Research interests
The life trajectory of a protein within a cell resembles that of a human life—from "birth" (synthesis) to "death" (degradation), it travels to different places at different times (spatiotemporal localization), encounters many "people and events" (interactions), and fulfills its own "social responsibilities" (functional execution). The long-term goal of the Qin laboratory is to systematically dissect the dynamic regulation of the proteome across multiple dimensions, including time, space, interactions, and function. Our group will broadly combine chemical biology and mass spectrometry-based proteomics to develop novel, function-driven, in vivo-compatible, and spatiotemporally resolved chemoproteomic technologies around key biological questions such as protein dynamics, biomolecular interactions, and post-translational modifications. Using these tools, we aim to map protein interaction and communication networks at multiple spatial and temporal resolutions and levels—molecular, organellar, and cellular. Specific research directions are as follows:
1. Development of in vivo-compatible enzymatic proximity labeling technologies
Protein functions undergo dynamic changes across time and space; multi-dimensional proteomic approaches can systematically delineate the life trajectories of different proteins within cells. Spatiotemporally resolved proximity labeling techniques have been widely applied to identify constituent proteins of specific cells and subcellular structures, as well as to dissect biomolecular interaction networks. However, enzymatic proximity labeling methods such as APEX2 and TurboID still suffer from inherent limitations that typically restrict their use to cultured cell systems—for example, hydrogen peroxide toxicity for APEX2 and high biotin background for TurboID. Achieving a technological leap from cell-level to in vivo proximity labeling is therefore critical for studying protein dynamics with greater physiological relevance. Our lab is dedicated to overcoming these challenges by developing enzyme-based chemical tools compatible with in vivo proximity labeling. Since its inception, we have successfully developed TyroID (Nat. Commun., 2025), a new enzyme-driven proximity labeling technique, and Hi-APEX (Nat. Chem. Biol., in press), a novel APEX2-based approach driven by a new chemical mechanism that eliminates the requirement for hydrogen peroxide. In the future, we will continue to develop novel in vivo-compatible enzymatic proximity labeling technologies and apply them to animal models of major diseases, such as neurodegenerative disorders and tumors, to elucidate pathological mechanisms and identify drug targets.
2. Development of in vivo-compatible photocatalytic proximity labeling technologies
Photocatalytic proximity labeling generates reactive species in situ upon light illumination, enabling protein labeling with high spatiotemporal resolution. However, current photocatalytic methods mostly rely on visible-light excitation and thus suffer from poor tissue penetration and phototoxicity, restricting their application largely to cultured cells or superficial tissues. To overcome these bottlenecks, we have developed SeeID (Nat. Commun., 2025), a near-infrared photocatalytic proximity labeling technique, and BRET-ID (ACS Cent. Sci., 2025), a bioluminescence-triggered photocatalytic proximity labeling approach, which use near-infrared light and bioluminescence as excitation sources, respectively, and effectively address the phototoxicity and tissue-penetration issues of photocatalytic labeling. In the future, we will further optimize the excitation wavelength and catalytic efficiency of photocatalysts to broaden the application of photocatalytic proximity labeling to deep tissues and living animal models.
3. Multi-scale omics dissection and mechanistic exploration of protein behaviors and communications
Proteins appear in different regions at different times, encounter other biomolecules, and form complex interaction networks to collectively fulfill their "social responsibilities" inside the cell, while extensive protein communication events between cells maintain homeostasis in multicellular organisms; these behaviors and communications are often modulated by post-translational modifications and the surrounding environment. To advance this area, Dr. Qin developed TransitID during his postdoctoral training (Cell, 2023), achieving the first large-scale analysis of protein trafficking both between organelles within cells and between different cells. Moreover, organelles—particularly membraneless biomolecular condensates—exhibit highly dynamic protein compositions and undergo transient, dynamic contacts that mediate material exchange; such events cannot be effectively studied by traditional biochemical fractionation, making high-spatiotemporal-resolution proximity labeling the method of choice. Toward this end, our group, in collaboration with others, developed Phase-APEX2 (BioRxiv, 2025), a multi-gated proximity labeling technique for high-precision mapping of core proteomes in membraneless organelles. After establishing his lab, Dr. Qin further developed PBSP (Nat. Commun., 2025), a post-translational modification-based secretome proteomics technique that identified itaconate-modified secreted proteins in macrophages and revealed how itaconation modulates exosomal secretion to mediate intercellular communication; developed RTPP (BioRxiv, 2026) for identifying RNA-regulated proteins and BRIEF (Angew, 2024) for activity-based screening of drug efflux pump substrates; and, in collaboration with others, established a nucleosome deubiquitinase identification method targeting protein–ubiquitination interactions (JACS, 2026). Collectively, these efforts enable multi-scale, multi-target mapping of protein interaction networks. In the future, we will identify and map organellar heterogeneity and transient dynamic interaction networks across various systems, detect and mechanistically dissect potential organelle transfer and communication between cells, and integrate chemical design with artificial intelligence to establish more sensitive, convenient, and systematic methodologies for studying multi-platform protein trafficking—ultimately delineating protein modifications, interactions, and communications in living organisms to aid disease diagnosis, therapy, and drug development.
Scientific contributions
1. Developed TransitID, a novel proximity labeling technique for mapping dynamic protein trafficking (Cell, 2023), and achieved the first large-scale analysis of protein trafficking both between organelles within cells and between different cells.
2. Developed a series of in vivo-compatible proximity labeling technologies—TyroID (Nat. Commun., 2025), Hi-APEX (Nat. Chem. Biol., in press), SeeID (Nat. Commun., 2025), and BRET-ID (ACS Cent. Sci., 2025)—overcoming technical bottlenecks such as APEX2 hydrogen peroxide toxicity and the penetration and phototoxicity issues of photocatalytic proximity labeling, thereby advancing proximity labeling from cell-level to in vivo animal-level applications.
Honors and awards
MIT Technology Review: Innovators Under 35 China
Bayer Investigator Award
Second Prize of the National Natural Science Award of China (fifth contributor)
RSC Chemical Biology Emerging Investigator
Tsinghua University Academic New Scholar Award
Selected publications：
(1) Chen, B.#; Guo, H.#; Yan, Z.; Lu, W.; Li, C.; Xu, S.; Zhang, Y.; Guo, H.; Sun, S.; Sun, X.; Zhao, S.; Shangguan, Q.; Chen, Y.; Lu, L.; Wu, Z.; Chen, Y.*; Qin, W.*. In vivo-compatible spatial multi-omics via hydrogen peroxide-independent APEX2 labeling. Nat. Chem. Biol. In press.
(2) Chen, YZ.#; Liu, ZY.#; Wang, YK.#; Lu, WJ.; Li, HY.; Wang, WJ.; Qiu, ZL.; Qiu, YJ.; Qing, H.; Xie, YX.; Liu, N.; Zhang, CG.*; Chen, Y.*; Qin, W.*. Multidimensional atlas of RNA-regulated proteins revealed by RNA-dependent thermal proteome profiling. BioRxiv, 2026.
(3) Chen, Z.#; Chen, YZ.#; Ding, HR.#; Huang, MD.#; Chen, WJ.; Fu, B.; Wang, MC.; Zhang, LQ.; Qin, W.*; Li, PL*. Mapping Core Components of Membrane-less Organelles in Living Cells by Phase-APEX2 Proximity Labeling. BioRxiv, 2025.
(4) Lu, WJ.#; Zhang, YL.#; Wang, P.; Ni, XR.; Zhuang, ST.*; Qin, W.*, Spatiotemporal profiling of modification-specific proteome secretion uncovers an itaconation-activated tyrosine kinase. Nat. Commun., 2025.
(5) Wang, WJ.#; Guo, HY.#; Yan, XS.#; Pan, XZ.; Wang, XF.; Rong, YM.; Bai, ZX.; Zhang, LW.; Wu, ZF.; Zhao, XY.; Huang, WR.; Qin, W.*; Chu, L.*, Silicon-rhodamine-enabled identification for near-infrared light controlled proximity labeling in vitro and in vivo.Nat. Commun., 2025.
(6) Sun, XG.#; Zhang, YL.#; Lu, WJ.#; Guo, HY.#; He, GD.; Luo, SY.; Guo, HD.; Zhang, ZJ.; Wang, WJ.; Chu, L.; Liu, XY.; Qin, W.*, Precise and in vivo-compatible spatial proteomics via bioluminescence-triggered photocatalytic proximity labeling. ACS Cent. Sci., 2025.
(7) Zhang, ZJ.#; Wang, YK.#; Lu, WJ.; Wang, XF.; Guo, HY.; Pan, XZ.; Liu, ZY.; Wu, ZF.; Qin, W.*, Spatiotemporally resolved mapping of extracellular proteomes via in vivo-compatible TyroID. Nat. Commun., 2025.
(8) Sun, XG.#; Chen, Y.#; Yang, C.; Yang, S.; Lin, W.; Quan, BY.; Ding, Q.; Chen, X.*; Wang, C.*; Qin, W.*, Chemical recording of pump-specific drug efflux in living cells. Angew Chem Int Ed., 2024.
(9) Qin, W. #; Cheah, JS. #; Xu, C.; Messing, J.; Freibaum, BD.; Boeynaems, S.; Taylor, JP.; Udeshi, ND.; Carr, SA.; Ting, AY*. Dynamic mapping of proteome trafficking within and between living cells by TransitID. Cell, 2023.
