Affinity-purification coupled to mass spectrometry: basic principles and strategies

Green fluorescent protein as a marker for gene expression

Chalfie, M., Tu, Y., Euskirchen, G., Ward, W. W., & Prasher, D. C. (1994) · Science · doi:10.1126/science.8303295 · Cited by 6,802 · see citing works

Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase

Smith, D. B., & Johnson, K. S. (1988) · Gene · doi:10.1016/0378-1119(88)90005-4 · Cited by 5,974 · 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

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

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C. A., Causton, H. C., et al. (2001) · Nature Genetics · doi:10.1038/ng1201-365 · Cited by 4,109 · 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

A Model for Random Sampling and Estimation of Relative Protein Abundance in Shotgun Proteomics

Liu, H., Sadygov, R. G., & Yates, J. R. (2004) · Analytical Chemistry · doi:10.1021/ac0498563 · Cited by 2,486 · see citing works

Isolation of monoclonal antibodies specific for human c-myc proto-oncogene product.

Evan, G. I., Lewis, G. K., Ramsay, G. M., & Bishop, J. M. (1985) · Molecular and Cellular Biology · doi:10.1128/mcb.5.12.3610 · Cited by 2,412 · 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

Interaction network containing conserved and essential protein complexes in Escherichia coli

Butland, G., Peregrín-Alvarez, J. M., Li, J., Yang, W., Yang, X., Canadien, V., Starostine, A., Richards, D., Beattie, B., Krogan, N., et al. (2005) · Nature · doi:10.1038/nature03239 · Cited by 1,201 · see citing works

The abc's (and xyz's) of peptide sequencing

Steen, H., & Mann, M. (2004) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1468 · Cited by 1,139 · see citing works

A protein interaction network for pluripotency of embryonic stem cells

Wang, J., Rao, S., Chu, J., Shen, X., Levasseur, D. N., Theunissen, T. W., & Orkin, S. H. (2006) · Nature · doi:10.1038/nature05284 · Cited by 1,094 · see citing works

ArrayExpress--a public repository for microarray gene expression data at the EBI

Parkinson, H. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki056 · Cited by 1,075 · see citing works

Genetic Approach to Facilitate Purification of Recombinant Proteins with a Novel Metal Chelate Adsorbent

Hochuli, E., Bannwarth, W., Döbeli, H., Gentz, R., & Stüber, D. (1988) · Nature Biotechnology · doi:10.1038/nbt1188-1321 · Cited by 1,050 · 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

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

Interpretation of Shotgun Proteomic Data

Nesvizhskii, A. I., & Aebersold, R. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r500012-mcp200 · Cited by 1,025 · see citing works

A Short Polypeptide Marker Sequence Useful for Recombinant Protein Identification and Purification

Hopp, T. P., Prickett, K. S., Price, V. L., Libby, R. T., March, C. J., Cerretti, D. P., Urdal, D. L., & Conlon, P. J. (1988) · Nature Biotechnology · doi:10.1038/nbt1088-1204 · Cited by 959 · see citing works

Purification of a RAS -Responsive Adenylyl Cyclase Complex from Saccharomyces cerevisiae by Use of an Epitope Addition Method

Field, J. M., Nikawa, J., Broek, D., MACDONALD, B. S., Rodgers, L., Wilson, I. A., Lerner, R. A., & Wigler, M. H. (1988) · Molecular and Cellular Biology · doi:10.1128/mcb.8.5.2159 · Cited by 949 · see citing works

An empirical framework for binary interactome mapping

Venkatesan, K., Rual, J.-F. M., Vázquez, A., Stelzl, U., Lemmens, I. H., Hirozane-Kishikawa, T., Hao, T., Zenkner, M., Xin, X., Goh, K. I., et al. (2008) · Nature Methods · doi:10.1038/nmeth.1280 · Cited by 907 · 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

A simple role for BDNF in learning and memory?

Cunha, C. (2010) · Frontiers in Molecular Neuroscience · doi:10.3389/neuro.02.001.2010 · Cited by 778 · see citing works

The minimum information about a proteomics experiment (MIAPE)

Taylor, C. F., Paton, N. W., Lilley, K. S., Binz, P., Julian, R. K., Jones, A. R., Zhu, W., Apweiler, R., Aebersold, R. H., Deutsch, E. W., et al. (2007) · Nature Biotechnology · doi:10.1038/nbt1329 · Cited by 769 · 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

CIP2A 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

Using Antibodies: A Laboratory Manual

Palmer, H. M. (2000) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/45.3.413 · Cited by 653 · 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

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

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

Saccharomyces cerevisiae Elongator mutations confer resistance to the Kluyveromyces lactis zymocin

Frohloff, F., Fichtner, L., Jablonowski, D., Breunig, K. D., & Schaffrath, R. (2001) · The EMBO Journal · doi:10.1093/emboj/20.8.1993 · Cited by 492 · 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

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

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

Systematic exploration of essential yeast gene function with temperature-sensitive mutants

Li, Z., Vizeacoumar, F. J., Bahr, S., Li, J., Warringer, J., Vizeacoumar, F. S., Min, R., VanderSluis, B., Bellay, J., DeVit, M. J., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1832 · Cited by 404 · see citing works

Large-scale identification of protein–protein interaction of <i>Escherichia coli</i> K-12

Arifuzzaman, M., Maeda, M., Itoh, A., Nishikata, K., Takita, C., Saito, R., Ara, T., Nakahigashi, K., Huang, H.-C., Hirai, A., et al. (2006) · Genome Research · doi:10.1101/gr.4527806 · Cited by 403 · 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

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

The KLHL12–Cullin-3 ubiquitin ligase negatively regulates the Wnt–β-catenin pathway by targeting Dishevelled for degradation

Angers, S., Thorpe, C. J., Biechele, T. L., Goldenberg, S. J., Zheng, N., MacCoss, M. J., & Moon, R. T. (2006) · Nature Cell Biology · doi:10.1038/ncb1381 · Cited by 364 · see citing works

A PP2A phosphatase high density interaction network identifies a novel striatin-interacting phosphatase and kinase complex linked to the cerebral cavernous malformation 3 (CCM3) protein

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 &amp; Cellular Proteomics · doi:10.1074/mcp.m800266-mcp200 · Cited by 359 · see citing works

Edgetic perturbation models of human inherited disorders

Zhong, Q., Simonis, N., Li, Q., Charloteaux, B., Heuze, F., Klitgord, N., Tam, S., Yu, H., Venkatesan, K., Mou, D., et al. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.80 · Cited by 359 · see citing works

The study of macromolecular complexes by quantitative proteomics

Ranish, J. A., Yi, E. C., Pedrioli, D. M. L., Purvine, S. O., Goodlett, D. R., Eng, J. K., & Aebersold, R. H. (2003) · Nature Genetics · doi:10.1038/ng1101 · Cited by 344 · see citing works

IκB Kinase (IKK)-Associated Protein 1, a Common Component of the Heterogeneous IKK Complex

Mercurio, F., Murray, B. W., Shevchenko, A., Bennett, B. L., Young, D. B., Li, J. W., Pascual, G., Motiwala, A., Zhu, H., Mann, M., et al. (1999) · Molecular and Cellular Biology · doi:10.1128/mcb.19.2.1526 · Cited by 325 · see citing works

Trim24 targets endogenous p53 for degradation

Allton, K., Jain, A. K., Herz, H.-M., Tsai, W.-W., Jung, S. Y., Qin, J., Bergmann, A., Johnson, R. L., & Barton, M. C. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0813177106 · Cited by 292 · see citing works

The random peptide library-assisted engineering of a C-terminal affinity peptide, useful for the detection and purification of a functional Ig Fv fragment

Schmidt, T. G. M., & Skerra, A. (1993) · Protein Engineering Design and Selection · doi:10.1093/protein/6.1.109 · Cited by 288 · see citing works

The minimum information required for reporting a molecular interaction experiment (MIMIx)

Orchard, S. E., Salwiński, Ł., Kerrien, S., Montecchi‐Palazzi, L., Oesterheld, M., Stümpflen, V., Ceol, A. G. M., Chatr‐aryamontri, A., Armstrong, J. T., Woollard, P. M., et al. (2007) · Nature Biotechnology · doi:10.1038/nbt1324 · Cited by 280 · see citing works

Targeted tandem affinity purification of PSD‐95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins

Fernández, E., Collins, M. O., Uren, R. T., Kopanitsa, M. V., Komiyama, N. H., Croning, M. D. R., Zografos, L., Armstrong, J. D., Choudhary, J. S., & Grant, S. G. N. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.27 · Cited by 275 · see citing works

Skp1 forms multiple protein complexes, including RAVE, a regulator of V-ATPase assembly

Seol, J. H., Shevchenko, A., Shevchenko, A., & Deshaies, R. J. (2001) · Nature Cell Biology · doi:10.1038/35070067 · Cited by 263 · see citing works

Comprehensive analysis of diverse ribonucleoprotein complexes

Oeffinger, M., Wei, K. E., Rogers, R. S., DeGrasse, J. A., Chait, B. T., Aitchison, J. D., & Rout, M. P. (2007) · Nature Methods · doi:10.1038/nmeth1101 · Cited by 261 · 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

Fluorescent Proteins as Proteomic Probes

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

The impact of cellular networks on disease comorbidity

Park, J. M., Lee, D., Christakis, N. A., & Barabási, A.-Ĺ. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.16 · Cited by 245 · see citing works

Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK)

Selbach, M., & Mann, M. (2006) · Nature Methods · doi:10.1038/nmeth972 · Cited by 240 · see citing works

Protein Profiling with Epstein-Barr Nuclear Antigen-1 Reveals an Interaction with the Herpesvirus-associated Ubiquitin-specific Protease HAUSP/USP7

Holowaty, M. N., Zeghouf, M., Wu, H., Tellam, J., Athanasopoulos, V., Greenblatt, J., & Frappier, L. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m303977200 · Cited by 228 · see citing works

Improved tandem affinity purification tag and methods for isolation of protein heterocomplexes from plants

Rohila, J. S., Chen, M. Y., Cerny, R. L., & Fromm, M. (2004) · The Plant Journal · doi:10.1111/j.1365-313x.2004.02031.x · Cited by 227 · 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

Sequential Peptide Affinity (SPA) System for the Identification of Mammalian and Bacterial Protein Complexes

Zeghouf, M., Li, J., Butland, G. P., Borkowska, A., Canadien, V., Richards, D. P., Beattie, B. K., Emili, A., & Greenblatt, J. (2004) · Journal of Proteome Research · doi:10.1021/pr034084x · Cited by 221 · see citing works

The interaction network of the chaperonin CCT

Dekker, C., Stirling, P. C., McCormack, E. A., Filmore, H., Paul, A., Brost, R. L., Costanzo, M., Boone, C., Leroux, M. R., & Willison, K. R. (2008) · The EMBO Journal · doi:10.1038/emboj.2008.108 · Cited by 220 · see citing works

A novel tandem affinity purification strategy for the efficient isolation and characterisation of native protein complexes

Gloeckner, C. J., Boldt, K., Schumacher, A., Roepman, R., & Ueffing, M. (2007) · PROTEOMICS · doi:10.1002/pmic.200700038 · Cited by 218 · see citing works

A Tandem Affinity Purification-based Technology Platform to Study the Cell Cycle Interactome in Arabidopsis thaliana

Leene, J. V., Stals, H., Eeckhout, D., Persiau, G., Slijke, E. V. D., Isterdael, G. V., Clercq, A. D., Bonnet, É., Laukens, K., Remmerie, N., et al. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700078-mcp200 · Cited by 217 · see citing works

Vitamin B 6 Is Required for Full Motility and Virulence in Helicobacter pylori

Grubman, A., Phillips, A. W., Thibonnier, M., Kaparakis‐Liaskos, M., Johnson, C. J., Thiberge, J.-M., Radcliff, F. J., Ecobichon, C., Labigne-Roussel, A., Reuse, H. D., et al. (2010) · mBio · doi:10.1128/mbio.00112-10 · Cited by 216 · see citing works

An efficient protein complex purification method for functional proteomics in higher eukaryotes

Forler, D., Köcher, T., Rode, M., Gentzel, M., Izaurralde, E., & Wilm, M. S. (2002) · Nature Biotechnology · doi:10.1038/nbt773 · Cited by 211 · 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

Drag&Drop cloning in yeast

Jansen, G., Wu, C., Schade, B., Thomas, D. Y., & Whiteway, M. S. (2004) · Gene · doi:10.1016/j.gene.2004.10.016 · Cited by 176 · see citing works

A Targeted Proteomic Analysis of the Ubiquitin-Like Modifier Nedd8 and Associated Proteins

Jones, J. A., Wu, K. K.-Y., Yang, Y., Guerrero, C., Nillegoda, N. B., Pan, Z., & Huang, L. (2008) · Journal of Proteome Research · doi:10.1021/pr700749v · Cited by 164 · see citing works

High confidence determination of specific protein–protein interactions using quantitative mass spectrometry

Vermeulen, M., Hubner, N. C., & Mann, M. (2008) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2008.06.001 · Cited by 163 · see citing works

EPITOPE TAGGING

Jarvik, J. W., & Telmer, C. A. (1998) · Annual Review of Genetics · doi:10.1146/annurev.genet.32.1.601 · Cited by 163 · see citing works

An integrated mass spectrometric and computational framework for the analysis of protein interaction networks

Rinner, 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

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

Identification of TFB5, a new component of general transcription and DNA repair factor IIH

Ranish, J. A., Hahn, S., Lu, Y., Yi, E. C., Li, X., Eng, J. K., & Aebersold, R. H. (2004) · Nature Genetics · doi:10.1038/ng1385 · Cited by 150 · see citing works

Transgenic Mouse Proteomics Identifies New 14-3-3-associated Proteins Involved in Cytoskeletal Rearrangements and Cell Signaling

Angrand, P., Segura, I., Völkel, P., Ghidelli, S., Terry, R. L., Brajenovic, M., Vintersten, K., Klein, R., Superti‐Furga, G., Drewes, G., et al. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m600147-mcp200 · Cited by 146 · see citing works

Proteomic and genomic characterization of chromatin complexes at a boundary

Tackett, A. J., Dilworth, D. J., Davey, M. J., O’Donnell, M. E., Aitchison, J. D., Rout, M. P., & Chait, B. T. (2005) · The Journal of Cell Biology · doi:10.1083/jcb.200502104 · Cited by 142 · see citing works

Vectors and gene targeting modules for tandem affinity purification in Schizosaccharomyces pombe

Tasto, J. J., Carnahan, R. H., McDonald, W. H., & Gould, K. L. (2001) · Yeast · doi:10.1002/yea.713 · Cited by 141 · see citing works

Gene fusion vectors based on the gene for staphylococcal protein A

Uhlén, M., Nilsson, B., Guss, B., Lindberg, M., Gatenbeck, S., & Philipson, L. (1983) · Gene · doi:10.1016/0378-1119(83)90025-2 · Cited by 138 · see citing works

Characterization of the brain 26S proteasome and its interacting proteins

Tai, H. (2010) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2010.00012 · Cited by 136 · see citing works

I-DIRT, A General Method for Distinguishing between Specific and Nonspecific Protein Interactions

Tackett, A. J., DeGrasse, J. A., Sekedat, M. D., Oeffinger, M., Rout, M. P., & Chait, B. T. (2005) · Journal of Proteome Research · doi:10.1021/pr050225e · Cited by 131 · see citing works

Identification of Glycan Structure Alterations on Cell Membrane Proteins in Desoxyepothilone B Resistant Leukemia Cells

Nakano, M., Saldanha, R. G., Göbel, A., Kavallaris, M., & Packer, N. H. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.009001 · Cited by 125 · see citing works

Identification of Novel Protein-Protein Interactions Using A Versatile Mammalian Tandem Affinity Purification Expression System

Knuesel, M. T., Wan, Y., Xiao, Z., Holinger, E. P., Lowe, N., Wang, W., & Liu, X. (2003) · Molecular & Cellular Proteomics · doi:10.1074/mcp.t300007-mcp200 · Cited by 122 · see citing works

A century of mass spectrometry: from atoms to proteomes

Yates, J. R. (2011) · Nature Methods · doi:10.1038/nmeth.1659 · Cited by 118 · 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 2× · see citing works

Quantitative Profiling of In Vivo-assembled RNA-Protein Complexes Using a Novel Integrated Proteomic Approach

Tsai, B. P., Wang, X., Huang, L., & Waterman, M. L. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.007385 · Cited by 112 · see citing works

Relative position of the hexahistidine tag effects binding properties of a tumor-associated single-chain Fv construct

Goel, A., Colcher, D. M., Koo, J.-S., Booth, B. J. M., Pavlínková, G., & Batra, S. K. (2000) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/s0304-4165(00)00086-6 · Cited by 111 · see citing works

Direct Ionization of Large Proteins and Protein Complexes by Desorption Electrospray Ionization-Mass Spectrometry

Ferguson, C. N., Benchaar, S. A., Miao, Z., Loo, J. A., & Chen, H. (2011) · Analytical Chemistry · doi:10.1021/ac201390w · Cited by 107 · see citing works

Extracting gene function from protein–protein interactions using Quantitative BAC InteraCtomics (QUBIC)

Hubner, N. C., & Mann, M. (2010) · Methods · doi:10.1016/j.ymeth.2010.12.016 · Cited by 107 · see citing works

The Protein Interaction Network of the Human Transcription Machinery Reveals a Role for the Conserved GTPase RPAP4/GPN1 and Microtubule Assembly in Nuclear Import and Biogenesis of RNA Polymerase II

Forget, D., Lacombe, A.-A., Cloutier, P., Al‐Khoury, R., Bouchard, A., Lavallée‐Adam, M., Faubert, D., Jerónimo, C., Blanchette, M., & Coulombe, B. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.003616 · Cited by 105 · see citing works

High‐throughput generation of tagged stable cell lines for proteomic analysis

Torres, J. Z., Miller, J. J., & Jackson, P. K. (2009) · PROTEOMICS · doi:10.1002/pmic.200800873 · Cited by 103 · see citing works

Quantitative Proteomic Analysis of Protein Complexes

Pflieger, D., Jünger, M. A., Müller, M., Rinner, O., Lee, H., Gehrig, P., Gstaiger, M., & Aebersold, R. H. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700282-mcp200 · Cited by 103 · see citing works

Combined Use of RNAi and Quantitative Proteomics to Study Gene Function in Drosophila

Bonaldi, T., Straub, T., Cox, J., Kumar, C., Becker, P. B., & Mann, M. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.07.018 · Cited by 96 · see citing works

Proteomic identification of ubiquitinated proteins from human cells expressing His‐tagged ubiquitin

Kirkpatrick, D. S., Weldon, S. F., Tsaprailis, G., Liebler, D. C., & Gandolfi, A. J. (2005) · PROTEOMICS · doi:10.1002/pmic.200401089 · Cited by 95 · see citing works

Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments

Nesvizhskii, A. I. (2012) · PROTEOMICS · doi:10.1002/pmic.201100537 · Cited by 93 · see citing works

Construction, verification and experimental use of two epitope‐tagged collections of budding yeast strains

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

Nuclear Import of Histone Deacetylase 5 by Requisite Nuclear Localization Signal Phosphorylation

Greco, T. M., Yu, F., Guise, A. J., & Cristea, I. M. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.004317 · Cited by 92 · see citing works

A Lentiviral Functional Proteomics Approach Identifies Chromatin Remodeling Complexes Important for the Induction of Pluripotency

Mak, A. B., Ni, Z., Hewel, J. A., Chen, G. I., Zhong, G., Karamboulas, K., Blakely, K., Smiley, S., Marcon, E., Roudeva, D., et al. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m000002-mcp201 · Cited by 92 · see citing works

RNA interference rescue by bacterial artificial chromosome transgenesis in mammalian tissue culture cells

Kittler, R., Pelletier, L., Ma, C., Poser, I., Fischer, S., Hyman, A. A., & Buchholz, F. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409861102 · Cited by 90 · see citing works

Affinity Purification of an Archaeal DNA Replication Protein Network

Li, Z., Santangelo, T. J., Čuboňová, L., Reeve, J. N., & Kelman, Z. (2010) · mBio · doi:10.1128/mbio.00221-10 · Cited by 87 · see citing works

An interaction network of the mammalian COP9 signalosome identifies Dda1 as a core subunit of multiple Cul4-based E3 ligases

Olma, M. H., Roy, M. M., Bihan, T. L., Sumara, I., Maerki, S., Larsen, B. G., Quadroni, M., Peter, M., Tyers, M., & Pintard, L. (2009) · Journal of Cell Science · doi:10.1242/jcs.043539 · Cited by 83 · 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

In Vivo Analysis of Proteomes and Interactomes Using Parallel Affinity Capture (iPAC) Coupled to Mass Spectrometry

Rees, J. S., Lowe, N., Armean, I. M., Roote, J., Johnson, G., Drummond, E., Spriggs, H. F., Ryder, E. J., Russell, S. R. H., Johnston, D. S., et al. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.002386 · Cited by 79 · see citing works

Molecular interaction databases

Orchard, S. E. (2012) · PROTEOMICS · doi:10.1002/pmic.201100484 · Cited by 78 · see citing works

Epitope Tagging

Brizzard, B. (2008) · BioTechniques · doi:10.2144/000112841 · Cited by 77 · see citing works

Tandem Affinity Purification of Protein Complexes from Mammalian Cells by the Strep/FLAG (SF)-TAP Tag

Gloeckner, C. J., Boldt, K., Schumacher, A., & Ueffing, M. (2009) · Methods in molecular biology · doi:10.1007/978-1-60761-157-8_21 · Cited by 75 · see citing works

Label‐free quantitative proteomics and SAINT analysis enable interactome mapping for the human Ser/Thr protein phosphatase 5

Skarra, 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

Subunit Stoichiometry, Evolution, and Functional Implications of an Asymmetric Plant Plastid ClpP/R Protease Complex in Arabidopsis

Olinares, P. D. B., Kim, J., Davis, J. I., & van Wijk, K. J. (2011) · The Plant Cell · doi:10.1105/tpc.111.086454 · Cited by 73 · 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 71 · see citing works

A human protein atlas based on antibody proteomics.

Persson, A., Hober, S., & Uhlén, M. (2006) · PubMed · Cited by 70 · see citing works

RPAP1, a Novel Human RNA Polymerase II-Associated Protein Affinity Purified with Recombinant Wild-Type and Mutated Polymerase Subunits

Jerónimo, C., Langelier, M.-F., Zeghouf, M., Cojocaru, M., Bergeron, D., Baali, D., Forget, D., Mnaimneh, S., Davierwala, A. P., Pootoolal, J., et al. (2004) · Molecular and Cellular Biology · doi:10.1128/mcb.24.16.7043-7058.2004 · Cited by 69 · see citing works

Tandem affinity purification of functional TAP-tagged proteins from human cells

Gregáň, J., Riedel, C. G., Petronczki, M. P., Čipák, L., Rumpf, C., Poser, I., Buchholz, F., Mechtler, K., & Nasmyth, K. (2007) · Nature Protocols · doi:10.1038/nprot.2007.172 · Cited by 59 · see citing works

Tandem affinity purification in Drosophila: the advantages of the GS-TAP system

Kyriakakis, P., Tipping, M., Abed, L., & Veraksa, A. N. (2008) · Fly · doi:10.4161/fly.6669 · Cited by 58 · see citing works

Interactome mapping for analysis of complex phenotypes: Insights from benchmarking binary interaction assays

Falter‐Braun, P. (2012) · PROTEOMICS · doi:10.1002/pmic.201100598 · Cited by 56 · see citing works

Two steps forward—one step back: Advances in affinity purification mass spectrometry of macromolecular complexes

Oeffinger, M. (2012) · PROTEOMICS · doi:10.1002/pmic.201100509 · Cited by 55 · see citing works

Resolving protein interactions and complexes by affinity purification followed by label‐based quantitative mass spectrometry

Trinkle‐Mulcahy, L. (2012) · PROTEOMICS · doi:10.1002/pmic.201100438 · Cited by 53 · see citing works

Studying protein–protein affinity and immobilized ligand–protein affinity interactions using MS-based methods

Kool, J., Jonker, N., Irth, H., & Niessen, W. M. A. (2011) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-011-5207-9 · Cited by 51 · 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

A modified tandem affinity purification strategy identifies cofactors of the Drosophila nuclear receptor dHNF4

Yang, P., Sampson, H. M., & Krause, H. M. (2006) · PROTEOMICS · doi:10.1002/pmic.200500230 · Cited by 43 · see citing works

Drug target deconvolution by chemical proteomics

Raida, M. (2011) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2011.06.016 · Cited by 43 · see citing works

RaPID: An Aptamer-Based mRNA Affinity Purification Technique for the Identification of RNA and Protein Factors Present in Ribonucleoprotein Complexes

Slobodin, B., & Gerst, J. E. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-005-8_24 · Cited by 40 · see citing works

Recombineering, transfection, Western, IP and ChIP methods for protein tagging via gene targeting or BAC transgenesis

Hofemeister, H., Ciotta, G., Fu, J., Seibert, P. M., Schulz, A., Maresca, M., Sarov, M., Anastassiadis, K., & Stewart, A. F. (2011) · Methods · doi:10.1016/j.ymeth.2010.12.026 · Cited by 38 · see citing works

[Drug target deconvolution by chemical proteomics].

Gong, L., & Kang, J. (2020) · PubMed · doi:10.3724/sp.j.1123.2019.12014 · Cited by 38 · see citing works

Recombineering BAC transgenes for protein tagging

Ciotta, G., Hofemeister, H., Maresca, M., Fu, J., Sarov, M., Anastassiadis, K., & Stewart, A. F. (2010) · Methods · doi:10.1016/j.ymeth.2010.09.003 · Cited by 36 · see citing works

Isolation of Transcription Factor Complexes by In Vivo Biotinylation Tagging and Direct Binding to Streptavidin Beads

Rodriguez, P., Braun, H., Kolodziej, K. E., de Boer, E., Campbell, J. A., Bonte, E. J., Grosveld, F. G., Philipsen, S., & Strouboulis, J. (2006) · Humana Press eBooks · doi:10.1385/1-59745-097-9:305 · Cited by 35 · see citing works

Rapid tagging of endogenous mouse genes by recombineering and ES cell complementation of tetraploid blastocysts

Zhou, D. (2004) · Nucleic Acids Research · doi:10.1093/nar/gnh128 · Cited by 35 · see citing works

A cost–benefit analysis of multidimensional fractionation of affinity purification‐mass spectrometry samples

Dunham, W. H., Larsen, B. G., Tate, S. A., Badillo, B. G., Goudreault, M., Tehami, Y., Kislinger, T., & Gingras, A. (2011) · PROTEOMICS · doi:10.1002/pmic.201000571 · Cited by 34 · see citing works

Affinity chromatography: history, perspectives, limitations and prospects.

Roque, A. C. A., & Lowe, C. R. (2008) · PubMed · Cited by 31 · see citing works

A Quantitative Proteomic Approach to Prion Disease Biomarker Research: Delving into the Glycoproteome

Wei, X. L., Herbst, A. J., Ma, D., Aiken, J. M., & Li, L. (2011) · Journal of Proteome Research · doi:10.1021/pr2000495 · Cited by 29 · see citing works

Proteomic Studies of Syk-Interacting Proteins Using a Novel Amine-Specific Isotope Tag and GFP Nanotrap

Galan, J. A., Paris, L. L., Zhang, H.-J., Adler, J. J., Geahlen, R. L., & Tao, W. A. (2011) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-010-0030-7 · Cited by 27 · see citing works

Identification of a host cell target for the thiazolide class of broad-spectrum anti-parasitic drugs

Müller, J., & Hemphill, A. F. (2011) · Experimental Parasitology · doi:10.1016/j.exppara.2011.02.007 · Cited by 26 · see citing works

From large analogical instruments to small digital black boxes: 40 years of progress in mass spectrometry and its role in proteomics. Part I 1965–1984

Gelpı́, E. (2008) · Journal of Mass Spectrometry · doi:10.1002/jms.1403 · Cited by 26 · see citing works

Comparison of Classical and Affinity Purification Techniques of Mason-Pfizer Monkey Virus Capsid Protein: The Alteration of the Product by an Affinity Tag

Rumlová, M., Benedı́ková, J., Cubı́nková, R., Pichová, I., & Ruml, T. (2001) · Protein Expression and Purification · doi:10.1006/prep.2001.1488 · Cited by 25 · see citing works

Tandem Affinity Purification of Ciliopathy-Associated Protein Complexes

Boldt, K., van Reeuwijk, J., Gloeckner, C. J., Ueffing, M., & Roepman, R. (2009) · Methods in cell biology · doi:10.1016/s0091-679x(08)91009-8 · Cited by 24 · see citing works

High‐sensitive protein analysis by FESI‐CE‐MALDI‐MS

Pourhaghighi, M. R., Busnel, J., & Girault, H. H. (2011) · Electrophoresis · doi:10.1002/elps.201100024 · Cited by 23 · see citing works

Mass Spectrometric Strategies and Their Applications for Molecular Mass Determination of Recombinant Therapeutic Proteins

Carini, M., Regazzoni, L., & Aldini, G. (2011) · Current Pharmaceutical Biotechnology · doi:10.2174/138920111798357348 · Cited by 22 · see citing works

Tagging genes with cassette-exchange sites

Cobellis, G. (2005) · Nucleic Acids Research · doi:10.1093/nar/gni045 · Cited by 22 · see citing works

From large analogical instruments to small digital black boxes: 40 years of progress in mass spectrometry and its role in proteomics. Part II 1985–2000

Gelpı́, E. (2009) · Journal of Mass Spectrometry · doi:10.1002/jms.1621 · Cited by 21 · see citing works

A Method for the Rapid and Efficient Elution of Native Affinity-Purified Protein A Tagged Complexes

Strambio‐De‐Castillia, C., Tetenbaum-Novatt, J. E., Imai, B. S., Chait, B. T., & Rout, M. P. (2005) · Journal of Proteome Research · doi:10.1021/pr0501517 · Cited by 17 · 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

Computational structural analysis of protein interactions and networks

Hooda, Y., & Kim, P. M. (2012) · PROTEOMICS · doi:10.1002/pmic.201100597 · Cited by 17 · see citing works

Towards a Rigorous Network of Protein-Protein Interactions of the Model Sulfate Reducer Desulfovibrio vulgaris Hildenborough

Chhabra, S. R., Joachimiak, M. P., Petzold, C. J., Zane, G. M., Price, M. N., Reveco, S. A., Fok, V., Johanson, A. R., Batth, T. S., Singer, M. E., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0021470 · Cited by 12 · see citing works

High throughput gene trapping and postinsertional modifications of gene trap alleles

Schnütgen, F., Ehrmann, F., Ruíz, P., & von Melchner, H. (2011) · Methods · doi:10.1016/j.ymeth.2010.12.037 · Cited by 10 · see citing works

Affinity Chromatography

Roque, A. C. A., & Lowe, C. R. (2008) · Humana Press eBooks · doi:10.1007/978-1-59745-582-4_1 · Cited by 5 · see citing works

Mass-spectrometric exploration of proteome structure and function

Aebersold, R., & Mann, M. (2016) · Nature · doi:10.1038/nature19949 · Cited by 2,334 · see citing works

The CRAPome: a contaminant repository for affinity purification–mass spectrometry data

Mellacheruvu, D., Wright, Z., Couzens, A. L., Lambert, J.-P., St-Denis, N. A., Li, T., Miteva, Y. V., Hauri, S., Sardiu, M. E., Low, T. Y., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2557 · Cited by 1,686 · see citing works

Deciphering molecular interactions by proximity labeling

Qin, W., Cho, K. F., Cavanagh, P. E., & Ting, A. Y. (2021) · Nature Methods · doi:10.1038/s41592-020-01010-5 · Cited by 671 · see citing works

NANOG-dependent function of TET1 and TET2 in establishment of pluripotency

Costa, Y., Ding, J., Theunissen, T. W., Faiola, F., Hore, T. A., Shliaha, P. V., Fidalgo, M., Saunders, A., Lawrence, M., Dietmann, S., et al. (2013) · Nature · doi:10.1038/nature11925 · Cited by 433 · see citing works

Modulating biomolecular condensates: a novel approach to drug discovery

Mitrea, D. M., Mittasch, M., Gomes, B. F., Klein, I. A., & Murcko, M. A. (2022) · Nature Reviews Drug Discovery · doi:10.1038/s41573-022-00505-4 · Cited by 408 · see citing works

Mapping the Degradable Kinome Provides a Resource for Expedited Degrader Development

Donovan, K. A., Ferguson, F. M., Bushman, J. W., Eleuteri, N. A., Bhunia, D., Ryu, S., Tan, L., Shi, K., Yue, H., Liu, X., et al. (2020) · Cell · doi:10.1016/j.cell.2020.10.038 · Cited by 359 · see citing works

Rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) for analysis of chromatin complexes

Mohammed, H., Taylor, C., Brown, G. D., Papachristou, E., Carroll, J., & D'Santos, C. (2016) · Nature Protocols · doi:10.1038/nprot.2016.020 · Cited by 316 · see citing works

The emerging landscape of single-molecule protein sequencing technologies

Alfaro, J., Bohländer, P. R., Dai, M.-J., Filius, M., Howard, C. J., van Kooten, X. F., Ohayon, S., Pomorski, A., Schmid, S., Aksimentiev, A., et al. (2021) · Nature Methods · doi:10.1038/s41592-021-01143-1 · Cited by 306 · see citing works

Fundamentals 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

An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations

Liu, X., Salokas, K., Tamene, F., Jiu, Y., Weldatsadik, R. G., Öhman, T., & Varjosalo, M. T. (2018) · Nature Communications · doi:10.1038/s41467-018-03523-2 · Cited by 259 · see citing works

Understudied proteins: opportunities and challenges for functional proteomics

Kustatscher, G., Collins, T., Gingras, A., Guo, T., Hermjakob, H., Ideker, T. E., Lilley, K. S., Lundberg, E. K., Marcotte, E. M., Ralser, M., et al. (2022) · Nature Methods · doi:10.1038/s41592-022-01454-x · Cited by 190 · see citing works

Affinity purification–mass spectrometry and network analysis to understand protein-protein interactions

Morris, 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

mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry

Teo, G., Kim, S., Tsou, C., Collins, B. C., Gingras, A., Nesvizhskii, A. I., & Choi, H. (2015) · Journal of Proteomics · doi:10.1016/j.jprot.2015.09.013 · Cited by 145 · see citing works

Characterization of Native Protein Complexes and Protein Isoform Variation Using Size-fractionation-based Quantitative Proteomics

Kirkwood, K. J., Ahmad, Y., Larance, M., & Lamond, A. I. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.032367 · Cited by 133 · see citing works

Protein-protein interaction networks: unraveling the wiring of molecular machines within the cell

Rivas, J. D. L., & Fontanillo, C. (2012) · Briefings in Functional Genomics · doi:10.1093/bfgp/els036 · Cited by 125 · see citing works

Protein–Protein Interaction Network Exploration Using Cytoscape

Majeed, A., & Mukhtar, S. M. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-3327-4_32 · Cited by 120 · see citing works

JMJ17–WRKY40 and HY5–ABI5 modules regulate the expression of ABA‐responsive genes in Arabidopsis

Wang, T., Huang, S., Zhang, A., Guo, P., Liu, Y., Xu, C., Cong, W., Liu, B., & Xu, Z. (2021) · New Phytologist · doi:10.1111/nph.17177 · Cited by 119 · see citing works

The RTK Interactome: Overview and Perspective on RTK Heterointeractions

Paul, M. D., & Hristova, K. A. (2018) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00467 · Cited by 114 · see citing works

Proteomics-based identification of low-abundance signaling and regulatory protein complexes in native plant tissues

Smaczniak, C., Li, N., Boeren, S. A., America, A. H. P., van Dongen, W. M. A. M., Goerdayal, S. S., de Vries, S. C., Angenent, G. C., & Kaufmann, K. (2012) · Nature Protocols · doi:10.1038/nprot.2012.129 · Cited by 107 · see citing works

Expanding the Genetic Code to Study Protein–Protein Interactions

Nguyen, T., Cigler, M., & Lang, K. (2018) · Angewandte Chemie International Edition · doi:10.1002/anie.201805869 · Cited by 107 · see citing works

A Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis

Rudolph, J. D., & Cox, J. (2019) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00927 · Cited by 105 · see citing works

Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins

Rafiee, M., Girardot, C., Sigismondo, G., & Krijgsveld, J. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.09.019 · Cited by 101 · see citing works

Proteomics turns functional

Monti, C., Zilocchi, M., Colugnat, I., & Alberio, T. (2018) · Journal of Proteomics · doi:10.1016/j.jprot.2018.12.012 · Cited by 100 · see citing works

Proximity-dependent biotinylation mediated by TurboID to identify protein–protein interaction networks in yeast

Larochelle, M., Bergeron, D., Arcand, B., & Bachand, F. (2019) · Journal of Cell Science · doi:10.1242/jcs.232249 · Cited by 92 · see citing works

Protein–protein interaction predictions using text mining methods

Papanikolaou, N., Pavlopoulos, G. A., Θεοδοσίου, Θ., & Iliopoulos, I. (2014) · Methods · doi:10.1016/j.ymeth.2014.10.026 · Cited by 91 · see citing works

Computational identification of protein-protein interactions in model plant proteomes

Ding, Z., & Kihara, D. (2019) · Scientific Reports · doi:10.1038/s41598-019-45072-8 · Cited by 90 · 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

Deciphering preferential interactions within supramolecular protein complexes: the proteasome case

Fabre, B., Lambour, T., Garrigues, L., Amalric, F., Vigneron, N., Menneteau, T., Stella, A., Monsarrat, B., den Eynde, B. J. V., Burlet‐Schiltz, O., et al. (2015) · Molecular Systems Biology · doi:10.15252/msb.20145497 · Cited by 87 · see citing works

Genetically encoded protein photocrosslinker with a transferable mass spectrometry-identifiable label

Yang, Y., Song, H., He, D., Zhang, S., Dai, S. A., Lin, S., Meng, R., Wang, C., & Chen, P. R. (2016) · Nature Communications · doi:10.1038/ncomms12299 · Cited by 85 · see citing works

Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein–Protein Interaction Networks in Vivo

Matzinger, M., & Mechtler, K. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00583 · Cited by 80 · see citing works

Protein‐protein interaction networks as miners of biological discovery

Wang, S., Wu, R., Lü, J., Jiang, Y., Huang, T., & Cai, Y. (2022) · PROTEOMICS · doi:10.1002/pmic.202100190 · Cited by 84 · see citing works

Dissecting ribosomal particles throughout the kingdoms of life using advanced hybrid mass spectrometry methods

van de Waterbeemd, M., Tamara, S., Fort, K. L., Damoc, E., Franc, V., Bieri, P., Itten, M. P., Makarov, A., Ban, N., & Heck, A. J. R. (2018) · Nature Communications · doi:10.1038/s41467-018-04853-x · Cited by 80 · see citing works

A census of pathway maps in cancer systems biology

Kuenzi, B. M., & Ideker, T. (2020) · Nature reviews. Cancer · doi:10.1038/s41568-020-0240-7 · Cited by 79 · see citing works

Recent advances in predicting and modeling protein–protein interactions

Durham, J., Zhang, J., Humphreys, I. R., Pei, J., & Cong, Q. (2023) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2023.03.003 · Cited by 80 · see citing works

The development of proximity labeling technology and its applications in mammals, plants, and microorganisms

Guo, J., Guo, S., Lu, S., Gong, J., Wang, L., Ding, L., Chen, Q., & Liu, W. (2023) · Cell Communication and Signaling · doi:10.1186/s12964-023-01310-1 · Cited by 83 · see citing works

Machine learning solutions for predicting protein–protein interactions

Casadio, R., Martelli, P. L., & Savojardo, C. (2022) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1618 · Cited by 80 · see citing works

Computational Methods for Predicting Protein‐Protein Interactions Using Various Protein Features

Ding, Z., & Kihara, D. (2018) · Current Protocols in Protein Science · doi:10.1002/cpps.62 · Cited by 77 · see citing works

Parallel Exploration of Interaction Space by BioID and Affinity Purification Coupled to Mass Spectrometry

Hesketh, G. G., Youn, J., Samavarchi‐Tehrani, P., Raught, B., & Gingras, A. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-6747-6_10 · Cited by 73 · see citing works

Measuring rank robustness in scored protein interaction networks

Bozhilova, L. V., Whitmore, A. V., Wray, J., Reinert, G., & Deane, C. M. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-3036-6 · Cited by 72 · see citing works

Genetically Encoded Residue-Selective Photo-Crosslinker to Capture Protein-Protein Interactions in Living Cells

Hu, W., Yuan, Y., Wang, C.-H., Tian, H., Guo, A., Nie, H., Hu, H., Tan, M., Tang, Z., & Chen, X. (2019) · Chem · doi:10.1016/j.chempr.2019.08.020 · Cited by 72 · see citing works

Interaction network of tobacco etch potyvirus NIa protein with the host proteome during infection

Martínez, F., Rodrigo, G., Aragonés, V., Ruiz, M., Lodewijk, I., Fernández, U., Elena, S. F., & Daròs, J. (2016) · BMC Genomics · doi:10.1186/s12864-016-2394-y · Cited by 72 · see citing works

Rapid, optimized interactomic screening

Hakhverdyan, Z., Domanski, M., Hough, L. E., Oroskar, A. A., Oroskar, A. R., Keegan, S., Dilworth, D. J., Molloy, K. R., Sherman, V., Aitchison, J. D., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3395 · Cited by 65 · see citing works

Proteomic approaches to the study of papillomavirus–host interactions

White, E. A., & Howley, P. M. (2012) · Virology · doi:10.1016/j.virol.2012.09.046 · Cited by 70 · see citing works

Next-generation Interactomics: Considerations for the Use of Co-elution to Measure Protein Interaction Networks

Salas, D., Stacey, R. G., Akinlaja, M. O., & Foster, L. J. (2019) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r119.001803 · Cited by 66 · see citing works

Proteomics to study DNA-bound and chromatin-associated gene regulatory complexes

Wierer, M., & Mann, M. (2016) · Human Molecular Genetics · doi:10.1093/hmg/ddw208 · Cited by 66 · see citing works

Target identification with quantitative activity based protein profiling (ABPP)

Chen, X., Wong, Y. K., Wang, J., Zhang, J., Lee, Y. M., Shen, H., Lin, Q., & Hua, Z. (2016) · PROTEOMICS · doi:10.1002/pmic.201600212 · Cited by 66 · see citing works

A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE)

Stacey, R. G., Skinnider, M. A., Scott, N. E., & Foster, L. J. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1865-8 · Cited by 65 · see citing works

Characterization of the CLASP2 Protein Interaction Network Identifies SOGA1 as a Microtubule-Associated Protein

Kruse, R., Krantz, J. L., Barker, N. K., Coletta, R. L., Rafikov, R., Luo, M., Højlund, K., Mandarino, L. J., & Langlais, P. R. (2017) · Molecular & Cellular Proteomics · doi:10.1074/mcp.ra117.000011 · Cited by 63 · see citing works

Affinity Proteomics to Study Endogenous Protein Complexes: Pointers, Pitfalls, Preferences and Perspectives

LaCava, J., Molloy, K. R., Taylor, M. S., Domanski, M., Chait, B. T., & Rout, M. P. (2015) · BioTechniques · doi:10.2144/000114262 · Cited by 58 · see citing works

CETSA in integrated proteomics studies of cellular processes

Prabhu, N., Dai, L., & Nordlund, P. (2019) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2019.11.004 · Cited by 60 · see citing works

Quantitative and Comparative Profiling of Protease Substrates through a Genetically Encoded Multifunctional Photocrosslinker

He, D., Xie, X., Yang, F., Zhang, H., Su, H., Ge, Y., Song, H., & Chen, P. R. (2017) · Angewandte Chemie International Edition · doi:10.1002/anie.201708151 · Cited by 59 · see citing works

Direct and Propagated Effects of Small Molecules on Protein–Protein Interaction Networks

Cesa, L. C., Mapp, A. K., & Gestwicki, J. E. (2015) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2015.00119 · Cited by 58 · see citing works

Exploring protein-protein interactions at the proteome level

Elhabashy, H., Merino, F., Alva, V., Kohlbacher, O., & Lupas, A. N. (2022) · Structure · doi:10.1016/j.str.2022.02.004 · Cited by 56 · see citing works

Cross-linking immunoprecipitation-MS (xIP-MS): Topological Analysis of Chromatin-associated Protein Complexes Using Single Affinity Purification

Makowski, M. M., Willems, E., Jansen, P. W. T. C., & Vermeulen, M. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m115.053082 · Cited by 57 · see citing works

Revealing Higher Order Protein Structure Using Mass Spectrometry

Chait, B. T., Cadène, M., Olinares, P. D. B., Rout, M. P., & Shi, Y. (2016) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-016-1385-1 · Cited by 55 · see citing works

Genetically encoded photocrosslinkers for identifying and mapping protein‐protein interactions in living cells

Yang, Y., Song, H., & Chen, P. R. (2016) · IUBMB Life · doi:10.1002/iub.1560 · Cited by 56 · see citing works

Comparison of label-free quantification methods for the determination of protein complexes subunits stoichiometry

Fabre, B., Lambour, T., Bouyssié, D., Menneteau, T., Monsarrat, B., Burlet‐Schiltz, O., & Bousquet, M. (2014) · EuPA Open Proteomics · doi:10.1016/j.euprot.2014.06.001 · Cited by 55 · see citing works

Interaction Analysis through Proteomic Phage Display

Sundell, G. N., & Ivarsson, Y. (2014) · BioMed Research International · doi:10.1155/2014/176172 · Cited by 55 · see citing works

Amino Acid Insertion Frequencies Arising from Photoproducts Generated Using Aliphatic Diazirines

Ziemianowicz, D. S., Bomgarden, R. D., Etienne, C. L., & Schriemer, D. C. (2017) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-017-1730-z · Cited by 53 · see citing works

Inferring protein-protein interaction networks from mass spectrometry-based proteomic approaches: a mini-review

Yugandhar, K., Gupta, S., & Yu, H. (2019) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2019.05.007 · Cited by 51 · see citing works

Identification of the interaction between vimentin and nucleocapsid protein of transmissible gastroenteritis virus

Zhang, X., Shi, H., Chen, J., Shi, D., Dong, H., & Feng, L. (2014) · Virus Research · doi:10.1016/j.virusres.2014.12.013 · Cited by 51 · see citing works

Analysis of protein complexes in Arabidopsis leaves using size exclusion chromatography and label-free protein correlation profiling

Aryal, U. K., McBride, Z., Chen, D., Xie, J. H., & Szymanski, D. B. (2017) · Journal of Proteomics · doi:10.1016/j.jprot.2017.06.004 · Cited by 51 · see citing works

A user-friendly platform for yeast two-hybrid library screening using next generation sequencing

Erffelinck, M., Ribeiro, B., Perassolo, M., Pauwels, L., Pollier, J., Storme, V., & Goossens, A. (2018) · PLoS ONE · doi:10.1371/journal.pone.0201270 · Cited by 51 · see citing works

Protein complexes and neighborhoods driving autophagy

Sankar, D. S., & Dengjel, J. (2020) · Autophagy · doi:10.1080/15548627.2020.1847461 · Cited by 51 · see citing works

Utilizing a Biology-Driven Approach to Map the Exposome in Health and Disease: An Essential Investment to Drive the Next Generation of Environmental Discovery

Chung, M. K., Rappaport, S. M., Wheelock, C. E., Nguyen, V. K., van der Meer, T. P., Miller, G. W., Vermeulen, R. C. H., & Patel, C. J. (2021) · Environmental Health Perspectives · doi:10.1289/ehp8327 · Cited by 48 · see citing works

The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein–Protein Interactions (PPIs)

Yakubu, R., Nieves, E., & Weiss, L. M. (2019) · Advances in experimental medicine and biology · doi:10.1007/978-3-030-15950-4_10 · Cited by 46 · see citing works

Protein-protein interactions involving enzymes of the mammalian methionine and homocysteine metabolism

Portillo, F., Vázquez, J., & Pajares, M. A. (2020) · Biochimie · doi:10.1016/j.biochi.2020.02.015 · Cited by 46 · see citing works

Marked by association: techniques for proximity-dependent labeling of proteins in eukaryotic cells

Roux, K. J. (2013) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-013-1287-3 · Cited by 43 · see citing works

MKRN3 Interacts With Several Proteins Implicated in Puberty Timing but Does Not Influence GNRH1 Expression

Yellapragada, V., Liu, X., Lund, C., Känsäkoski, J., Pulli, K., Vuoristo, S., Lundin, K., Tuuri, T., Varjosalo, M. T., & Raivio, T. (2019) · Frontiers in Endocrinology · doi:10.3389/fendo.2019.00048 · Cited by 42 · see citing works

Fam83h null mice support a neomorphic mechanism for human ADHCAI

Wang, S., Hu, Y., Yang, J., Smith, C. E., Richardson, A. S., Yamakoshi, Y., Lee, Y., Seymen, F., Koruyucu, M., Gençay, K., et al. (2015) · Molecular Genetics & Genomic Medicine · doi:10.1002/mgg3.178 · Cited by 41 · see citing works

Recent Advances in Mass Spectrometry-Based Protein Interactome Studies

Wu, S.-W., Zhang, S., Liu, C., Fernie, A., & Yan, S.-J. (2024) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2024.100887 · Cited by 37 · see citing works

A Versatile Lentiviral Delivery Toolkit for Proximity-dependent Biotinylation in Diverse Cell Types

Samavarchi‐Tehrani, P., Abdouni, H. S., Samson, R., & Gingras, A. (2018) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir118.000902 · Cited by 39 · see citing works

Combining Genomic and Proteomic Approaches for Epigenetics Research

Han, Y., & Garcia, B. A. (2013) · Epigenomics · doi:10.2217/epi.13.37 · Cited by 38 · see citing works

The calcified eggshell matrix proteome of a songbird, the zebra finch (Taeniopygia guttata)

Mann, K. (2015) · Proteome Science · doi:10.1186/s12953-015-0086-1 · Cited by 38 · see citing works

Surfaceome nanoscale organization and extracellular interaction networks.

Bausch-Fluck, D., Milani, E., & Wollscheid, B. (2019) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2018.09.020 · Cited by 35 · see citing works

Impact of inherent biases built into proteomic techniques: Proximity labeling and affinity capture compared

Moreira, C. M. D. N., Kelemen, C. D., Obado, S. O., Zahedifard, F., Zhang, N., Holetz, F., Gauglitz, L., Dallagiovanna, B., Field, M. C., Krämer, S., et al. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.102726 · Cited by 36 · see citing works

Next-Generation Sequencing for Binary Protein–Protein Interactions

Suter, B., Zhang, X., Pesce, C. G., Mendelsohn, A. R., Dinesh‐Kumar, S. P., & Mao, J. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00346 · Cited by 37 · see citing works

From proteomes to complexomes in the era of systems biology

Clancy, T., & Hovig, E. J. (2013) · PROTEOMICS · doi:10.1002/pmic.201300230 · Cited by 36 · see citing works

Target Identification of Kinase Inhibitor Alisertib (MLN8237) by Using DNA‐Programmed Affinity Labeling

Wang, D., Cao, Y. W., Zheng, L., Chen, L., Chen, X., Hong, Z., Zhu, Z., Li, X., & Chai, Y. (2017) · Chemistry - A European Journal · doi:10.1002/chem.201702033 · Cited by 36 · see citing works

Systematic identification of structure-specific protein–protein interactions

(2024) · doi:10.1038/s44320-024-00037-6 · Cited by 34 · see citing works

Proteomics of effector-triggered immunity (ETI) in plants

Hurley, B. A., Subramaniam, R., Guttman, D. S., & Desveaux, D. (2014) · Virulence · doi:10.4161/viru.36329 · Cited by 34 · see citing works

Interactomics: toward protein function and regulation

Feng, S., Zhou, L., Huang, C., Xie, K., & Nice, E. C. (2015) · Expert Review of Proteomics · doi:10.1586/14789450.2015.1000870 · Cited by 34 · see citing works

Protein complex analysis: From raw protein lists to protein interaction networks

Meysman, P., Titeca, K., Eyckerman, S., Tavernier, J. H., Goethals, B., Martens, L., Valkenborg, D., & Laukens, K. (2015) · Mass Spectrometry Reviews · doi:10.1002/mas.21485 · Cited by 33 · see citing works

Genetically encoded releasable photo-cross-linking strategies for studying protein–protein interactions in living cells

Yang, Y., Song, H., He, D., Zhang, S., Dai, S. A., Xie, X., Lin, S., Hao, Z., Zheng, H., & Chen, P. R. (2017) · Nature Protocols · doi:10.1038/nprot.2017.090 · Cited by 33 · see citing works

Stressor-induced proteome alterations in zebrafish: A meta-analysis of response patterns

Groh, K. J., & Suter, M. J. ‐. (2014) · Aquatic Toxicology · doi:10.1016/j.aquatox.2014.11.013 · Cited by 33 · see citing works

An Inducible Retroviral Expression System for Tandem Affinity Purification Mass-Spectrometry-Based Proteomics Identifies Mixed Lineage Kinase Domain-like Protein (MLKL) as an Heat Shock Protein 90 (HSP90) Client

Bigenzahn, J. W., Fauster, A., Rebsamen, M., Kandasamy, R. K., Scorzoni, S., Vladimer, G. I., Müller, A. C., Gstaiger, M., Zuber, J. A., Bennett, K. L., et al. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o115.055350 · Cited by 33 · see citing works

Mapping oncogenic protein interactions for precision medicine

Tabar, M. S., Francis, H., Yeo, D., Bailey, C. G., & Rasko, J. E. J. (2022) · International Journal of Cancer · doi:10.1002/ijc.33954 · Cited by 30 · see citing works

Integrative analysis of human omics data using biomolecular networks

Robinson, J. L., & Nielsen, J. (2016) · Molecular BioSystems · doi:10.1039/c6mb00476h · Cited by 32 · 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

Incorporating DNA shearing in standard affinity purification allows simultaneous identification of both soluble and chromatin-bound interaction partners

Lambert, J., Tucholska, M., Pawson, T. J., & Gingras, A. (2014) · Journal of Proteomics · doi:10.1016/j.jprot.2013.12.022 · Cited by 31 · see citing works

MASS SPECTROMETRY IN VIROLOGICAL SCIENCES

Milewska, A., Ner‐Kluza, J., Dąbrowska, A., Bodzoń‐Kułakowska, A., Pyrć, K., & Suder, P. (2019) · Mass Spectrometry Reviews · doi:10.1002/mas.21617 · Cited by 31 · see citing works

The cell-free system: A new apparatus for affordable, sensitive, and portable healthcare

Copeland, C. E., Langlois, A., Kim, J., & Kwon, Y. (2021) · Biochemical Engineering Journal · doi:10.1016/j.bej.2021.108124 · Cited by 31 · see citing works

Increased WD-repeat containing protein 1 in interstitial fluid from ovarian carcinomas shown by comparative proteomic analysis of malignant and healthy gynecological tissue

Haslene‐Hox, H., Oveland, E., Woie, K., Salvesen, H. B., Wiig, H., & Tenstad, O. (2013) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2013.05.011 · Cited by 31 · see citing works

Navigating the landscape of plant proteomics

Sang, T., Zhang, Z., Liu, G., & Wang, P. (2025) · Journal of Integrative Plant Biology · doi:10.1111/jipb.13841 · Cited by 29 · see citing works

Rapid Identification of Protein‐Protein Interactions in Plants

Zhang, Y., Natale, R., Júnior, A. P. D., Toleco, M. R., Siemiątkowska, B., Fàbregas, N., & Fernie, A. R. (2019) · Current Protocols in Plant Biology · doi:10.1002/cppb.20099 · Cited by 30 · see citing works

An optimized co-immunoprecipitation protocol for the analysis of endogenous protein-protein interactions in cell lines using mass spectrometry

Lagundžin, D., Krieger, K. L., Law, H. C.-H., & Woods, N. T. (2022) · STAR Protocols · doi:10.1016/j.xpro.2022.101234 · Cited by 30 · see citing works

Methods for Studying Interactions Between Atg8/LC3/GABARAP and LIR-Containing Proteins

Johansen, T., Birgisdottir, Å. B., Huber, J., Kniss, A., Dötsch, V., Kirkin, V., & Rogov, V. V. (2017) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2016.10.023 · Cited by 29 · see citing works

Recent Advances in Fluorescent Detection of Pesticides in Environmental and Food Matrices: From Molecular Probes to Nanoparticle-Based Sensors

Xiong, J., Ma, C., Qu, H., Zhang, H., He, Q. Z., Zhao, Z., Liu, Y., Zhou, Z., Noruzi, E. B., & Li, H. (2025) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.5c07935 · Cited by 29 · see citing works

Analysis of Human Nuclear Protein Complexes by Quantitative Mass Spectrometry Profiling

Connelly, K. E., Hedrick, V., Sobreira, T. J. P., Dykhuizen, E. C., & Aryal, U. K. (2018) · PROTEOMICS · doi:10.1002/pmic.201700427 · Cited by 28 · see citing works

Protein Complex Identification and quantitative complexome by CN-PAGE

Górka, M., Swart, C., Siemiątkowska, B., Martínez-Jaime, S., Skirycz, A., Streb, S., & Graf, A. (2019) · Scientific Reports · doi:10.1038/s41598-019-47829-7 · Cited by 29 · see citing works

Quantitative proteomics: A strategic ally to map protein interaction networks

Marcilla, M., & Albar, J. P. (2012) · IUBMB Life · doi:10.1002/iub.1081 · Cited by 22 · see citing works

Affinity Purification couple to Mass Spectrometry (AP-MS)

Inglés‐Prieto, Á., Liñeiro, E., Bensimon, A., Frommelt, F., & Mueller, A. C. (2022) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.7457415

Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments

Nesvizhskii, A. I. (2012) · PROTEOMICS · doi:10.1002/pmic.201100537 · Cited by 93 · see citing works

Analyzing protein–protein interactions by quantitative mass spectrometry

Paul, F. E., Hosp, F., & Selbach, M. (2011) · Methods · doi:10.1016/j.ymeth.2011.03.001 · Cited by 61 · see citing works

Accurate Protein Complex Retrieval by Affinity Enrichment Mass Spectrometry (AE-MS) Rather than Affinity Purification Mass Spectrometry (AP-MS)

Keilhauer, E. C., Hein, M. Y., & Mann, M. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.041012 · Cited by 254 · see citing works