●个人简历
秦为博士2014年本科毕业于北京理工大学生命学院，2019年毕业于北京大学前沿交叉学科研究院，获博士学位。博士期间师从北京大学化学与分子工程学院王初教授和陈兴教授，发展了一系列化学蛋白质组学策略研究O-GlcNAc糖基化修饰和衣康酸修饰。2019年到2023年在美国斯坦福大学从事博士后研究工作，合作导师为著名化学生物学家Alice Y. Ting教授, 从事邻近标记等化学生物学研究。在此期间发展了具有时空分辨率的功能性邻近标记技术，实现亚细胞区域内特定蛋白类型的大规模分析。同时发展了针对蛋白质空间动态转运的新型邻近标记技术TransitID，并利用该方法首次实现了细胞内不同细胞器之间以及不同细胞之间蛋白转运的大规模分析。秦为博士于2023年3月加入清华大学药学院展开独立研究，研究方向为发展活体兼容的时空化学蛋白质组学技术，并以此为基础解析蛋白质等生物大分子在分子水平、细胞器水平及细胞水平上的互作与通讯。独立以来，课题组成功开发了多种化学蛋白质组学工具（详情见下），并有多篇通讯作者文章发表于JACS, Angew, Nat. Commun.等期刊，此外还有多篇通讯作者文章于 Nat. Methods, Mol. Cell等期刊在审，并有文章已被 Nat. Chem. Biol. 接收。更详细信息请参考课题组主页：thu-qin-lab.org
●研究方向
一个蛋白质在细胞内的生命轨迹就如同人的一生，从“出生”(合成)到“死亡”(降解)，会在不同的时间去到不同的地方(时空定位)，遇到很多的“人和事” (相互作用)，并承担着自己的“社会责任” (功能执行)。秦为课题组长期的研究目标是系统解析蛋白质组在时间，空间，相互作用和功能等多个维度中的动态调控。本课题组将广泛地结合化学生物学和基于质谱的蛋白质组学，围绕蛋白质动态调控，生物大分子相互作用，翻译后修饰等重要生物学问题，进一步发展功能驱动的，活体兼容的，具有时空动态分辨率的的新型化学蛋白质组学技术，并以此工具箱为基础，绘制时空分辨率多维度多水平的蛋白质互作及通讯图谱，分别从分子水平、细胞器水平和细胞水平对蛋白质的互作与通讯进行解析。具体研究大方向如下：
1. 活体兼容酶催化邻近标记技术的开发
蛋白质的功能在时间和空间等多个维度上发生着动态变化，发展多维度的蛋白质组学方法可以系统解析细胞内不同蛋白质的生命轨迹。其中，基于邻近标记的时空分辨组学技术已被广泛应用于鉴定特定细胞和亚细胞结构的组成蛋白，以及解析生物分子间的相互作用网络。然而，以 APEX2、TurboID 为代表的酶催化邻近标记技术仍存在自身局限，其应用通常局限于培养细胞体系，例如 APEX2 的过氧化氢毒性、TurboID 的生物素背景等。实现邻近标记从细胞水平到活体水平的技术革新，对于解析更具生理意义的蛋白质动态调控过程至关重要。本课题组致力于解决上述问题，开发可用于活体邻近标记的酶催化化学工具：课题组自成立以来，成功开发了新酶驱动的新型邻近标记技术 TyroID (Nat. Commun., 2025)，以及基于新化学机理、无需过氧化氢的 APEX2 邻近标记技术 Hi-APEX (Nat. Chem. Biol., in press)，摆脱了 APEX2 对过氧化氢的依赖。未来，本课题组将持续关注新型活体兼容酶催化邻近标记技术的开发，并将其应用于神经退行性疾病、肿瘤等重大疾病的动物模型中，解析病理机制，寻找药物靶点。
2. 活体兼容光催化邻近标记技术的开发
光催化邻近标记利用光催化剂在光照下原位产生活性物种，从而实现对蛋白质的高时空分辨率标记。然而，现有光催化邻近标记多依赖可见光激发，组织穿透性差且存在光毒性风险，其应用往往局限于培养细胞体系或浅表组织。为突破上述瓶颈，本课题组开发了近红外光催化邻近标记 SeeID (Nat. Commun., 2025) 与生物发光催化的邻近标记 BRET-ID (ACS Cent. Sci., 2025)，分别以近红外光与生物发光作为激发光源，克服了光催化邻近标记的光毒性和组织穿透性问题。未来，本课题组将进一步优化光催化剂的激发波长与催化效率，推动光催化邻近标记在深层组织及活体动物模型中的广泛应用。
3. 多尺度蛋白质行为与通讯的组学解析和机制探索
细胞内的蛋白质会在不同时间出现在不同的细胞区域，遇到其它生物分子并形成复杂的相互作用网络，共同承担细胞内的“社会责任”；细胞之间同样存在大量的蛋白质通讯与互作事件，共同维持多细胞生物的机体稳态，而蛋白质的行为与通讯往往受到其自身修饰及所处环境等多重因素的调控。为推进这一问题的解决，秦为博士在博士后期间开发了 TransitID 技术 (Cell, 2023)，首次实现了细胞内不同细胞器之间以及不同细胞之间蛋白转运的大规模分析。细胞内的各种细胞器，尤其是无膜包裹的生物凝聚体，蛋白质组成高度动态，且细胞器之间会发生瞬时动态的接触与互作、介导物质交流——这类事件难以通过传统生化分离方法研究，邻近标记的高时空分辨率使其成为理想工具。为此，课题组与合作者开发了多重门控邻近标记技术 Phase-APEX2 (BioRxiv, 2025)，实现了对无膜细胞器核心蛋白质组的高精准度解析。课题组成立以来，还开发了基于翻译后修饰的分泌蛋白质组学技术 PBSP (Nat. Commun., 2025)，鉴定了巨噬细胞中携带衣康酸修饰的分泌蛋白，并揭示了衣康酸修饰经外泌体分泌参与细胞间通讯的潜在调控机制；此外开发了基于蛋白质热稳定性的 RNA 调控蛋白鉴定技术 RTPP (BioRxiv, 2026) 和基于活性的药物外排泵底物筛选技术 BRIEF (Angew, 2024)，并与合作者开发了核小体去泛素化酶鉴定技术 (JACS, 2026)，实现了对蛋白质互作图谱的多尺度、多目标综合绘制。未来，本课题组将进一步鉴定并绘制不同体系中细胞器的异质性与瞬时动态相互作用图谱，对细胞间潜在的细胞器迁移与通讯进行检测鉴定与机理挖掘，同时结合化学设计与人工智能，建立更灵敏、更系统、更便捷的蛋白质多尺度转运研究方法与范式，在活体水平系统解析蛋白质的修饰、互作与通讯，为疾病的诊疗与药物开发提供助力。
●主要科学贡献
1. 开发了新型邻近标记技术TransitID解析蛋白动态转运(Cell, 2023) ，并利用该方法首次实现了细胞内不同细胞器之间以及不同细胞之间蛋白转运的大规模分析。
2. 开发了TyroID (Nat. Commun., 2025), Hi-APEX (Nat. Chem. Biol., in press), SeeID (Nat. Commun., 2025), BRET-ID (ACS Cent. Sci., 2025)等一系列活体兼容的邻近标记技术,克服了APEX2的过氧化氢毒性及光催化邻近标记的穿透性和光毒性等技术瓶颈，推动了邻近标记技术从细胞水平到活体动物水平的技术革新
●荣誉与奖励
麻省理工科技评论中国区35岁以下35人
拜耳研究员奖
国家自然科学二等奖（第五完成人）
英国皇家化学学会化学生物学新锐科学家
清华大学学术新人奖
●代表性论文
(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.
Wei Qin, PhD
Keywords: Chemical Biology, Proteomics, Intracellular and Intercellular Protein Communication
Dr. Wei Qin received his B.S. from the School of Life Sciences at Beijing Institute of Technology in 2014 and his Ph.D. from the Academy for Advanced Interdisciplinary Studies at Peking University in 2019. During his doctoral studies, under the supervision of Professors Chu Wang and Xing Chen at the College of Chemistry and Molecular Engineering, Peking University, he developed a series of chemoproteomic strategies to study O-GlcNAc glycosylation and itaconate modification. From 2019 to 2023, he conducted postdoctoral research at Stanford University, working with Professor Alice Y. Ting, a renowned chemical biologist, on proximity labeling and other chemical biology approaches. During this period, he developed functional proximity labeling technologies with spatiotemporal resolution for large-scale profiling of specific proteome within subcellular regions. He also invented TransitID, a novel proximity labeling technique for spatial protein dynamics, and used it to achieve the first large-scale analysis of protein trafficking both between organelles within cells and between different cells. Dr. Qin joined the School of Pharmaceutical Sciences at Tsinghua University in March 2023 as an independent principal investigator. His research focuses on developing in vivo-compatible spatiotemporal chemoproteomic technologies to dissect the interactions and communications of proteins and other biomacromolecules at the molecular, organellar, and cellular levels. Since establishing his lab, his group has successfully developed multiple chemoproteomic tools (see below) and published several papers as corresponding author in journals such as JACS, Angew, and Nat. Commun.; additional manuscripts as corresponding author are under review or in revision at Nat. Methods, Nat. Chem. Biol., and Mol. Cell. For more information, please access the official lab website:thu-qin-lab.org
Research Directions
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.
Major 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.