ArticleNature protocols2020
Combined proximity labeling and affinity purification-mass spectrometry workflow for mapping and visualizing protein interaction networks.
Article in Nature protocols, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed.
- Review
- BHLHE40 and ChREBP associate with hepatic enhancer clusters containing PPARα, RXRα, and HNF4 nuclear receptors.Endocrinology · 2026Article
- Paradoxical non-catalytic kinase functions are driven by inhibitor-induced displacement of autoinhibitory domains.Molecular systems biology · 2026Article
- A proximity ligation screen identifies SNAT2 as a novel target of the MARCH1 E3 ubiquitin ligase.Biology open · 2026Article
- BST-2 inhibits SARS-CoV-2 egress at intracellular membranes and is neutralized by ORF7a.Scientific reports · 2026Article
- Proximity proteomics reveals a co-evolved LRRK2-regulatory network linked to centrosomes.EMBO reports · 2026Article
- Regulation of lineage reprogramming by dynamic chromatin SUMOylation.Cellular and molecular life sciences : CMLS · 2026Article
- ADAR1 and ADAR2 associate with the RNA exosome and modulate RNA stability.Nucleic acids research · 2026Article
- ProtFormer-Site: Ultra-fast and Accurate Prediction of Protein-Protein Interaction Sites with Protein Language Model.Interdisciplinary sciences, computational life sciences · 2026Article
- The Disordered Region of ASXL1 Acts as an Auto-Regulator Through Condensation.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- An enzymatic cascade enables sensitive and specific proximity labeling proteomics in challenging biological systems.Nature communications · 2025Article
- Mechanisms and Research Methods of Protein Modification in Virus Entry.Applied biochemistry and biotechnology · 2025Review
- State-of-the-Art and Future Directions in Structural Proteomics.Molecular & cellular proteomics : MCP · 2025Review
- Sensitive and specific affinity purification-mass spectrometry assisted by PafA-mediated proximity labeling.Cell reports methods · 2025Article
- An engineered redox-switchable streptavidin mutein enables the high-affinity capture and efficient elution of biotinylated ligands.Protein science : a publication of the Protein Society · 2025Article
- G Protein-Coupled Receptor 35 Suppresses Oxidative Stress Responsive Kinase 1 in Diabetic Wound Healing.Diabetes · 2025Article
- Proximity labelling of internalizing influenza A viruses reveals a role for neogenin in virus uptake.PLoS pathogens · 2025Article
- SUMOylation inhibition potentiates the glucocorticoid receptor to program growth arrest of acute lymphoblastic leukemia cells.Oncogene · 2025Article
- Engineered Proteins and Chemical Tools to Probe the Cell Surface Proteome.Chemical reviews · 2025Review
- Characterizing host-microbe interactions with bacterial effector proteins using proximity-dependent biotin identification (BioID).Communications biology · 2025Review
23 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
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Abstract
Affinity purification coupled with mass spectrometry (AP-MS) and proximity-dependent biotinylation identification (BioID) methods have made substantial contributions to interaction proteomics studies. Whereas AP-MS results in the identification of proteins that are in a stable complex, BioID labels and identifies proteins that are in close proximity to the bait, resulting in overlapping yet distinct protein identifications. Integration of AP-MS and BioID data has been shown to comprehensively characterize a protein's molecular context, but interactome analysis using both methods in parallel is still labor and resource intense with respect to cell line generation and protein purification. Therefore, we developed the Multiple Approaches Combined (MAC)-tag workflow, which allows for both AP-MS and BioID analysis with a single construct and with almost identical protein purification and mass spectrometry (MS) identification procedures. We have applied the MAC-tag workflow to a selection of subcellular markers to provide a global view of the cellular protein interactome landscape. This localization database is accessible via our online platform ( http://proteomics.fi ) to predict the cellular localization of a protein of interest (POI) depending on its identified interactors. In this protocol, we present the detailed three-stage procedure for the MAC-tag workflow: (1) cell line generation for the MAC-tagged POI; (2) parallel AP-MS and BioID protein purification followed by MS analysis; and (3) protein interaction data analysis, data filtration and visualization with our localization visualization platform. The entire procedure can be completed within 25 d.
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