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

ClusterM: a scalable algorithm for computational prediction of conserved protein complexes across multiple protein interaction networks

Wang, Y., Jeong, H., Yoon, B.-J., & Qian, X. (2020) · BMC Genomics · doi:10.1186/s12864-020-07010-1 · Cited by 7

Analysis of the SARS-CoV-2-host protein interaction network reveals new biology and drug candidates: focus on the spike surface glycoprotein and RNA polymerase

Sokullu, E., Pinard, M., Gauthier, M., & Coulombe, B. (2021) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2021.1909566 · Cited by 7

Extracting Protein-Protein Interactions (PPIs) from Biomedical Literature using Attention-based Relational Context Information

Park, G., McCorkle, S. M., Soto, C., Blaby, I. K., & Yoo, S. (2022) · IEEE International Conference on Big Data (BigData) · doi:10.1109/bigdata55660.2022.10021099 · Cited by 8

Identification and Quantification of Affinity-Purified Proteins with MaxQuant, Followed by the Discrimination of Nonspecific Interactions with the CRAPome Interface

Lee, P. Y., & Low, T. Y. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-3327-4_25 · Cited by 7

Challenges in Separations of Proteins and Small Biomolecules and the Role of Modern Mass Spectroscopy Tools for Solving Them, as Well as Bypassing Them, in Structural Analytical Studies of Complex Biomolecular Mixtures

Jovanović, M. (2018) · Separations · doi:10.3390/separations5010011 · Cited by 5

Proteomic approaches for cancer epigenetics research

Marchione, D. M., Garcia, B. A., & Wojcik, J. B. (2018) · Expert Review of Proteomics · doi:10.1080/14789450.2019.1550363 · Cited by 7

Probing Protein Interaction Networks by Combining MS-Based Proteomics and Structural Data Integration

Postic, G., Marcoux, J., Reys, V., Andréani, J., Vandenbrouck, Y., Bousquet, M., Mouton‐Barbosa, E., Cianférani, S., Burlet‐Schiltz, O., Guérois, R., et al. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00066 · Cited by 8

Network-Based Analysis for Biological Discovery

Tripathi, L. P., Chen, Y. A., Mizuguchi, K., & Murakami, Y. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.20674-2 · Cited by 7

Network-Based Analysis of Host-Pathogen Interactions

Tripathi, L. P., Chen, Y. A., Mizuguchi, K., & Morita, E. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.20170-2 · Cited by 7

PPIscreenML: Structure-based screening for protein-protein interactions using AlphaFoldPreprint

Mischley, V., Maier, J., Chen, J., & Karanicolas, J. (2024) · eLife · doi:10.7554/elife.98179.1 · Cited by 7

Myosin Va, a Novel Interaction Partner of STXBP1, Is Required to Transport Syntaxin1A to the Plasma Membrane

Taura, Y., Tozawa, T., Fujimoto, T., Ichise, E., Chiyonobu, T., Itoh, K., & Iehara, T. (2023) · Neuroscience · doi:10.1016/j.neuroscience.2023.05.031 · Cited by 7

Answering open questions in biology using spatial genomics and structured methods

Jena, S. G., Verma, A., & Engelhardt, B. E. (2024) · BMC Bioinformatics · doi:10.1186/s12859-024-05912-5 · Cited by 7

Next-Generation Techniques for Determination of Protein-Protein Interactions: Beyond the Crystal Structure

Carter, R., Luchini, A., Liotta, L. A., & Haymond, A. N. (2019) · Current Pathobiology Reports · doi:10.1007/s40139-019-00198-2 · Cited by 6

Proteo3Dnet: a web server for the integration of structural information with interactomics data

Postic, G., Andréani, J., Marcoux, J., Reys, V., Guérois, R., Rey, J., Mouton‐Barbosa, E., Vandenbrouck, Y., Cianférani, S., Burlet‐Schiltz, O., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab332 · Cited by 6

Interactomics in plant defence: progress and opportunities

Mostaffa, N. H., Suhaimi, A. H., & Al-Idrus, A. (2023) · Molecular Biology Reports · doi:10.1007/s11033-023-08345-0 · Cited by 5

Cracking Lysine Crotonylation (Kcr): Enlightening a Promising Post‐Translational Modification

Westerveld, M., Besermenji, K., Aidukas, D., Ostrovitsa, N., & Petracca, R. (2024) · ChemBioChem · doi:10.1002/cbic.202400639 · Cited by 6

Proteomic profiling and network biology of colorectal cancer liver metastasis

Bartolomé, R. A., & Casal, J. I. (2023) · Expert Review of Proteomics · doi:10.1080/14789450.2023.2275681 · Cited by 5

Tyrosine-phosphorylation of the scaffold protein ADAP and its role in T cell signaling

Kuropka, B., Schraven, B. L., Kliche, S., Krause, E., & Freund, C. (2016) · Expert Review of Proteomics · doi:10.1080/14789450.2016.1187565 · Cited by 5

Using proteomics to identify host cell interaction partners for VgrG and IglJ

Prokšová, M., Řehulková, H., Řehulka, P., Lays, C., Lenčo, J., & Stulík, J. (2020) · Scientific Reports · doi:10.1038/s41598-020-71641-3 · Cited by 5

Metabolic control of glycosylation forms for establishing glycan-dependent protein interaction networks

Liu, X., Yi, L., Lin, Z., Chen, S., Wang, S., Sheng, Y., Lebrilla, C. B., Garcia, B. A., & Xie, Y. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2422936122 · Cited by 4

High-Efficiency Enrichment by Saturating Nanoliters of Protein Affinity Media

Raval, S., Douglas, P., Laurent, D., Khan, M. F., Lees‐Miller, S. P., & Schriemer, D. C. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.3c01736 · Cited by 4

A Tandem-Affinity Purification Method for Identification of Primary Intracellular Drug-Binding Proteins

Islam, S., Gour, J., Beer, T., Tang, H., Cassel, J. A., Salvino, J. M., & Busino, L. (2024) · ACS Chemical Biology · doi:10.1021/acschembio.3c00570 · Cited by 5

A brief guide to analyzing TurboID-based proximity labeling-mass spectrometry in plants

Park, T., & Kim, T. (2025) · Molecules and Cells · doi:10.1016/j.mocell.2025.100236 · Cited by 4

Comparative Evaluation of Smart Sampling for hCG Determination: A New Potential Direction in Protein Biomarker Analysis From Dried Microsamples

Mrsa, A., Matijevic, M., Dehnes, Y., Halvorsen, T. G., & Reubsaet, L. (2025) · Drug Testing and Analysis · doi:10.1002/dta.3948 · Cited by 4

Systems Pharmacology: Enabling Multidimensional Therapeutics

Maudsley, S. R., Leysen, H., van Gastel, J., & Martin, B. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-820472-6.00017-7 · Cited by 5

A Combination of Bio‐Orthogonal Supramolecular Clicking and Proximity Chemical Tagging as a Supramolecular Tool for Discovery of Putative Proteins Associated with Laminopathic Disease

Sim, J., Lee, A., Kim, D., Kim, K. L., Park, B., Park, K. M., & Kim, K. (2023) · Small · doi:10.1002/smll.202208088 · Cited by 5

Affinity Anchors: Overview of Popular Tags for Modern Molecular Biology

Kryukova, P. A., Kiseleva, O. I., Kurbatov, I. Y., & Poverennaya, E. V. (2024) · Biology Bulletin Reviews · doi:10.1134/s2079086424600644 · Cited by 4

Transitioning from concept to application: Comprehensive analytical validation of antibody-based smart sampling

Mrsa, A., Ishaq, R., Brandoli, L., Halvorsen, T. G., & Reubsaet, L. (2025) · Journal of Pharmaceutical and Biomedical Analysis · doi:10.1016/j.jpba.2025.116825 · Cited by 4

Protein networks and activation of lymphocytes

Helou, Y. A., & Salomon, A. R. (2015) · Current Opinion in Immunology · doi:10.1016/j.coi.2015.01.019 · Cited by 4

Interactions by 2D Gel Electrophoresis Overlap (iGEO): a novel high fidelity approach to identify constituents of protein complexes

Yoshigi, M., Pronovost, S. M., & Kadrmas, J. L. (2013) · Proteome Science · doi:10.1186/1477-5956-11-21 · Cited by 4

Proteomic approaches to investigate gammaherpesvirus biology and associated tumorigenesis

Chappell, D. L., White, M. C., & Damania, B. (2020) · Advances in virus research · doi:10.1016/bs.aivir.2020.10.001 · Cited by 4

Identification of Inflammatory Proteomics Networks of Toll-like Receptor 4 through Immunoprecipitation-Based Chemical Cross-Linking Proteomics

Shahinuzzaman, A. D. A., Kamal, A. H. M., Chakrabarty, J. K., Rahman, A., & Chowdhury, S. M. (2022) · Proteomes · doi:10.3390/proteomes10030031 · Cited by 4

PPIscreenML is a method for structure-based screening of protein-protein interactions using AlphaFold

(2026) · doi:10.7554/elife.98179.2 · Cited by 8

Mechanisms and Research Methods of Protein Modification in Virus Entry

Xiao, Y., Gao, M., Mo, X., Lang, J., Wang, Z., Ma, Z., Meng, Y., Tang, B.-L., Liu, D., & He, H. (2025) · Applied Biochemistry and Biotechnology · doi:10.1007/s12010-025-05333-x · Cited by 5

Studying Cellular Dynamics Using Proximity-Dependent Biotinylation: Somatic Cell Reprogramming

Samson, R., Zangari, F., & Gingras, A. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-3457-8_3 · Cited by 3

High-Resolution Proteomics Unravel a Native Functional Complex of Cav1.3, SK3, and Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels in Midbrain Dopaminergic Neurons

Belghazi, M., Iborra, C., Toutendji, O., Lasserre, M., Debanne, D., Goaillard, J., & Marquèze‐Pouey, B. (2024) · Cells · doi:10.3390/cells13110944 · Cited by 3

A Case Study on the Keap1 Interaction with Peptide Sequence Epitopes Selected by the Peptidomic mRNA Display

Hirose, H., Hideshima, T., Katoh, T., & Suga, H. (2019) · ChemBioChem · doi:10.1002/cbic.201900039 · Cited by 3

Proteomics contribution to the elucidation of the steroid hormone receptors functions

Agbo, L., & Lambert, J. (2019) · The Journal of Steroid Biochemistry and Molecular Biology · doi:10.1016/j.jsbmb.2019.105387 · Cited by 3

Advanced Technologies for Protein Complex Production and Characterization

Vega, M. C., & Fernández, F. J. (2024) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-52193-5 · Cited by 2

Utility of Computational Structural Biology in Mass Spectrometry

Roy, U., Woods, A. G., Sokolowska, I., & Darie, C. C. (2014) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-06068-2_6 · Cited by 3

Lysis buffer selection guidance for mass spectrometry-based global proteomics including studies on the intersection of signal transduction and metabolismPreprint

Helm, B., Hansen, P., Lai, L., Schwarzmüller, L. E., Clas, S. M., Richter, A., Ruwolt, M., Liu, F., Frey, D. L., D’Alessandro, L. A., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.19.580971 · Cited by 3

Fast tracking native mass spectrometry: Skipping over buffer exchangePreprint

Grün, A. F. R., Said, F.-A., Schamoni-Kast, K., Damjanović, T., Berikkara, A., Schroeder, J., Brockmann, F. K., Lichtenberg, T., Bosse, J. B., & Uetrecht, C. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.22.639503 · Cited by 3

IP-to-MS: An Unbiased Workflow for Antigen Profiling

Biedka, S., Yablonska, S., Peng, X., Alkam, D., Hartoyo, M., VanEvery, H., Kass, D. J., Byrum, S. D., Xiao, K., Zhang, Y., et al. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00837 · Cited by 2

Research Progress of Protein-Protein Interaction Based on Liquid Chromatography Mass Spectrometry※

Chen, Y., Zhou, W., Li, X., Yang, K., Liang, Z., Zhang, L., & Zhang, Y. (2022) · 化学学报 · doi:10.6023/a22010055 · Cited by 2

Antibody for Serine 65 Phosphorylated Ubiquitin Identifies PLK1-Mediated Phosphorylation of Mitotic Proteins and APC1

Mann, G., Sulkshane, P., Sadhu, P., Ziv, T., Glickman, M., & Brik, A. (2022) · Molecules · doi:10.3390/molecules27154867 · Cited by 2

Discovery and Characterization of Linear Motif Mediated Protein-Protein Complexes

Zeke, A., Alexa, A., & Reményi, A. (2024) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-52193-5_5 · Cited by 2

A series of reviews in familial cancer: genetic cancer risk in context variants of uncertain significance in MMR genes: which procedures should be followed?

Lucas, M. C., Keßler, T., Scharf, F., Steinke‐Lange, V., Klink, B., Laner, A., & Holinski‐Feder, E. (2025) · Familial Cancer · doi:10.1007/s10689-025-00470-y · Cited by 2

Proteomic Applications of Polymeric Nanoparticles with Engineered Affinity towards Select Target

Thangavel, H. (2017) · Journal of Nanomedicine Research · doi:10.15406/jnmr.2017.05.00124 · Cited by 2

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-v · Cited by 2

Combination of Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Substrate Trapping for the Detection of Transient Protein Interactions

Duda, J. M., & Thomas, S. N. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2863-8_18 · Cited by 2

Generation and Utilization of a Monoclonal Antibody against Hepatitis B Virus Core Protein for a Comprehensive Interactome Analysis

Nakai, Y., Miyakawa, K., Yamaoka, Y., Hatayama, Y., Nishi, M., Suzuki, H., Kimura, H., Takahashi, H., Kimura, Y., & Ryo, A. (2022) · Microorganisms · doi:10.3390/microorganisms10122381 · Cited by 2

Tandem Affinity Purification (TAP) of Interacting Prey Proteins with FLAG- and HA-Tagged Bait Proteins

Low, T. Y., & Lee, P. Y. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-3327-4_6 · Cited by 2

Prediction of genes and protein-protein interaction networking for miR-221-5p using bioinformatics analysis

Shanmugapriya, S., Othman, N., & Sasidharan, S. (2019) · Gene Reports · doi:10.1016/j.genrep.2019.100426 · Cited by 2

Methods of Computational Interactomics for Investigating Interactions of Human Proteoforms

Poverennaya, E. V., Kiseleva, O. I., Ivanov, A. S., & Ponomarenko, E. A. (2020) · Biochemistry (Moscow) · doi:10.1134/s000629792001006x · Cited by 3

Proteomics

Suna, G., & Mayr, M. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-809657-4.99573-5 · Cited by 2

Introducing weak affinity chromatography to drug discovery with focus on fragment screening

Duong‐Thi, M. (2013) · DiVA (Linnaeus University) · Cited by 2

Mass Spectrometry for Biomarker Development

Wu, C., Liu, T., Baker, E. S., Rodland, K., & Smith, R. D. (2014) · Springer eBooks · doi:10.1007/978-94-007-7740-8_21-1 · Cited by 2

RAPIDS, a method for sub-compartmental identification of protein interactomes

James, C., Lenz, C., & Kehlenbach, R. H. (2022) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2022.07.006 · Cited by 1

TurboID-Based Proximity Labeling: A Method to Decipher Protein–Protein Interactions in Plants

Li, Y., Zhang, Y., & Dinesh‐Kumar, S. P. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-3485-1_19 · Cited by 1

Searching for EGF Fragments Recreating the Outer Sphere of the Growth Factor Involved in Receptor Interactions

Czerczak-Kwiatkowska, K., Kaminska, M., Frączyk, J., Majsterek, I., & Kolesińska, B. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25031470 · Cited by 1

MAGPIE: A Machine Learning Approach to Decipher Protein–Protein Interactions in Human Plasma

Hashimoto-Roth, E., Forget, D., Gaspar, V. P., Bennett, S. A. L., Gauthier, M., Coulombe, B., & Lavallée‐Adam, M. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00160 · Cited by 1

TurboID-based mapping of organelle membrane protein interactomes with digitonin-permeabilization

Sun, Y., Yang, L., Zhang, J., Tian, P., Chen, S., Fang, L., & Hong, Z. (2025) · Biophysics Reports · doi:10.52601/bpr.2025.240051 · Cited by 1

Construction of a proximity labeling vector to identify protein-protein interactions in human stem cells

Gomes-Júnior, R., Moreira, C. M. D. N., & Dallagiovanna, B. (2025) · PLoS ONE · doi:10.1371/journal.pone.0324779 · Cited by 1

Identification of Virus–Host Protein Interactions Via Proteomic Techniques

Zhao, X., Zheng, X., Liang, Z., Zheng, C., & Shang, P. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4615-1_14 · Cited by 1

Biosensors for Detecting Small Rho GTPases: Monitoring Expression and Activation

Hasnizan, N. Y. U., Fung, C. C., Chuan, S. K., Fizal, N. S., Idros, N., & Mokhtar, A. M. A. (2025) · BioEssays · doi:10.1002/bies.70069 · Cited by 1

A novel Halo Tag-based photo-crosslinking system for efficient drug target identification via chemoproteomic profiling

Liu, X., Ji, W., Tao, Y., Gong, Y., Zhang, Q., Lin, R., Yang, Y., Wang, Y., Li, S., Zhang, Y., et al. (2025) · Analytica Chimica Acta · doi:10.1016/j.aca.2025.344720 · Cited by 1

Comprehensive Approaches to Protein Detection and Analysis in Mycobacterium tuberculosis

Farnia, P., Velayati, A. A., Ghanavi, J., & Farnia, P. (2025) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-96883-9_2 · Cited by 1

Spatial Mapping of Membrane Protein Interactions Using a DNA Origami Rubbing

Tang, Q., Yu, H., Hou, J., Jiang, M., Zhang, Z., Wang, J., Zhang, M., Han, D., & Guo, P. (2026) · Angewandte Chemie International Edition · doi:10.1002/anie.202513795 · Cited by 2

Phage ImmunoPrecipitation sequencing (PhIP-Seq) in autoimmunity research: From high-resolution epitope mapping to multi-omics integration

Yu, R., Lu, R., Xue, C., Bai, Y., Li, M., & Hu, C. (2026) · Autoimmunity Reviews · doi:10.1016/j.autrev.2026.104094 · Cited by 1

Hierarchical Contrastive Learning for Protein–Protein Interaction Prediction Across Organisms

Liu, S., Liang, B., Fang, Y., Jiang, Z., & Xu, R. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27146242 · Cited by 1

Identification of DNA Damage Checkpoint-Dependent Protein Interactions in Saccharomyces cerevisiae Using Quantitative Mass Spectrometry

de Oliveira, F. M. B., & Smolka, M. B. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-0685-7_17 · Cited by 1

A Systems Perspective of Complex Diseases: From Reductionism to Integration

Bandesh, K., Dhar, P. K., & Bharadwaj, D. (2018) · RNA technologies · doi:10.1007/978-3-319-92967-5_2 · Cited by 1

Fluorescent Labeling of a Target Protein with an Alkyl Diazirine Photocrosslinker Bearing a Cinnamate Moiety

Nakashima, T., Iwanabe, T., Tanimoto, H., & Tomohiro, T. (2024) · Chemistry - An Asian Journal · doi:10.1002/asia.202400288 · Cited by 1

Extraction method combining saponin and trehalose useful for analyzing fragile intermolecular association

Fujimoto, T., Okamura, T., & Itoh, K. (2024) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2024.150323 · Cited by 1

Long Non-Coding RNAs, Nuclear Receptors and Their Cross-Talks in Cancer—Implications and Perspectives

Tiwari, P., & Tripathi, L. P. (2024) · Cancers · doi:10.3390/cancers16162920 · Cited by 1

Constructing Reliable Protein-Protein Interaction (PPI) Networks

Srihari, S., Yong, C. H., & Wong, L. (2017) · doi:10.1145/3064650.3064653 · Cited by 2

Analysis of biological networks in the endothelium with biomimetic microsystem platform

Kruse, K. J., Klomp, J. A., Sun, M., Chen, Z., Santana, D., Huang, F., Kanabar, P. N., Maienschein‐Cline, M., & Komarova, Y. A. (2019) · American Journal of Physiology-Lung Cellular and Molecular Physiology · doi:10.1152/ajplung.00392.2018 · Cited by 1

BEHIND THE SCENES OF HOST-MICROBE INTERACTIONS

Prokšová, M., Stulík, J., & Kubelková, K. (2020) · Military Medical Science Letters · doi:10.31482/mmsl.2020.010 · Cited by 1

Effective and transient mapping of protein–protein interactions: Application of novel releasable photoaffinity linkers

Wang, J., Ma, Y., Li, J., Zhang, Q., Pan, X., Lu, W. Z., & Zhang, J. (2021) · Drug Development Research · doi:10.1002/ddr.21866 · Cited by 1

Proteomanalyse

Lottspeich, F., Jooß, K., Kelleher, N. L., Götze, M., Friedrich, B., & Aebersold, R. H. (2021) · Springer eBooks · doi:10.1007/978-3-662-61707-6_42 · Cited by 1

Mass Spectrometry for Biomarker Development

Wu, C., Liu, T., Baker, E. S., Rodland, K., & Smith, R. D. (2015) · Biomarkers in disease · doi:10.1007/978-94-007-7696-8_21 · Cited by 2

EvoPPI 2: A Web and Local Platform for the Comparison of Protein–Protein Interaction Data from Multiple Sources from the Same and Distinct Species

Reboiro‐Jato, M., Vieira, J., Rocha, S., Sousa, A. D., López-Fernández, H., & Vieira, C. P. (2022) · Lecture notes in networks and systems · doi:10.1007/978-3-031-17024-9_10 · Cited by 1

Romantic surfaces : Zwitterionic polymer brushes for biomedical applications

van Andel, E. (2018) · doi:10.18174/459827 · Cited by 1

Regulation of Hippo Pathway Kinases MST1/2 by DLG5 and Other Signaling Factors

Kwan, J. (2017) · TSpace (University of Toronto) · Cited by 1

Region-Specific PSD-95 Interactomes Contribute to Functional Diversity of Excitatory Synapses in Human BrainPreprint

Funk, A. J., Labilloy, G., Reigle, J. K., Alnafisah, R. S., Heaven, M. R., Roberts, R. C., Shamsaei, B., Greis, K. D., Meller, J., & McCullumsmith, R. E. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.04.076844 · Cited by 1

P-PPI: accurate prediction of peroxisomal protein-protein interactions (P-PPI) using deep learning-based protein sequence embeddingsPreprint

Anteghini, M., dos Santos, V. A. P. M., & Saccenti, E. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.30.547177 · Cited by 1

Network-Based Analysis for Biological Knowledge Discovery

Tripathi, L. P., Osorio, R. S. A., Murakami, Y., Chen, Y. A., & Mizuguchi, K. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-95502-7.00272-4 · Cited by 1

Membrane mimetic thermal proteome profiling (MM-TPP) towards mapping membrane protein-ligand dynamicsPreprint

Jandu, R. S., Al‐Seragi, M., Aoki, H., Babu, M., & Duong, F. (2025) · eLife · doi:10.7554/elife.104549.1 · Cited by 1

Mass Spectrometry‐Based Methods to Investigate Protein–Protein Interactions in Cells and Their Application in Drug Discovery

Branon, T. C. (2025) · Wiley eBooks · doi:10.1002/9781394236145.ch16 · Cited by 1

Membrane mimetic thermal proteome profiling (MM-TPP) towards mapping membrane protein-ligand dynamic interactionsPreprint

Jandu, R. S., Bhattacharya, A., Antony, F., Al‐Seragi, M., Aoki, H., Babu, M., & Duong, F. (2025) · eLife · doi:10.7554/elife.104549.2 · Cited by 1

Mass spectrometry in clinical protein biomarker discovery

Parviainen, V. (2014) · Työväentutkimus Vuosikirja

Global Approaches to Understanding Protein Kinase Functions

Gorman, J. L., & Woodgett, J. R. (2015) · Wiley eBooks · doi:10.1002/9783527683031.ch1

A Computational and Informatics Framework for the Analysis of Affinity Purification Mass Spectrometry Data and Reconstruction of Protein Interaction Networks.

Mellacheruvu, D. (2015) · Deep Blue (University of Michigan)

Interrogation of In Vivo Protein–Protein Interactions Using Transgenic Mouse Models and Stable Isotope Labeling

Dey, A., Wu, J., & Kirkpatrick, D. S. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-0992-6_15

Delineating the Molecular Mechanisms of KIF7 in Vertebrate Hedgehog Signal Transduction

Liu, Y. C. (2015) · TSpace (University of Toronto)

The Path to Personalized Cardiovascular Medicine

Marı́n-Garcı́a, J. (2014) · Elsevier eBooks · doi:10.1016/b978-0-12-404599-6.00024-x

Methodologies in the Era of Cardiovascular “Omics”

Marı́n-Garcı́a, J. (2014) · Elsevier eBooks · doi:10.1016/b978-0-12-404599-6.00002-0 · Cited by 1

FOCUS: MASS SPECTROMETRY AS A PROBE OF HIGHER ORDER PROTEIN STRUCTURE: ACCOUNT & PERSPECTIVE Revealing Higher Order Protein Structure Using Mass Spectrometry

Chait, B. T., Cadène, M., Olinares, P. D. B., Rout, M. P., & Shi, Y. (2016)

Elucidating The Mechanism Of Phenylpropanoid Regulation By The Arabidopsis Mediator Complex

Zeng, W. (2014) · Purdue e-Pubs (Purdue University System)

Identifying Evolutionarily Conserved Protein Complexes

Srihari, S., Yong, C. H., & Wong, L. (2017) · doi:10.1145/3064650.3064658

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 23

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 95

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 66

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 260