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

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 5,844

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

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

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

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 2,964

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

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 2,570

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 2,534

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

Alternative proteins are functional regulators in cell reprogramming by PKA activation

Cardon, T., Franck, J., Coyaud, É., Laurent, E. M. N., D’Amato, M., Maffia, M., Vergara, D., Fournier, I., & Salzet, M. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa277 · Cited by 30

The role of cell proteins in dengue virus infection

Salazar, M. I., del Ángel, R. M., Lanz‐Mendoza, H., Ludert, J. E., & Pando-Robles, V. (2014) · Journal of Proteomics · doi:10.1016/j.jprot.2014.06.002 · Cited by 29

Mapping of Plasma Membrane Proteins Interacting With Arabidopsis thaliana Flotillin 2

Junková, P., Daněk, M., Kocourková, D., Brouzdová, J., Kroumanová, K., Zelazny, E., Janda, M., Hynek, R., Martinec, J., & Valentová, O. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2018.00991 · Cited by 28

Identification of Tomato Proteins That Interact With Replication Initiator Protein (Rep) of the Geminivirus TYLCV

Maio, F., Helderman, T. A., Arroyo‐Mateos, M., van der Wolf, M., Boeren, S. A., Prins, M., & van den Burg, H. A. (2020) · Frontiers in Plant Science · doi:10.3389/fpls.2020.01069 · Cited by 27

A toolbox for systematic discovery of stable and transient protein interactors in baker's yeast

Fenech, E. J., Cohen, N., Kupervaser, M., Gazi, Z., & Schuldiner, M. (2023) · Molecular Systems Biology · doi:10.15252/msb.202211084 · Cited by 27

Global discovery of protein kinases and other nucleotide‐binding proteins by mass spectrometry

Xiao, Y., & Wang, Y. (2014) · Mass Spectrometry Reviews · doi:10.1002/mas.21447 · Cited by 27

Multiplex Protein Imaging with Secondary Ion Mass Spectrometry Using Metal Oxide Nanoparticle-Conjugated Antibodies

Moon, D. W., Park, Y. H., Lee, S. Y., Lim, H., Kwak, S., Kim, M. S., Kim, H., Kim, E., Jung, Y., Hoe, H.-S., et al. (2020) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.9b21800 · Cited by 28

Dynamics of protein complex components

Rattray, D., & Foster, L. J. (2018) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2018.11.003 · Cited by 26

Proximity Labeling, Quantitative Proteomics, and Biochemical Studies Revealed the Molecular Mechanism for the Inhibitory Effect of Indisulam on the Proliferation of Gastric Cancer Cells

Lü, J., Jiang, H., Li, D., Chen, T., Wang, Y., Pu, Z., & Xu, G. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.1c00437 · Cited by 26

The application of proteomic approaches to the study of mammalian spermatogenesis and sperm function

MacLeod, G. D. A. H., & Varmuza, S. (2013) · FEBS Journal · doi:10.1111/febs.12461 · Cited by 28

Proteomic analysis of the NOS2 interactome in human airway epithelial cells

Foster, M. W., Thompson, J. W., Forrester, M. T., Sha, Y., McMahon, T. J., Bowles, D. E., Moseley, M. A., & Marshall, H. E. (2013) · Nitric Oxide · doi:10.1016/j.niox.2013.02.079 · Cited by 25

Discovery of RSV-Induced BRD4 Protein Interactions Using Native Immunoprecipitation and Parallel Accumulation—Serial Fragmentation (PASEF) Mass Spectrometry

Mann, M. W., Roberts, D. S., Zhu, Y., Li, Y., Zhou, J., Ge, Y., & Brasier, A. R. (2021) · Viruses · doi:10.3390/v13030454 · Cited by 23

OGT Protein Interaction Network (OGT-PIN): A Curated Database of Experimentally Identified Interaction Proteins of OGT

Ma, J., Hou, C., Li, Y., Chen, S., & Wu, C. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22179620 · Cited by 29

A New Cellular Interactome of SARS-CoV-2 Nucleocapsid Protein and Its Biological Implications

Min, Y., Huang, M., Feng, K., Jia, Y., Sun, X., & Ning, Y. (2023) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2023.100579 · Cited by 25

Phosphoinositide-specific Phospholipase C β 1b (PI-PLCβ1b) Interactome: Affinity Purification-Mass Spectrometry Analysis of PI-PLCβ1b with Nuclear Protein

Piazzi, M., Blalock, W. L., Bavelloni, A., Faenza, I., D’Angelo, A., Maraldi, N. M., & Cocco, L. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.029686 · Cited by 25

Characterization of L1-Ribonucleoprotein Particles

Taylor, M. S., LaCava, J., Dai, L., Mita, P., Burns, K. H., Rout, M. P., & Boeke, J. D. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-3372-3_20 · Cited by 23

Conditional Chaperone–Client Interactions Revealed by Genetically Encoded Photo-cross-linkers

Zhang, S., He, D., Lin, Z., Yang, Y., Song, H., & Chen, P. R. (2017) · Accounts of Chemical Research · doi:10.1021/acs.accounts.6b00647 · Cited by 25

Oxidative Stress and Cell Death in Cardiovascular Disease

Marı́n-Garcı́a, J. (2014) · Elsevier eBooks · doi:10.1016/b978-0-12-404599-6.00014-7 · Cited by 26

Validation of a Novel Shotgun Proteomic Workflow for the Discovery of Protein–Protein Interactions: Focus on ZNF521

Bernaudo, F., Monteleone, F., Mesuraca, M., Krishnan, S., Chiarella, E., Scicchitano, S., Cuda, G., Morrone, G., Bond, H. M., & Gaspari, M. (2015) · Journal of Proteome Research · doi:10.1021/pr501288h · Cited by 24

Proximity‐dependent biotinylation approaches to study apicomplexan biology

Kimmel, J., Kehrer, J., Frischknecht, F., & Spielmann, T. (2021) · Molecular Microbiology · doi:10.1111/mmi.14815 · Cited by 24

Detecting Membrane Protein‐protein Interactions Using the Mammalian Membrane Two‐hybrid (MaMTH) Assay

Saraon, P., Grozavu, I., Lim, S. H., Snider, J. D., Yao, Z., & Štagljar, I. (2017) · Current Protocols in Chemical Biology · doi:10.1002/cpch.15 · Cited by 24

Antibody based affinity capture LC-MS/MS in quantitative determination of proteins in biological matrices

Halvorsen, T. G., & Reubsaet, L. (2017) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2017.08.009 · Cited by 24

Protein–Protein Interaction Methods and Protein Phase Separation

Savojardo, C., Martelli, P. L., & Casadio, R. (2020) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-011720-104428 · Cited by 26

A Novel Immuno-Competitive Capture Mass Spectrometry Strategy for Protein–Protein Interaction Profiling Reveals That LATS Kinases Regulate HCV Replication Through NS5A Phosphorylation*

Meistermann, H., Gao, J., Golling, S., Lamerz, J., Pogam, S. L., Tzouros, M., Sankabathula, S., Gruenbaum, L. M., Nájera, I., Langen, H., et al. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.028977 · Cited by 24

Facilitating identification of minimal protein binding domains by cross-linking mass spectrometry

Liu, Q., Remmelzwaal, S., Heck, A. J. R., Akhmanova, A. S., & Liu, F. (2017) · Scientific Reports · doi:10.1038/s41598-017-13663-y · Cited by 23

Exploring dinoflagellate biology with high-throughput proteomics

Morse, D., Tse, S. P.-K., & Lo, S. C. (2018) · Harmful Algae · doi:10.1016/j.hal.2018.03.010 · Cited by 25

A Guide to Mass Spectrometry-Based Quantitative Proteomics

Smith, B. J., Martins‐de‐Souza, D., & Fioramonte, M. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-8994-2_1 · Cited by 24

Chemo‐proteomics in antimalarial target identification and engagement

Bailey, B. L., Nguyen, W., Cowman, A. F., & Sleebs, B. E. (2023) · Medicinal Research Reviews · doi:10.1002/med.21975 · Cited by 21

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

Rochette, S., Diss, G., Filteau, M., Leducq, J., Dubé, A. K., & Landry, C. R. (2015) · Journal of Visualized Experiments · doi:10.3791/52255 · Cited by 21

Exploring Protein Interactome Data with IPinquiry: Statistical Analysis and Data Visualization by Spectral Counts

Kühn, L., Vincent, T., Hammann, P., & Zuber, H. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1967-4_11 · Cited by 20

Recent advances in quantitative and chemical proteomics for autophagy studies

Wong, Y., Zhang, J., Hua, Z., Lin, Q., Shen, H., & Wang, J. (2017) · Autophagy · doi:10.1080/15548627.2017.1313944 · Cited by 20

Analysis of Protein Complexes in the Unicellular Cyanobacterium Cyanothece ATCC 51142

Aryal, U. K., Ding, Z., Hedrick, V., Sobreira, T. J. P., Kihara, D., & Sherman, L. A. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00170 · Cited by 20

Tandem Affinity Purification and Mass Spectrometry (TAP‐MS) for the Analysis of Protein Complexes

Adelmant, G., Garg, B. K., Tavares, M., Card, J. D., & Marto, J. A. (2019) · Current Protocols in Protein Science · doi:10.1002/cpps.84 · Cited by 19

Twenty years of protein interaction studies for biological function deciphering

Legrain, P., & Rain, J. (2014) · Journal of Proteomics · doi:10.1016/j.jprot.2014.03.038 · Cited by 21

Structural proteomics, electron cryo-microscopy and structural modeling approaches in bacteria–human protein interactions

Chowdhury, S., Happonen, L., Khakzad, H., Malmström, L., & Malmström, J. A. (2020) · Medical Microbiology and Immunology · doi:10.1007/s00430-020-00663-5 · Cited by 18

The TGEV Membrane Protein Interacts with HSC70 To Direct Virus Internalization through Clathrin-Mediated Endocytosis

Ji, Z., Dong, H., Jiao, R., Zhu, X., Shi, H., Chen, J., Shi, D., Liu, J., Jing, Z., Zhang, J., et al. (2023) · Journal of Virology · doi:10.1128/jvi.00128-23 · Cited by 19

Decoding the functional impact of the cancer genome through protein–protein interactions

Fu, H., Mo, X., & Ivanov, A. A. (2025) · Nature reviews. Cancer · doi:10.1038/s41568-024-00784-6 · Cited by 22

Steap4 attenuates high glucose and S100B‐induced effects in mesangial cells

Chuang, C., Guh, J., Lu, C., Wang, Y., Chen, H., & Chuang, L. (2015) · Journal of Cellular and Molecular Medicine · doi:10.1111/jcmm.12472 · Cited by 19

How do oncoprotein mutations rewire protein–protein interaction networks?

Bowler-Barnett, E., Wang, Z., & Ewing, R. M. (2015) · Expert Review of Proteomics · doi:10.1586/14789450.2015.1084875 · Cited by 19

Studying epigenetic complexes and their inhibitors with the proteomics toolbox

Weigt, D., Hopf, C., & Médard, G. (2016) · Clinical Epigenetics · doi:10.1186/s13148-016-0244-z · Cited by 18

Affinity Purification of Protein Complexes from Drosophila Embryos in Cell Cycle Studies

Lipinszki, Z., Wang, P., Grant, R., Lindon, C., Dzhindzhev, N. S., D’Avino, P. P., Przewloka, M. R., Glover, D. M., & Archambault, V. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-0888-2_33 · Cited by 18

Mapping the Polarity Interactome

Pires, H. R., & Boxem, M. (2017) · Journal of Molecular Biology · doi:10.1016/j.jmb.2017.12.017 · Cited by 20

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

MS/MS‐based strategies for proteomic profiling of invasive cell structures

Havrylov, S., & Park, M. (2014) · PROTEOMICS · doi:10.1002/pmic.201400220 · Cited by 18

Computational Prediction of Protein Complexes from Protein Interaction Networks

Srihari, S., Yong, C. H., & Wong, L. (2017) · doi:10.1145/3064650 · Cited by 17

Expanding the Genetic Code to Study Protein–Protein Interactions

Nguyen, T., Cigler, M., & Lang, K. (2018) · Angewandte Chemie · doi:10.1002/ange.201805869 · Cited by 17

Protein interactome mapping in Caenorhabditis elegans

Remmelzwaal, S., & Boxem, M. (2018) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2018.08.006 · Cited by 17

Host cell protein detection gap risk mitigation: quantitative IAC-MS for ELISA antibody reagent coverage determination

Waldera-Lupa, D. M., Jasper, Y., Köhne, P., Schwichtenhövel, R., Falkenberg, H., Flad, T., Happersberger, P., Reisinger, B., Dehghani, A., Moussa, R., et al. (2021) · mAbs · doi:10.1080/19420862.2021.1955432 · Cited by 16

Highly Specific Protein Identification by Immunoprecipitation–Mass Spectrometry Using Antifouling Microbeads

van Andel, E., Roosjen, M., van der Zanden, S., Lange, S. C., Weijers, D., Smulders, M. M. J., Savelkoul, H. F. J., Zuilhof, H. T., & Tijhaar, E. J. (2022) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.1c22734 · Cited by 16

Activity-based proteomic profiling: application of releasable linker in photoaffinity probes

Wang, J., Chen, Q., Shan, Y., Pan, X., & Zhang, J. (2019) · Drug Discovery Today · doi:10.1016/j.drudis.2019.10.016 · Cited by 16

CDC20-Mediated hnRNPU Ubiquitination Regulates Chromatin Condensation and Anti-Cancer Drug Response

Wavelet-Vermuse, C., Odnokoz, O., Xue, Y., Lu, X., Cristofanilli, M., & Wan, Y. (2022) · Cancers · doi:10.3390/cancers14153732 · Cited by 16

Virus-host interactome: Putting the accent on how it changes

Rodrigo, G., Daròs, J., & Elena, S. F. (2016) · Journal of Proteomics · doi:10.1016/j.jprot.2016.12.007 · Cited by 16

Native MS-guided lipidomics to define endogenous lipid microenvironments of eukaryotic receptors and transporters

Wu, D., Tang, H., Qiu, X., Song, S., Chen, S., & Robinson, C. V. (2024) · Nature Protocols · doi:10.1038/s41596-024-01037-4 · Cited by 20

A composite filter for low FDR of protein-protein interactions detected by in vivo cross-linking

de Jong, L., Roseboom, W., & Kramer, G. (2020) · Journal of Proteomics · doi:10.1016/j.jprot.2020.103987 · Cited by 15

Proteomics Insights Into the Molecular Basis of SARS-CoV-2 Infection: What We Can Learn From the Human Olfactory Axis

Lachén‐Montes, M., Corrales, F. J., Fernández‐Irigoyen, J., & Santamaría, E. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.02101 · Cited by 15

From Affinity to Proximity Techniques to Investigate Protein Complexes in Plants

Kerbler, S. M., Natale, R., Fernie, A. R., & Zhang, Y. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22137101 · Cited by 19

Sample Preparation for Mass Spectrometry Analysis of Protein–Protein Interactions in Cancer Cell Lines and Tissues

Beigbeder, A., Vélot, L., James, D. A., & Bisson, N. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-3801-8_23 · Cited by 15

The Arabidopsis Proteins AtNHR2A and AtNHR2B Are Multi-Functional Proteins Integrating Plant Immunity With Other Biological Processes

Singh, R. P., Liyanage, R., Gupta, C., Lay, J. O., Pereira, A., & Rojas, C. M. (2020) · Frontiers in Plant Science · doi:10.3389/fpls.2020.00232 · Cited by 15

Mapping the in vitro interactome of cardiac sodium (Na+)‐calcium (Ca2+) exchanger 1 (NCX1)

Hafver, T. L., Wanichawan, P., Manfra, O., de Souza, G. A., Lunde, M., Martinsen, M., Louch, W. E., Sejersted, O. M., & Carlson, C. R. (2017) · PROTEOMICS · doi:10.1002/pmic.201600417 · Cited by 14

Protocol for establishing a protein-protein interaction network using tandem affinity purification followed by mass spectrometry in mammalian cells

Bian, W., Jiang, H., Feng, S., Chen, J., Wang, W., & Li, X. (2022) · STAR Protocols · doi:10.1016/j.xpro.2022.101569 · Cited by 13

Shedding light on complexity of protein–protein interactions in cancer

Yoon, T., & Lee, H.-W. (2019) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2019.07.001 · Cited by 14

Smart sampling as the “Spot‐on” Method for LC‐MS protein analysis from dried blood spots

Johannsen, C., Mrsa, A., Halvorsen, T. G., & Reubsaet, L. (2023) · Journal of Separation Science · doi:10.1002/jssc.202300394 · Cited by 14

Insights from protein-protein interaction studies on bacterial pathogenesis

Gagarinova, A. G., Phanse, S., Cygler, M., & Babu, M. (2017) · Expert Review of Proteomics · doi:10.1080/14789450.2017.1365603 · Cited by 14

Contribution of Mass Spectrometry-Based Proteomics to the Understanding of TNF-α Signaling

Ciuffa, R., Caron, É., Leitner, A., Uliana, F., Gstaiger, M., & Aebersold, R. H. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00728 · Cited by 14

In vivo cross-linking-based affinity purification and mass spectrometry for targeting intracellular protein-protein interactions.

Zhong, B.-W., An, Y., Gao, H., Zhao, L., Li, X., Liang, Z., Zhang, Y.-K., Zhao, Q., & Zhang, L. (2023) · Analytica Chimica Acta · doi:10.1016/j.aca.2023.341273 · Cited by 10

A comprehensive protein–protein interactome for yeast PAS kinase 1 reveals direct inhibition of respiration through the phosphorylation of Cbf1

DeMille, D., Bikman, B. T., Mathis, A. D., Prince, J. T., Mackay, J. T., Sowa, S. W., Hall, T. D., & Grose, J. H. (2014) · Molecular Biology of the Cell · doi:10.1091/mbc.e13-10-0631 · Cited by 15

Magnetite nanoparticles coated with chitosan and polyethylenimine as anion exchanger for sorptive enrichment of phosphopeptides

Hussain, D., Musharraf, S. G., Fatima, B., Saeed, A., Jabeen, F., Ashiq, M. N., & Haq, M. N. U. (2019) · Microchimica Acta · doi:10.1007/s00604-019-3971-y · Cited by 13

Predicting Functions of Uncharacterized Human Proteins: From Canonical to Proteoforms

Poverennaya, E. V., Kiseleva, O. I., Romanova, A., & Pyatnitskiy, M. A. (2020) · Genes · doi:10.3390/genes11060677 · Cited by 12

Cracking chromatin with proteomics: From chromatome to histone modifications

Sigismondo, G., Papageorgiou, D. N., & Krijgsveld, J. (2022) · PROTEOMICS · doi:10.1002/pmic.202100206 · Cited by 13

High throughput methods to study protein-protein interactions during host-pathogen interactions

Chandrasekharan, G., & Unnikrishnan, M. (2024) · European Journal of Cell Biology · doi:10.1016/j.ejcb.2024.151393 · Cited by 13

Higher-Order Structural Organization of the Mitochondrial Proteome Charted by In Situ Cross-Linking Mass Spectrometry

Hevler, J. F., & Heck, A. J. R. (2023) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2023.100657 · Cited by 12

Bidirectional linkage of DNA barcodes for the multiplexed mapping of higher-order protein interactions in cells

Liu, Y., Sundah, N. R., Ho, N. R. Y., Shen, W. X., Xu, Y., Natalia, A., Yu, Z., Seet, J. E., Chan, C. W., Loh, T. P., et al. (2024) · Nature Biomedical Engineering · doi:10.1038/s41551-024-01225-3 · Cited by 13

Monitoring light/dark association dynamics of multi-protein complexes in cyanobacteria using size exclusion chromatography-based proteomics

Guerreiro, A. C. L., Penning, R., Raaijmakers, L. M., Axmann, I. M. I., Heck, A. J. R., & Altelaar, M. A. F. (2016) · Journal of Proteomics · doi:10.1016/j.jprot.2016.04.030 · Cited by 14

Integrative network analysis reveals USP7 haploinsufficiency inhibits E-protein activity in pediatric T-lineage acute lymphoblastic leukemia (T-ALL)

Shaw, T. I., Dong, L., Tian, L., Qian, C., Liu, Y., Ju, B., High, A. A., Kavdia, K., Pagala, V., Shaner, B., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-84647-2 · Cited by 13

Targeted proteomics analyses of phosphorylation-dependent signalling networks

Banerjee, S. L., Dionne, U., Lambert, J., & Bisson, N. (2018) · Journal of Proteomics · doi:10.1016/j.jprot.2018.02.004 · Cited by 14

Profiling Optimal Conditions for Capturing EDEM Proteins Complexes in Melanoma Using Mass Spectrometry

Munteanu, C. V. A., Chirițoiu, G. N., Petrescu, A., & Petrescu, S. M. (2019) · Advances in experimental medicine and biology · doi:10.1007/978-3-030-15950-4_9 · Cited by 12

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 · doi:10.1002/ange.201708151 · Cited by 11

Pre- and Post-Processing Workflow for Affinity Purification Mass Spectrometry Data

Fischer, M., Zilkenat, S., Gerlach, R. G., Wagner, S., & Renard, B. Y. (2014) · Journal of Proteome Research · doi:10.1021/pr401249b · Cited by 11

Identification of intracellular glycosaminoglycan-interacting proteins by affinity purification mass spectrometry

Großkopf, H., Vogel, S., Müller, C. D., Köhling, S., Dürig, J., Möller, S., Schnabelrauch, M., Rademann, J., Hempel, U., von Bergen�, M., et al. (2021) · Biological Chemistry · doi:10.1515/hsz-2021-0167 · Cited by 11

Rapid isolation of respiring skeletal muscle mitochondria using nitrogen cavitation

Younis, A. Z., Lavery, G. G., Christian, M., & Doig, C. L. (2023) · Frontiers in Physiology · doi:10.3389/fphys.2023.1114595 · Cited by 10

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

Open Science Resources for the Mass Spectrometry-Based Analysis of SARS-CoV-2

Bittremieux, W., Adams, C., Laukens, K., Dorrestein, P. C., & Bandeira, N. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00929 · Cited by 11

A Proteomic Approach Identifies Isoform-Specific and Nucleotide-Dependent RAS Interactions

Miller, S. P., Maio, G. E., Zhang, X., Soto, F. S. B., Zhu, J., Ramirez, S. Z., & Lin, H. (2022) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2022.100268 · Cited by 11

Affinity-Based Interactome Analysis of Endogenous LINE-1 Macromolecules

Stefano, L. H. D., Saba, L. J., Oghbaie, M., Jiang, H. L., McKerrow, W., Benitez‐Guijarro, M., Taylor, M. S., & LaCava, J. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2883-6_12 · Cited by 9

Analysis of affinity purification-related proteomic data for studying protein–protein interaction networks in cells

Kattan, R. E., Ayesh, D., & Wang, W. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad010 · Cited by 11

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CeLINC, a fluorescence-based protein–protein interaction assay in Caenorhabditis elegans

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A Systems-Level Understanding of Cardiovascular Disease through Networks

Farber, C. R., & Mesner, L. D. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-799961-6.00003-2 · Cited by 12

A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research

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Proximity-dependent biotin labeling in testicular germ cells identified TESMIN-associated proteins

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Proximity labeling approaches to study protein complexes during virus infection

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High throughput platform to explore RNA–protein interactomes

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Protein Interactome Profiling of Stable Molecular Complexes in Biomaterial Lysate

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Topology-driven negative sampling enhances generalizability in protein–protein interaction prediction

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Affinity Purification couple to Mass Spectrometry (AP-MS)

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

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Analyzing protein–protein interactions by quantitative mass spectrometry

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

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