Proteomics-Based Methods for Discovery, Quantification, and Validation of Protein–Protein Interactions

DAVID: Database for Annotation, Visualization, and Integrated Discovery

Dennis, G., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., & Lempicki, R. A. (2003) · Genome Biology · doi:10.1186/gb-2003-4-5-p3 · Cited by 9,327 · see citing works

Universal sample preparation method for proteome analysis

Wiśniewski, J. R., Zougman, A., Nagaraj, N., & Mann, M. (2009) · Nature Methods · doi:10.1038/nmeth.1322 · Cited by 8,352 · see citing works

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

Bindea, G., Mlecnik, B., Hackl, H., Charoentong, P., Tosolini, M., Kirilovsky, A., Fridman, W.-H., Pagès, F., Trajanoski, Z., & Galon, J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp101 · Cited by 6,280 · see citing works

Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics

Ong, S.-E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., & Mann, M. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m200025-mcp200 · Cited by 5,574 · see citing works

Cytoscape 2.8: new features for data integration and network visualization

Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P., & Ideker, T. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq675 · Cited by 4,770 · see citing works

Quantitative analysis of complex protein mixtures using isotope-coded affinity tags

Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., & Aebersold, R. (1999) · Nature Biotechnology · doi:10.1038/13690 · Cited by 4,683 · see citing works

Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents

Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., et al. (2004) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m400129-mcp200 · Cited by 4,401 · see citing works

BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks

Maere, S., Heymans, K., & Kuiper, M. (2005) · Bioinform. · doi:10.1093/bioinformatics/bti551 · Cited by 4,251 · see citing works

Global analysis of protein localization in budding yeast

Huh, W.-K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S., & O'Shea, E. K. (2003) · Nature · doi:10.1038/nature02026 · Cited by 4,248 · see citing works

A Genomic Perspective on Protein Families

Tatusov, R. L., Koonin, E. V., & Lipman, D. J. (1997) · Science · doi:10.1126/science.278.5338.631 · Cited by 3,552 · see citing works

STRING: a database of predicted functional associations between proteins

von Mering, C. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg034 · Cited by 2,942 · 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

A generic protein purification method for protein complex characterization and proteome exploration

Rigaut, G., Shevchenko, A., Rutz, B., Wilm, M., Mann, M., & Séraphin, B. (1999) · Nature Biotechnology · doi:10.1038/13732 · Cited by 2,707 · 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

The Database of Interacting Proteins: 2004 update

Salwinski, L. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh086 · Cited by 2,271 · see citing works

Mass Spectrometry and Protein Analysis

Domon, B., & Aebersold, R. H. (2006) · Science · doi:10.1126/science.1124619 · Cited by 2,188 · see citing works

GO::TermFinder–open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes

Boyle, E. I., Weng, S., Gollub, J., Jin, H., Botstein, D., Cherry, J. M., & Sherlock, G. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth456 · Cited by 2,067 · 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

CORUM: the comprehensive resource of mammalian protein complexes—2009

Ruepp, A., Wägele, B., Lechner, M., Brauner, B., Dunger-Kaltenbach, I., Fobo, G., Frishman, G., Montrone, C., & Mewes, H. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp914 · Cited by 1,320 · see citing works

Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions

Goldberg, A. D., Banaszynski, L. A., Noh, K., Lewis, P. W., Elsässer, S. J., Stadler, S. C., Dewell, S. B., Law, M. J., Guo, X., Li, X., et al. (2010) · Cell · doi:10.1016/j.cell.2010.01.003 · Cited by 1,281 · see citing works

GoMiner: a resource for biological interpretation of genomic and proteomic data

Zeebèrg, B. R., Feng, W., Wang, G., Wang, M. D., Fojo, A. T., Sunshine, M., Narasimhan, S., Kane, D. W., Reinhold, W. C., Lababidi, S., et al. (2003) · Genome biology · doi:10.1186/gb-2003-4-4-r28 · Cited by 1,198 · 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

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

Pruitt, K. D., Tatusova, T., Brown, G. R., & Maglott, D. R. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1079 · Cited by 1,149 · see citing works

The protein–protein interaction map of Helicobacter pylori

Rain, J., Selig, L., Reuse, H. D., Battaglia, V., Reverdy, C., Simon, S., Lenzen, G., Petel, F. X., Wojcik, J., Schächter, V., et al. (2001) · Nature · doi:10.1038/35051615 · Cited by 1,142 · see citing works

FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes

Al‐Shahrour, F., Díaz‐Uriarte, R., & Dopazo, J. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg455 · Cited by 1,118 · see citing works

Development of Human Protein Reference Database as an Initial Platform for Approaching Systems Biology in HumansPreprint

Kristiansen, T. Z., Navarro, J. D., Amanchy, R., Kristiansen, T. Z., Jonnalagadda, C. K., Surendranath, V., Niranjan, V., Muthusamy, B., Gandhi, T. K. B., Gronborg, M., et al. (2003) · Genome Research · doi:10.1101/gr.1680803 · Cited by 1,078 · see citing works

The molecular architecture of the nuclear pore complex

Alber, F., Dokudovskaya, S., Veenhoff, L. M., Zhang, W., Kipper, J., Devos, D. P., Suprapto, A., Karni-Schmidt, O., Williams, R., Chait, B. T., et al. (2007) · Nature · doi:10.1038/nature06405 · Cited by 1,059 · see citing works

Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors

Bantscheff, M., Eberhard, D., Abraham, Y., Bastuck, S., Böesche, M., Hobson, S., Mathieson, T., Perrin, J., Raida, M., Rau, C., et al. (2007) · Nature Biotechnology · doi:10.1038/nbt1328 · Cited by 1,036 · see citing works

MINT: the Molecular INTeraction database

Chatr‐aryamontri, A., Ceol, A. G. M., Montecchi‐Palazzi, L., Nardelli, G., Schneider, M. V., Castagnoli, L., & Cesareni, G. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl950 · Cited by 1,027 · see citing works

IntAct: an open source molecular interaction database

Hermjakob, H. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh052 · Cited by 1,013 · see citing works

Accurate quantitation of protein expression and site-specific phosphorylation.

Oda, Y., Huang, K., Cross, F., Cowburn, D., & Chait, B. (1999) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.96.12.6591 · Cited by 1,011 · 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

Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map

Collins, S. R., Miller, K. M., Maas, N. L., Roguev, A., Fillingham, J., Chu, C. S., Schuldiner, M., Gebbia, M., Recht, J., Shales, M., et al. (2007) · Nature · doi:10.1038/nature05649 · Cited by 869 · 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

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

Toward a Comprehensive Atlas of the Physical Interactome of Saccharomyces cerevisiae

Collins, S. R., Kemmeren, P., Zhao, X.-C., Greenblatt, J. F., Spencer, F., Holstege, F. C. P., Weissman, J. S., & Krogan, N. J. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m600381-mcp200 · Cited by 795 · see citing works

Global 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

Ongoing and future developments at the Universal Protein Resource

The UniProt Consortium (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1020 · Cited by 730 · see citing works

MIPS: analysis and annotation of proteins from whole genomes

Mewes, H. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh092 · Cited by 713 · 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

A Versatile Nanotrap for Biochemical and Functional Studies with Fluorescent Fusion Proteins

Rothbauer, U., Zolghadr, K., Muyldermans, S., Schepers, A., Cardoso, M. C., & Leonhardt, H. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700342-mcp200 · Cited by 678 · see citing works

Mapping intact protein isoforms in discovery mode using top-down proteomics

Tran, J. C., Zamdborg, L., Ahlf, D. R., Lee, J. E., Catherman, A. D., Durbin, K. R., Tipton, J. D., Vellaichamy, A., Kellie, J. F., Li, M., et al. (2011) · Nature · doi:10.1038/nature10575 · Cited by 665 · see citing works

Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes

Bantscheff, M., Hopf, C., Savitski, M. M., Dittmann, A., Grandi, P., Michon, A.-M., Schlegl, J., Abraham, Y., Becher, I., Bergamini, G., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1759 · Cited by 659 · see citing works

GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop

Montojo, J., Zuberi, K., Rodriguez, H., Kazi, F. I., Wright, G., Donaldson, S. L., Morris, Q., & Bader, G. D. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq562 · Cited by 633 · see citing works

The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data

Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C., et al. (2004) · Nature Biotechnology · doi:10.1038/nbt926 · Cited by 630 · see citing works

Online Predicted Human Interaction Database

Brown, K. R., & Jurišica, I. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti273 · Cited by 601 · see citing works

BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals

Poser, I., Sarov, M., Hutchins, J. R. A., Hèriché, J.-K., Toyoda, Y., Pozniakovsky, A., Weigl, D., Nitzsche, A., Hegemann, B., Bird, A. W., et al. (2008) · Nature Methods · doi:10.1038/nmeth.1199 · Cited by 597 · see citing works

The Biomolecular Interaction Network Database and related tools 2005 update

Alfarano, C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki051 · Cited by 587 · see citing works

Identification of cross-linked peptides from complex samples

Yang, B., Wu, Y.-J., Zhu, M., Fan, S., Lin, J., Zhang, K., Li, S., Chi, H., Li, Y., Chen, H., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2099 · Cited by 574 · see citing works

The GOA database in 2009--an integrated Gene Ontology Annotation resource

Barrell, D. G., Dimmer, E. C., Huntley, R. P., Binns, D., O’Donovan, C., & Apweiler, R. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn803 · Cited by 554 · see citing works

Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors

Paoletti, A. C., Parmely, T. J., Tomomori‐Sato, C., Sato, S., Zhu, D., Conaway, R. C., Conaway, J. W., Florens, L. A., & Washburn, M. P. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0606379103 · Cited by 541 · see citing works

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

Orchard, S. E., Kerrien, S., Abbani, S., Aranda, B., Bhate, J., Bidwell, S. L., Bridge, A. J., Briganti, L., Brinkman, F. S. L., Cesareni, G., et al. (2012) · Nature Methods · doi:10.1038/nmeth.1931 · Cited by 538 · see citing works

A gene network for navigating the literature

Hoffmann, R., & Valencia, A. (2004) · Nature Genetics · doi:10.1038/ng0704-664 · Cited by 535 · see citing works

The Brd4 Extraterminal Domain Confers Transcription Activation Independent of pTEFb by Recruiting Multiple Proteins, Including NSD3

Rahman, S., Sowa, M. E., Ottinger, M., Smith, J. A., Shi, Y., Harper, J. W., & Howley, P. M. (2011) · Molecular and Cellular Biology · doi:10.1128/mcb.01341-10 · Cited by 532 · 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

Photo-leucine and photo-methionine allow identification of protein-protein interactions in living cells

Suchanek, M., Radzikowska, A., & Thiele, C. (2005) · Nature Methods · doi:10.1038/nmeth752 · Cited by 487 · 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

A perspective on the use of iTRAQTM reagent technology for protein complex and profiling studies

Zieske, L. R. (2006) · Journal of Experimental Botany · doi:10.1093/jxb/erj168 · Cited by 468 · see citing works

Paxdb, a database of protein abundance averages across all three domains of life

Wang, M., Weiss, M., Simonovic, M., Haertinger, G., Schrimpf, S. P., Hengartner, M. O., & von Mering, C. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o111.014704 · Cited by 466 · see citing works

High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry

Young, M. M., Tang, N., Hempel, J. C., Oshiro, C. M., Taylor, E. W., Kuntz, I. D., Gibson, B. W., & Dollinger, G. D. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.090099097 · Cited by 460 · 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

The Protein Information Resource

Wu, C. H. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg040 · Cited by 455 · see citing works

Network visualization and analysis of gene expression data using BioLayout Express3D

Theocharidis, A., van Dongen, S., Enright, A. J., & Freeman, T. C. (2009) · Nature Protocols · doi:10.1038/nprot.2009.177 · Cited by 453 · see citing works

Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes

Trinkle‐Mulcahy, L., Boulon, S., Lam, Y. W., Urcia, R., Boisvert, F., Vandermoere, F., MORRICE, N. A., Swift, S., Rothbauer, U., Leonhardt, H., et al. (2008) · The Journal of Cell Biology · doi:10.1083/jcb.200805092 · Cited by 446 · see citing works

Systematic Analysis of the Protein Interaction Network for the Human Transcription Machinery Reveals the Identity of the 7SK Capping Enzyme

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

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

Identification of cross-linked peptides from large sequence databases

Rinner, O., Seebacher, J., Walzthoeni, T., Mueller, L. N., Beck, M., Schmidt, A., Mueller, M., & Aebersold, R. H. (2008) · Nature Methods · doi:10.1038/nmeth.1192 · Cited by 430 · see citing works

Proteomics: a pragmatic perspective

Mallick, P., & Küster, B. (2010) · Nature Biotechnology · doi:10.1038/nbt.1658 · Cited by 428 · see citing works

Stepwise evolution of protein native structure with electrospray into the gas phase, 10 −12 to 10 2 s

Breuker, K., & McLafferty, F. W. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0807005105 · Cited by 422 · see citing works

The beginning of a beautiful friendship: Cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes

Rappsilber, J. (2010) · Journal of Structural Biology · doi:10.1016/j.jsb.2010.10.014 · Cited by 414 · see citing works

A conserved protein network controls assembly of the outer kinetochore and its ability to sustain tensionPreprint

Cheeseman, I. M., Niessen, S., Anderson, S., Barron, F. E., Yates, J. R., Oegema, K., & Desai, A. B. (2004) · Genes & Development · doi:10.1101/gad.1234104 · Cited by 413 · see citing works

Mass spectrometry–based proteomics in cell biology

Walther, T. C., & Mann, M. (2010) · The Journal of Cell Biology · doi:10.1083/jcb.201004052 · Cited by 411 · see citing works

Development of a Novel Cross-linking Strategy for Fast and Accurate Identification of Cross-linked Peptides of Protein Complexes

Kao, A., Chiu, C., Vellucci, D., Yang, Y., Patel, V. R., Guan, S., Randall, A. Z., Baldi, P., Rychnovsky, S. D., & Huang, L. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.002212 · Cited by 405 · see citing works

An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells

Bürckstümmer, T., Bennett, K. L., Preradovic, A., Schütze, G. A., Hantschel, O. D., Superti‐Furga, G., & Bauch, A. (2006) · Nature Methods · doi:10.1038/nmeth968 · Cited by 391 · see citing works

Architecture of the RNA polymerase II–TFIIF complex revealed by cross‐linking and mass spectrometry

Chen, Z. A., Jawhari, A., Fischer, L., Buchen, C., Tahir, S., Kamenski, T., Rasmussen, M. I., Larivière, L., Wills, J. C., Nilges, M., et al. (2010) · The EMBO Journal · doi:10.1038/emboj.2009.401 · Cited by 391 · see citing works

Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry

Herzog, F., Kahraman, A., Boehringer, D., Mak, R., Bracher, A., Walzthoeni, T., Leitner, A., Beck, M., Hartl, F. U., Ban, N., et al. (2012) · Science · doi:10.1126/science.1221483 · Cited by 372 · see citing works

MPact: the MIPS protein interaction resource on yeast

Güldener, U. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj003 · Cited by 353 · see citing works

Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection

Jäger, S., Kim, D. Y., Hultquist, J. F., Shindo, K., LaRue, R. S., Kwon, E., Li, M., Anderson, B. D., Yen, L., Stanley, D., et al. (2012) · Nature · doi:10.1038/nature10693 · Cited by 352 · see citing works

Integrated network analysis platform for protein-protein interactions

Wu, J., Vallenius, T., Ovaska, K., Westermarck, J. K., Mäkelä, T. P., & Hautaniemi, S. (2008) · Nature Methods · doi:10.1038/nmeth.1282 · Cited by 320 · see citing works

Native protein mass spectrometry: from intact oligomers to functional machineries

van den Heuvel, R. H. H., & Heck, A. J. R. (2004) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2004.08.006 · Cited by 303 · see citing works

False discovery rate estimation for cross-linked peptides identified by mass spectrometry

Walzthoeni, T., Claassen, M., Leitner, A., Herzog, F., Bohn, S., Förster, F. G., Beck, M., & Aebersold, R. H. (2012) · Nature Methods · doi:10.1038/nmeth.2103 · Cited by 301 · see citing works

Acetylation modulates cellular distribution and DNA sensing ability of interferon-inducible protein IFI16

Li, T., Diner, B. A., Chen, J., & Cristea, I. M. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1203447109 · Cited by 297 · see citing works

Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions

Kerrien, S., Orchard, S., Montecchi-Palazzi, L., Aranda, B., Quinn, A. F., Vinod, N., Bader, G. D., Xenarios, I., Wojcik, J., Sherman, D., et al. (2007) · BMC Biology · doi:10.1186/1741-7007-5-44 · Cited by 266 · see citing works

An Integrated Mass Spectrometry-based Proteomic Approach

Guerrero, C., Tagwerker, C., Kaiser, P., & Huang, L. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500303-mcp200 · Cited by 258 · see citing works

An Interaction Network Predicted from Public Data as a Discovery Tool: Application to the Hsp90 Molecular Chaperone Machine

Echeverría, P. C., Bernthaler, A., Dupuis, P., Mayer, B., & Picard, D. (2011) · PLoS ONE · doi:10.1371/journal.pone.0026044 · Cited by 252 · see citing works

Fluorescent Proteins as Proteomic Probes

Cristea, I. M., Williams, R., Chait, B. T., & Rout, M. P. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500227-mcp200 · Cited by 251 · see citing works

Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae

Babu, M., Vlasblom, J., Pu, S., Guo, X., Graham, C., Bean, B. D. M., Burston, H. E., Vizeacoumar, F. J., Snider, J. D., Phanse, S., et al. (2012) · Nature · doi:10.1038/nature11354 · Cited by 251 · see citing works

Human immunodeficiency virus type 1, human protein interaction database at NCBI

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A Combined Approach for the Localization and Tandem Affinity Purification of Protein Complexes from Metazoans

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