J., Laister, R. C., Mulligan, V. K., Kean, M. J., Goudreault, M., Scott, I. C., Derry, W. B., Chakrabartty, A., Gingras, A., & Sicheri, F. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.213777 · Cited by 74 · see citing works
Self-citationSkarra, D. V., Goudreault, M., Choi, H., Mullin, M. J., Nesvizhskii, A. I., Gingras, A., & Honkanen, R. E. (2011) · PROTEOMICS · doi:10.1002/pmic.201000770 · Cited by 73 · see citing works
Self-citationStengel, F., Aebersold, R. H., & Robinson, C. V. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r111.014027 · Cited by 71 · see citing works
Defining the budding yeast chromatin‐associated interactome
Lambert, J., Fillingham, J., Siahbazi, M., Greenblatt, J., Baetz, K., & Figeys, D. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.104 · Cited by 69 · see citing works
Choi, H., Glatter, T., Gstaiger, M., & Nesvizhskii, A. I. (2012) · Journal of Proteome Research · doi:10.1021/pr201185r · Cited by 68 · see citing works
Mousson, F., Kolkman, A., Pijnappel, W. W. M. P., Timmers, H. T. M., & Heck, A. J. R. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700306-mcp200 · Cited by 67 · see citing works
Literature curation of protein interactions: measuring agreement across major public databases
Turinsky, A. L., Razick, S., Turner, B., Donaldson, I. M., & Wodak, S. J. (2010) · Database · doi:10.1093/database/baq026 · Cited by 64 · see citing works
Glatter, T., Schittenhelm, R. B., Rinner, O., Roguska, K., Wepf, A., Jünger, M. A., Köhler, K., Jevtov, I., Choi, H., Schmidt, A., et al. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.79 · Cited by 62 · see citing works
Falter‐Braun, P. (2012) · PROTEOMICS · doi:10.1002/pmic.201100598 · Cited by 56 · see citing works
Trinkle‐Mulcahy, L. (2012) · PROTEOMICS · doi:10.1002/pmic.201100438 · Cited by 53 · see citing works
Modeling Contaminants in AP-MS/MS Experiments
Lavallée‐Adam, M., Cloutier, P., Coulombe, B., & Blanchette, M. (2010) · Journal of Proteome Research · doi:10.1021/pr100795z · Cited by 49 · see citing works
Michnick, S. W., Ear, P. H., Landry, C. R., Malleshaiah, M. K., & Messier, V. (2010) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(10)70014-8 · Cited by 46 · see citing works
The full-ORF clone resource of the German cDNA Consortium
Bechtel, S., Rosenfelder, H., Duda, A., Schmidt, C., Ernst, U., Wellenreuther, R., Mehrle, A., Schuster, C., Bahr, A., Blöcker, H., et al. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-399 · Cited by 45 · see citing works
Oeljeklaus, S., Reinartz, B. S., Wolf, J., Wiese, S., Tonillo, J., Podwojski, K., Kuhlmann, K., Stephan, C., Meyer, H. E., Schliebs, W., et al. (2012) · Journal of Proteome Research · doi:10.1021/pr3000333 · Cited by 45 · see citing works
New dimensions in the study of protein complexes using quantitative mass spectrometry
Oeljeklaus, S., Meyer, H. E., & Warscheid, B. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.04.018 · Cited by 41 · see citing works
Michnick, S. W., Ear, P. H., Landry, C. R., Malleshaiah, M. K., & Messier, V. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-160-4_25 · Cited by 37 · see citing works
Sardiu, M. E., Gilmore, J. M., Carrozza, M. J., Li, B., Workman, J. L., Florens, L. A., & Washburn, M. P. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007310 · Cited by 36 · see citing works
Strategies for membrane interaction proteomics: No mass spectrometry required
Lam, M. H. Y., & Štagljar, I. (2012) · PROTEOMICS · doi:10.1002/pmic.201100471 · Cited by 28 · see citing works
Automated production of recombinant human proteins as resource for proteome research
Kohl, T., Schmidt, C., Wiemann, S., Poustka, A., & Korf, U. (2008) · Proteome Science · doi:10.1186/1477-5956-6-4 · Cited by 27 · see citing works
A Biomedically Enriched Collection of 7000 Human ORF Clones
Rolfs, A., Hu, Y., Ebert, L., Hoffmann, D., Zuo, D., Ramachandran, N., Raphael, J., Kelley, F., McCarron, S., Jepson, D. A., et al. (2008) · PLoS ONE · doi:10.1371/journal.pone.0001528 · Cited by 21 · see citing works
Systematic Cloning of an ORFeome Using the Gateway System
Matsuyama, A., & Yoshida, M. (2009) · Methods in molecular biology · doi:10.1007/978-1-60761-232-2_2 · Cited by 19 · see citing works
Mapping physical interactions within chromatin by proteomic approaches
Lambert, J., Pawson, T. J., & Gingras, A. (2012) · PROTEOMICS · doi:10.1002/pmic.201100547 · Cited by 17 · see citing works
Self-citationProfiling Protein Interaction Networks with Functional Protein Microarrays
Mattoon, D., & Schweitzer, B. I. (2009) · Methods in molecular biology · doi:10.1007/978-1-60761-175-2_4 · Cited by 12 · see citing works
Flagged first, then by citations
Cited by
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Protein Analysis by Shotgun/Bottom-up Proteomics
Zhang, Y., Fonslow, B. R., Shan, B., Baek, M.-C., & Yates, J. R. (2013) · Chemical Reviews · doi:10.1021/cr3003533 · Cited by 1,491 · see citing works
Lambert, J.-P., Ivosev, G., Couzens, A. L., Larsen, B., Taipale, M., Lin, Z.-Y., Zhong, Q., Lindquist, S., Vidal, M., Aebersold, R., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2702 · Cited by 318 · see citing works
Self-citationFundamentals of protein interaction network mapping
Snider, J. D., Kotlyar, M., Saraon, P., Yao, Z., Jurišica, I., & Štagljar, I. (2015) · Molecular Systems Biology · doi:10.15252/msb.20156351 · Cited by 301 · see citing works
Gingras, A., Abe, K. T., & Raught, B. (2018) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2018.10.017 · Cited by 290 · see citing works
Self-citationLambert, J., Tucholska, M., Go, C. D., Knight, J. D. R., & Gingras, A. (2014) · Journal of Proteomics · doi:10.1016/j.jprot.2014.09.011 · Cited by 253 · see citing works
Self-citationZhou, Y., Liu, Y., Gupta, S., Paramo, M. I., Hou, Y., Mao, C., Luo, Y., Judd, J., Wierbowski, S. D., Bertolotti, M., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01474-0 · Cited by 203 · see citing works
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Samavarchi‐Tehrani, P., Samson, R., & Gingras, A. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r120.001941 · Cited by 201 · see citing works
Self-citationMorris, J. H., Knudsen, G. M., Verschueren, E., Johnson, J. R., Cimermančič, P., Greninger, A. L., & Pico, A. R. (2014) · Nature Protocols · doi:10.1038/nprot.2014.164 · Cited by 200 · see citing works
Characterizing Protein–Protein Interactions Using Mass Spectrometry: Challenges and Opportunities
Smits, A. H., & Vermeulen, M. (2016) · Trends in biotechnology · doi:10.1016/j.tibtech.2016.02.014 · Cited by 162 · see citing works
Edgotype: a fundamental link between genotype and phenotype
Sahni, N., Yi, S. S., Zhong, Q., Jailkhani, N., Charloteaux, B., Cusick, M. E., & Vidal, M. (2013) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2013.11.002 · Cited by 147 · see citing works
Mutations in Disordered Regions Can Cause Disease by Creating Dileucine Motifs
Meyer, K., Kirchner, M., Uyar, B., Cheng, J.-Y., Russo, G., Hernandez-Miranda, L. R., Szymborska, A., Zauber, H., Rudolph, I.-M., Willnow, T. E., et al. (2018) · Cell · doi:10.1016/j.cell.2018.08.019 · Cited by 132 · see citing works
Quantitative Interaction Proteomics of Neurodegenerative Disease Proteins
Hosp, F., Voßfeldt, H., Heinig, M., Vasiljević, D., Arumughan, A., Wyler, E., Landthaler, M., Hübner, N., Wanker, E. E., Lannfelt, L., et al. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.04.030 · Cited by 101 · see citing works
Integration of Mass Spectrometry Data for Structural Biology
Britt, H. M., Cragnolini, T., & Thalassinos, K. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00356 · Cited by 84 · see citing works
Meyer, K., & Selbach, M. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00237 · Cited by 70 · see citing works
The Impact of Mass Spectrometry–Based Proteomics on Fundamental Discoveries in Virology
Greco, T. M., Diner, B. A., & Cristea, I. M. (2014) · Annual Review of Virology · doi:10.1146/annurev-virology-031413-085527 · Cited by 67 · see citing works
Somewhat in control — the role of transcription in regulating microbial metabolic fluxes
Kochanowski, K., Sauer, U., & Chubukov, V. (2013) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2013.03.014 · Cited by 59 · see citing works
Bode, D., Yu, L., Tate, P., Pardo, M., & Choudhary, J. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m115.053207 · Cited by 50 · see citing works
Rouwette, T., Sondermann, J. R., Avenali, L., Gómez‐Varela, D., & Schmidt, M. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m116.058966 · Cited by 38 · see citing works
Merkley, E. D., Cort, J., & Adkins, J. (2013) · Journal of Structural and Functional Genomics · doi:10.1007/s10969-013-9160-z · Cited by 34 · see citing works
Highly effective proximate labeling in <i>Drosophila</i>
Zhang, B., Zhang, Y., & Liu, J.-L. (2021) · G3 Genes|Genomes|Genetics · doi:10.1093/g3journal/jkab077 · Cited by 32 · see citing works
Banerjee, S. L., Lessard, F., Chartier, F. J.-M., Jacquet, K., Osornio-Hernandez, A. I., Teyssier, V., Ghani, K., Lavoie, N., Lavoie, J. N., Caruso, M., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111031 · Cited by 20 · see citing works
Mapping the Polarity Interactome
Pires, H. R., & Boxem, M. (2017) · Journal of Molecular Biology · doi:10.1016/j.jmb.2017.12.017 · Cited by 19 · see citing works
TurboID‐mediated proximity labeling for screening interacting proteins of FIP37 in Arabidopsis
Li, X., Wei, Y., Fei, Q., Fu, G., Gan, Y., & Shi, C. (2023) · Plant Direct · doi:10.1002/pld3.555 · Cited by 10 · see citing works
Tóth, B. B., Barta, Z., Barta, Á. B., & Fésüs, L. (2021) · BMC Genomics · doi:10.1186/s12864-021-08126-8 · Cited by 6 · see citing works
Use of Proximity Labeling in Cardiovascular Research
Kushner, J., Papa, A. E., & Marx, S. O. (2021) · JACC Basic to Translational Science · doi:10.1016/j.jacbts.2021.01.005 · Cited by 7 · see citing works
Protein networks and activation of lymphocytes
Helou, Y. A., & Salomon, A. R. (2015) · Current Opinion in Immunology · doi:10.1016/j.coi.2015.01.019 · Cited by 4 · see citing works
Li, S., & Dorf, M. E. (2012) · Journal of Proteomics and Genomics research · doi:10.14302/issn.2326-0793.jpgr-12-100 · Cited by 2 · see citing works
Banerjee, S. L., Lavoie, N., Jacquet, K., Lessard, F., Osornio-Hernandez, A. I., Lavoie, J. N., Elowe, S., Lambert, J., Laprise, P., & Bisson, N. (2020) · SSRN Electronic Journal · doi:10.2139/ssrn.3720004
Bio-functional Analysis of Ubiquitin Ligase UBE3D
Penn, A. W. (2020) · TSpace (University of Toronto)
Tóth, B. B., Barta, Z., Barta, Á. B., & Fésüs, L. (2021) · Figshare · doi:10.6084/m9.figshare.17163062
Tóth, B. B., Barta, Z., Barta, Á. B., & Fésüs, L. (2021) · Figshare · doi:10.6084/m9.figshare.17163056
Tóth, B. B., Barta, Z., Barta, Á. B., & Fésüs, L. (2021) · Figshare · doi:10.6084/m9.figshare.17163065
Tóth, B. B., Barta, Z., Barta, Á. B., & Fésüs, L. (2021) · Figshare · doi:10.6084/m9.figshare.17163032
Tóth, B. B., Barta, Z., Barta, Á. B., & Fésüs, L. (2021) · Figshare · doi:10.6084/m9.figshare.17163059
- Authors
- Gingras, A.-C., & Raught, B.
- Affiliations
- Mount Sinai Hospital (CA)
- University of Toronto (CA)
- Corresponding author
- Gingras, Anne-Claude
- Venue
- FEBS Letters
- Publisher
- Wiley
- Published
- 2012-04-10
- Volume
- 586
- Issue
- 17
- Pages
- 2723-2731
- ISSN
- 0014-5793 (ISSN-L)
- 1873-3468
- PMC
- PMC3669394
- OpenAlex
- W2064661383
- Cited by
- 34
- References
- 117
- Citations by year
- 2023: 1 · 2022: 2 · 2021: 9 · 2020: 3 · 2018: 2 · 2017: 1 · 2016: 2 · 2015: 5 · 2014: 3 · 2013: 5 · 2012: 1
- FWCI
- 0.42
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- FEBS Letters (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- CIHR (MOP-84314, MOP-81268, MOP-119289)
- NIH (R01RR024031)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Biotin and Related Studies
- Keywords
- protein-protein interaction, affinity purification mass spectrometry, quantitative mass spectrometry, protein complex organization, interaction dynamics, interaction mapping, data curation
- MeSH terms
- Animals, Cell Line, Humans, Models, Biological, Peptides, Proteins, Software, Mass Spectrometry, Open Reading Frames, DNA, Complementary, Computational Biology, Protein Interaction Mapping, Databases, Protein, Proteomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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