biostudies-literatureLi Xthe Major Program of National Natural Science Foundation of ChinaGuangdong Province Fund for Distinguished Young ScholarsNational Key R&D Program of Chinathe General Program of National Natural Science Foundation of ChinaNatural Science Foundation of Guangdong ProvinceNational Natural Science Foundation of ChinaGuangdong Provincial Key Laboratory of Synthetic Genomics87-100https://www.ebi.ac.uk/biostudies/studies/S-EPMC9510856biostudies-literatureUnknown20(1)Proximity labeling catalyzed by promiscuous enzymes, such as APEX2, has emerged as a powerful approach to characterize multiprotein complexes and protein-protein interactions. However, current methods depend on the expression of exogenous fusion proteins and cannot be applied to identify proteins surrounding post-translationally modified proteins. To address this limitation, we developed a new method to label proximal proteins of interest by antibody-mediated protein A-ascorbate peroxidase 2 (pA-APEX2) labeling (AMAPEX). In this method, a modified protein is bound in situ by a specific antibody, which then tethers a pA-APEX2 fusion protein. Activation of APEX2 labels the nearby proteins with biotin; the biotinylated proteins are then purified using streptavidin beads and identified by massGenomics, proteomics & bioinformaticsDefining Proximity Proteome of Histone Modifications by Antibody-mediated Protein A-APEX2 Labeling.PMC951085631971354320706102021B1515020109320900312019YFA0903803320005802020B15151200342019B030301006Bouchonville KJChan KZhao WWen QGan HLi NPeng HLi XOffer SMGao YWang WWang ZZhou JfalseDefining Proximity Proteome of Histone Modifications by Antibody-mediated Protein A-APEX2 Labeling.Proximity labeling catalyzed by promiscuous enzymes, such as APEX2, has emerged as a powerful approach to characterize multiprotein complexes and protein-protein interactions. However, current methods depend on the expression of exogenous fusion proteins and cannot be applied to identify proteins surrounding post-translationally modified proteins. To address this limitation, we developed a new method to label proximal proteins of interest by antibody-mediated protein A-ascorbate peroxidase 2 (pA-APEX2) labeling (AMAPEX). In this method, a modified protein is bound in situ by a specific antibody, which then tethers a pA-APEX2 fusion protein. Activation of APEX2 labels the nearby proteins with biotin; the biotinylated proteins are then purified using streptavidin beads and identified by mass2022-01-01T00:00:00Z2022 Feb2026-05-27T22:53:37.873Z2025-04-06T12:12:58.717ZS-EPMC95108563455549610.1016/j.gpb.2021.09.003