Shui Research Group

Publications

2024

1. Dang T, Yu J, Cao Z, Zhang B, Li S, Xin Y, Yang L, Lou R, Zhuang M*, Shui W*. Endogenous cell membrane interactome mapping for the GLP-1 receptor in different cell types. Nature Chemical Biology. 2024 Sep 3.
2. Liu H, Yan P, Zhang Z, Han H, Zhou Q, Zheng J, Zhang J, Xu F*, Shui W*. Structural Mass Spectrometry Captures Residue-Resolved Comprehensive Conformational Rearrangements of a G Protein-Coupled Receptor. JACS. 2024 Jul 13.
3. Li S, Luo H, Tang P, Tian C, Hu J*, Lu H*, Shui W*. Generation of a deep mouse brain spectral library for transmembrane proteome profiling in mental disease models. Molecular & Cellular Proteomics. 2024 Apr 24:100777.
4. Lou R*, Shui W*. Acquisition and analysis of DIA-based proteomic data: a comprehensive survey in 2023. Molecular & Cellular Proteomics. 2024 Jan 3:100712.

2023

1. Jiang G, Zhang B, Zhang X, Chen F, Qin W, Chen J-L, Tian S, Shui W*, Ye N*. Identification of Spiro[chromene-2,4'-piperidine]s as Potent, Selective, and Gq-Biased 5-HT2C Receptor Partial Agonists. ACS Medicinal Chemistry Letters. 2023 Dec 18;15(1):99-106.
2. Yuan S, Xia L, Wang C, Wu F, Zhang B, Pan C, Fan Z, Lei X, Stevens R C, Sali A, Sun L*, Shui W*. Conformational Dynamics of the Activated GLP-1 Receptor-Gs Complex Revealed by Cross-Linking Mass Spectrometry and Integrative Structure Modeling. ACS Central Science. 2023 Apr 24;9(5):992-1007.
3. Xin Y, Liu S, Liu Y, Qian Z, Liu H, Zhang B, Guo T, Thompson G J, Stevens R C, Sharpless K B*, Dong J*, Shui W*. Affinity selection of double-click triazole libraries for rapid discovery of allosteric modulators for GLP-1 receptor. PNAS. 2023 Mar 14;120(11):e2220767120.
4. Pan C, Li J, Yuan S, Shui W*. Probing the structures of G protein-coupled receptors with mass spectrometry-based techniques. International Journal of Mass Spectrometry. 2023 Jan;483:116968.
5. Lou R, Cao Y, Li S, Lang X, Li Y, Zhang Y*, Shui W*. Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics. Nature Communications. 2023 Jan 6;14(1):94.

2022

1. Hart J R, Liu X, Pan C, Liang A, Ueno L, Xu Y, Quezada A, Zou X, Yang S, Zhou Q, Schoonooghe S, Hassanzadeh-Ghassabeh G, Xia T, Shui W*, Yang D*, Vogt P K*, Wang M-W*. Nanobodies and chemical cross-links advance the structural and functional analysis of PI3Kα. PNAS. 2022 Sep 20;119(38):e2210769119.
2. Mao Q, Zhang Z, Tian S, Qin W, Chen J, Huang X-P, Xin Y, Yang H, Zhen X-C*, Shui W*, Ye N*. Structural optimizations and bioevaluation of N-H aporphine analogues as Gq-biased and selective serotonin 5-HT2C receptor agonists. Bioorganic Chemistry. 2022 Jun;123:105795.
3. Qu X, Qiu N, Wang M, Zhang B, Du J, Zhong Z, Xu W, Chu X, Ma L, Yi C, Han S, Shui W*, Zhao Q*, Wu B*. Structural basis of tethered agonism of the adhesion GPCRs ADGRD1 and ADGRF1. Nature. 2022 Apr;604(7907):779-785.
4. Zhang B, Li S, Shui W*. Post-Translational Modifications of G Protein-Coupled Receptors Revealed by Proteomics and Structural Biology. Frontiers in Chemistry. 2022 Mar 10;10:843502.

2021

1. Lou R, Liu W, Li R, Li S, He X*, Shui W*. DeepPhospho accelerates DIA phosphoproteome profiling through in silico library generation. Nature Communications. 2021 Nov 18;12(1):6685.
2. Li S, Luo H, Lou R, Tian C, Miao C, Xia L, Pan C, Duan X, Dang T, Li H, Fan C, Tang P, Zhang Z, Liu Y, Li Y, Xu F, Zhang Y, Zhong G*, Hu J*, Shui W*. Multiregional profiling of the brain transmembrane proteome uncovers novel regulators of depression. Science Advances. 2021 Jul 21;7(30):eabf0634.
3. Zhou Q, Guo W, Dai A, Cai X, Vass M, Graaf C, Shui W, Zhao S*, Yang D*, Wang MW*. Discovery of Novel Allosteric Modulators Targeting an Extra-Helical Binding Site of GLP-1R Using Structure- and Ligand-Based Virtual Screening. Biomolecules. 2021 Jun 23;11(7):929.
4. Lu Y, Liu H, Yang D, Zhong L, Xin Y, Zhao S, Wang MW*, Zhou Q*, Shui W*. Affinity Mass Spectrometry-Based Fragment Screening Identified a New Negative Allosteric Modulator of the Adenosine A2A Receptor Targeting the Sodium Ion Pocket. ACS Chemical Biology. 2021 May 28.
5. Yang D, Zhou Q, Labroska V, Qin S, Darbalaei S, Wu Y, Yuliantie E, Xie L, Tao H, Cheng J, Liu Q, Zhao S, Shui W*, Jiang Y*, Wang MW*. G protein-coupled receptors: structure- and function-based drug discovery. Signal Transduction and Targeted Therapy. 2021, 6(1):7.

2020

1. Ma M, Guo S, Lin X, Li S, Wu Y, Zeng Y, Hu Y, Zhao S, Xu F, Xie X, Shui W*. Targeted Proteomics Combined with Affinity Mass Spectrometry Analysis Reveals Antagonist E7 Acts As an Intracellular Covalent Ligand of Orphan Receptor GPR52. ACS Chemical Biology. 2020, 15, 12, 3275–3284.
2. Li H, Yang J, Tian C, Diao M, Wang Q, Zhao S, Li S, Tan F, Hua T, Qin Y, Lin CP, Deska-Gauthier D, Thompson GJ., Zhang Y, Shui W, Liu ZJ, Wang T, Zhong G*. Organized cannabinoid receptor distribution in neurons revealed by super-resolution fluorescence imaging. Nature Communications. 2020, 11(1):5699.
3. Lou R, Tang P, Ding K, Li S, Tian C, Li Y, Zhao S*, Zhang Y*, Shui W*. Hybrid spectral library combining DIA-MS data and a targeted virtual library substantially deepens the proteome coverage. iScience. 2020: 100903.
4. Mao Q, Zhang B, Li W, Tian S, Shui W*, and Na Ye*. Identification of novel 1-O-substituted aporphine analogues as potent 5-HT2C receptor agonists. ACS Chemical Neuroscience. 2020, 11, 549-559.
5. Zhang B, Zhao S, Yang D, Wu Y, Xin Y, Cao H, Huang X, Cai X, Sun W, Ye N, Xu Y, Peng Y, Zhao S, Liu Z, Zhong G*, Wang M*, Shui W*. A novel G protein-biased and subtype selective agonist for a G protein-coupled receptor discovered from screening herbal extracts. ACS Central Science. 2020, 6, 213-225.
6. Xia L, Ma Z, Tong J, Tang Y, Li S, Qin S, Lou R, Zhao S, Lei X*, Shui W*. Evaluation of chemical cross-linkers for In-depth structural analysis of G protein-coupled receptors through cross-linking mass spectrometry. Analytica Chimica Acta. 2020, 1102, 53-62.

2019

1. Li S, Shui W*. Systematic mapping of protein-metabolite interactions with mass spectrometry-based techniques. Current Opinion in Biotechnology. 2019, 64, 24-31.
2. Lu Y, Qin S, Zhang B, Dai A, Cai X, Ma M, Gao ZG, Yang D, Stevens RC, Jacobson KA, Wang MW*, Shui W*. Accelerating the throughput of affinity mass spectrometry-based ligand screening toward a G protein-coupled receptor. Analytical Chemistry. 2019, 91, 8162-8169.
3. Wang Z, Liang H, Cao H, Zhang B, Li J, Wang W, Qin S, Wang Y, Xuan L, Lai L*, Shui W*. Efficient ligand discovery from natural herbs by integrating virtual screening, affinity mass spectrometry and targeted metabolomics. Analyst. 2019, 144, 2881–2890.
4. Abernathy M, Wan N, Shui W, Tang Y*. Dynamic 13C-labeling of fast turnover metabolites for analysis of metabolic fluxes and metabolite channeling. Methods in Molecular Biology. 2019, 1859, 301-316.
5. Li Z, Li Y, Tang YJ, Shui W*. Exploiting high-resolution mass spectrometry for targeted metabolite quantification and 13C-labeling metabolism analysis. Methods in Molecular Biology. 2019, 1859, 171-184.
6. Audet M, White KL, Breton B, Zarzycka B, Han GW, Lu Y, Gati C, Batyuk A, Popov P, Velasquez J, Manahan D, Hu H, Weierstall U, Liu W, Shui W, Katritch V, Cherezov V, Hanson MA, Stevens RC*. Crystal structure of misoprostol bound to the labor inducer prostaglandin E2 receptor. Nature Chemical Biology. 2019, 15, 11-17.

2018

1. Li Z, Lu Y, Guo Y, Cao H, Wang Q, Shui W*. Comprehensive evaluation of untargeted metabolomics data processing software in feature detection, quantiﬁcation and discriminating marker selection. Analytica Chimica Acta 2018, 1029, 50-57.
2. Miao C, Yang Y, Li S, Guo Y, Shui W*, Cao Q*. Discrimination and quantification of homologous keratins from goat and sheep with dual protease digestion and PRM assays. Journal of Proteomics 2018, 186, 38-46.
3. Yang S, Wu Y, Xu TH, de Waal PW, He Y, Pu M, Chen Y, DeBruine ZJ, Zhang B, Zaidi SA, Popov P, Guo Y, Han GW, Lu Y, Suino-Powell K, Dong S, Harikumar KG, Miller LJ, Katritch V, Xu HE, Shui W, Stevens RC, Melcher K, Zhao S, Xu F*. Crystal structure of the Frizzled 4 receptor in a ligand-free state. Nature 2018, 560, 666-670.
4. Qin S, Meng M, Yang D, Bai W, Lu Y, Peng Y, Song G, Wu Y, Zhou Q, Zhao S, Huang X, McCorvy JD, Cai X, Dai A, Roth BL, Hanson MA, Liu ZJ, Wang MW*, Stevens RC, Shui W*. High-throughput identification of G protein-coupled receptor modulators through affinity mass spectrometry screening. Chemical Science. 2018, 9, 3192-3199.
5. Peng Y, Zhao S, Wu Y, Cao H, Xu Y, Liu X, Shui W, Cheng J, Zhao S, Shen L, Ma J, Quinn RJ, Stevens RC, Zhong G*, Liu ZJ*. Identification of natural products as novel ligands for the human 5-HT2C receptor. Biophysics Reports. 2018, 4, 50-61.
6. Xiao W, Duan X, Lin Y, Cao Q, Li S, Guo Y, Gan Y, Qi X, Zhou Y, Guo L, Qin P, Wang Q*, Shui W*. Distinct Proteome Remodeling of Industrial Saccharomyces cerevisiae in Response to Prolonged Thermal Stress or Transient Heat Shock. Journal of Proteome Research. 2018, 17, 1812-1825.

2017

1. Ma J, Lu Y, Wu D, Peng Y, Loa-Kum-Cheung W, Peng C, Quinn RJ*, Shui W* and Liu ZJ*. Ligand identification of the adenosine A2A receptor in self-assembled nanodiscs by affinity mass spectrometry. Analytical Methods 2017, 9, 5851–5858.
2. Wang X, Li S, Wang H, Shui W* & Hu J*. Quantitative proteomics reveal proteins enriched in tubular endoplasmic reticulum of Saccharomyces cerevisiae. Elife 2017, 6, e23816.
3. Su C, Gao X, Yang W, Zhao Y, Fu X, Cui X, Zhang C, Xin L, Ren Y, Li L, Shui W, Yang X, Wei M & Yang J*. Phosphorylation of Tudor-SN, a novel substrate of JNK, is involved in the efficient recruitment of Tudor-SN into stress granules. Biochim Biophys Acta 2017, 1864, 562-571.
4. Li Z, Li Y, Chen W, Cao Q, Guo Y, Wan N, Jiang X, Tang Y, Wang Q & Shui W*. Integrating MS1 and MS2 scans in high-resolution parallel reaction monitoring assays for targeted metabolite quantification and dynamic 13C-labeling metabolism analysis. Analytical Chemistry 2017, 89, 877-885.
5. Li S, Cao Q, Xiao W, Guo Y, Yang Y, Duan X & Shui W*. Optimization of acquisition and data-processing parameters for improved proteomic quantification by sequential window acquisition of all theoretical fragment ion mass spectrometry. Journal of Proteome Research 2017, 16, 738-747.

2016

1. Fu X, Wang Z, Li L, Dong S, Li Z, Jiang Z, Wang Y, Shui W*. Novel chemical ligands to Ebola virus and Marburg virus nucleoproteins identified by combining affinity mass spectrometry and metabolomics approaches. Scientific Reports 2016, 6, 29680.
2. Hua T, Vemuri K, Pu M, Qu L, Han GW, Wu Y, Zhao S, Shui W, Li S, Korde A, Laprairie RB, Stahl EL, Ho JH, Zvonok N, Zhou H, Kufareva I, Wu B, Zhao Q, Hanson MA, Bohn LM, Makriyannis A*, Stevens RC*, Liu ZJ*. Crystal structure of the human cannabinoid receptor CB1. Cell 2016, 167, 750-762.
3. Luo Y, Ran J, Xie S, Yang Y, Chen J, Li S, Shui W, Li D, Liu M & Zhou J*. ASK1 controls spindle orientation and positioning by phosphorylating EB1 and stabilizing astral microtubules. Cell Discovery 2016, 2, 16033.
4. Xiong Y, Guo Y, Xiao W, Cao Q, Li S, Qi X, Zhang Z, Wang Q, Shui W*. An NGS-independent strategy for proteome-wide iIdentification of single amino acid polymorphisms by mass spectrometry. Analytical Chemistry 2016, 88, 2784-2791.
5. Li Z, Yang A, Li Y, Liu P, Zhang Z, Zhang X*, Shui W*. Targeted cofactor quantification in metabolically engineered E. coli using solid phase extraction and hydrophilic interaction liquid chromatography-mass spectrometry. Journal of Chromatography B (Analytical Technologies in the Biomedical and Life Sciences) 2016, 1014, 107-115.
6. Li S, Zhang Y, Wang J, Yang Y, Miao C, Guo Y, Zhang Z, Cao Q*, Shui W*. Combining untargeted and targeted proteomic strategies for discrimination and quantification of cashmere fibers. PLoS One 2016, 11, e0147044.

2015

1. Liu N, Xiong Y, Li S, Ren Y, He Q, Gao S, Zhou J*, Shui W*. New HDAC6-mediated deacetylation sites of tubulin in the mouse brain identified by quantitative mass spectrometry. Scientific Reports 2015, 5, 16869.
2. He X, Liu Z, He Q, Qin J, Liu N, Zhang L, Li D, Zhou J, Shui W*, Liu M*. Identification of novel microtubule-binding proteins by taxol-mediated microtubule stabilization and mass spectrometry analysis. Thorac Cancer 2015, 6, 649-654.
3. Qin S, Ren Y, Fu X, Shen J, Chen X, Wang Q, Bi X, Liu W, Li L, Liang G, Yang C, Shui W*. Multiple ligand detection and affinity measurement by ultrafiltration and mass spectrometry analysis applied to fragment mixture screening. Analytica Chimica Acta 2015, 886, 98-106.
4. Liu N, Xiong Y, Ren Y, Zhang L, He X, Wang X, Liu M, Li D, Shui W*, Zhou J*. Proteomic profiling and functional characterization of multiple post-translational modifications of tubulin. Journal of Proteome Research 2015, 14, 3292-3304.
5. Shui W*, Xiong Y, Xiao W, Qi X, Zhang Y, Lin Y, Guo Y, Zhang Z, Wang Q*, Ma Y. Understanding the mechanism of thermotolerance distinct from heat shock response through proteomic analysis of industrial strains of Saccharomyces cerevisiae. Molecular & Cellular Proteomics 2015, 14, 1885-1897.
6. Chen X, Qin S, Chen S, Li J, Li L, Wang Z, Wang Q, Lin J, Yang C*, Shui W*. A ligand-observed mass spectrometry approach integrated into the fragment based lead discovery pipeline. Scientific Reports 2015, 5, 8361.
7. Zhang L, Liu S, Liu N, Zhang Y, Liu M, Li D, Seto E, Yao T, Shui W*, Zhou J*. Proteomic identification and functional characterization of MYH9, Hsc70, and DNAJA1 as novel substrates of HDAC6 deacetylase activity. Protein & Cell 2015, 6, 42-54.

2014

1. Li D, Gao J, Yang Y, Sun L, Suo S, Luo Y, Shui W, Zhou J*, Liu M*. CYLD coordinates with EB1 to regulate microtubule dynamics and cell migration. Cell Cycle 2014, 13, 974-983.
2. Chen J, Luo Y, Li L, Ran J, Wang X, Gao S, Liu M, Li D, Shui W*, Zhou J*. Phosphoregulation of the dimerization and functions of end-binding protein 1. Protein & Cell 2014, 5, 795-799.
3. Wang Y, Li Z, Liu D, Xua J, Wei X, Yan L, Yang C, Lou Z, Shui W*. Assessment of BAK1 activity in different plant receptor-like kinase complexes by quantitative profiling of phosphorylation patterns. Journal of Proteomics, 2014, 108, 484-493.
4. Liu S, Chen X, Yan Z, Qin S, Xu J, Lin J, Yang C, Shui W*. Exploring skyline for both MSE-based label-free proteomics and HRMS quantification of small molecules. Proteomics 2014, 14, 169-180.

2013

1. Sun X, Liu M, Hao J, Li D, Luo Y, Wang X, Yang Y, Li F, Shui W, Chen Q, Zhou J*. Parkin deficiency contributes to pancreatic tumorigenesis by inducing spindle multipolarity and misorientation. Cell Cycle 2013, 12, 1133-1141.
2. Xu J, Wei X, Yan L, Liu D, Ma Y, Guo Y, Peng C, Zhou H, Yang C, Lou Z, Shui W*. Identification and functional analysis of phosphorylation residues of the Arabidopsis BOTRYTIS-INDUCED KINASE1. Protein & Cell 2013, 4, 771-781.
3. Chen X, Li L, Chen S, Xu Y, Xia Q, Guo Y, Liu X, Tang Y, Zhang T, Chen Y, Yang C*, Shui W*. Identiﬁcation of inhibitors of the antibiotic-resistance target new Delhi metallo-β-lactamase 1 by both nanoelectrospray ionization mass spectrometry and ultrafiltration-LC/MS approaches. Analytical Chemistry 2013, 85, 7957-7965.
4. Hao J, Li W, Dan J, Ye X, Wang F, Zeng X, Wang L, Wang H, Cheng C, Liu L*, Shui W*. Reprogramming- and pluripotency-associated membrane proteins in mouse stem cells revealed by label-free quantitative proteomics. Journal of Proteomics 2013, 86, 70-84.
5. Li Y, Wen T, Zhu M, Li L, Wei J, Wu X, Guo M, Liu S, Zhao H, Xia S, Huang W, Wang P, Wu Z, Zhao L, Shui W*, Li Z*, Yin Z*. Glycoproteomic analysis of tissues from patients with colon cancer using lectin microarrays and nanoLC-MS/MS. Molecular Biosystems 2013, 9, 1877-1887.

2012

1. Yan L, Ma Y, Liu D, Wei X, Sun Y, Chen X, Zhao H, Zhou J, Wang Z, Shui W*, Lou Z*. Structural basis for the impact of phosphorylation on plant receptor-like kinase BAK1 activation. Cell Research 2012, 8, 1304-1308.

2011

1. Shui W*, Lin S, Zhang A, Chen Y, Huang Y, Sanders M. Driving efficiency in a high-throughput metabolic stability assay through a generic high-resolution accurate mass method and automated data mining. Protein & Cell 2011, 8, 680-688.
2. Shui W*, Petzold C, Redding A, Liu J, Pitcher A, Keasling J*, Bertozzi C*. Organelle Membrane Proteomics Reveals Differential Influence of Mycobacterial Lipoglycans on Macrophage Phagosome Maturation and Autophagosome Accumulation. Journal of Proteome Research 2011, 10, 339-348.
3. Guo Y, Wan, J, Niu G, Shui W, Sun Y, Zhou H, Zhang Y, Yang C, Lou Z*, Rao Z. A structural view of the antibiotic degradation enzyme NDM-1 from a superbug. Protein & Cell 2011, 5, 384-394.

2009

1. Shui W, Gilmore S, Sheu L, Liu J, Keasling J*, Bertozzi C*. Quantitative proteomic profiling of host-pathogen interactions: the macrophage response to Mycobacterium tuberculosis lipids. Journal of Proteome Research 2009, 8, 282-289.
2. Wu P, Shui W, Carlson B, Bertozzi C*. Site-specific chemical modification of recombinant proteins produced in mammalian cells using the genetically-encoded aldehyde tag. Proceedings of the National Academy of Sciences 2009, 106, 3000-3005.
3. Tang Y#, Shui W#, Myers S, Kang Y, Ouellet M, Bertozzi C, Keasling J*. Central metabolism in Mycobacterium smegmatis during the transition from O2-rich to O2-poor conditions as studied by isotopomer-assisted metabolite analysis. Biotechnology Letter 2009, 31, 1233-1240.

2008

1. Shui W, Sheu L, Liu J, Smart B, Keasling J*, Bertozzi C*. Membrane proteomics of phagosomes suggests a connection to autophagy. PNAS 2008, 105, 16952-16957.

2006

1. Shui W, Fan J, Yang P, Liu C, Zhai J, Lei J, Yan Y*, Zhao D*, Chen X*. Nanopore-based proteolytic reactor for sensitive and comprehensive proteomic analyses. Analytical Chemistry 2006, 78, 4811-4819.

2005

1. Shui W, Liu Y, Fan H, Bao H, Liang S, Yang P*, Chen X*. Enhancing TOF/TOF-based de novo sequencing capability for high throughput protein identification with amino acid-coded mass tagging. Journal of Proteome Research 2005, 4, 83-90.
2. Fan J#, Shui W#, Yang P, Wang X, Xu Y, Wang H, Chen X*, Zhao D*. Mesoporous silica nanoreactors for highly efficient proteolysis. Chemistry-A European Journal 2005, 11, 5391-5396.

2004

1. Zhai J, Shui W, Xu X, Yu Y, Bao H, Chen X*, Yang P*. A modified nanospray tip coupled to a mass spectrometer for analyzing enzymatic peptides. Rapid Communications in Mass Spectrometry 2004, 18, 1177-1179.

2003

1. Shui W, Yu Y, Xu X, Huang Z, Xu G, Yang P*. Micro-electrospray with stainless steel emitters. Rapid Communications in Mass Spectrometry 2003, 17, 1541-1547.

2002

1. Wei J, Shui W, Zhou F, Lu Y, Chen K, Xu G, Yang P*. Naturally and externally pulsed electrospray. Mass Spectrometry Review 2002, 21, 48-162.
2. Zhou F, Shui W, Lu Y, Yang P*, Guo Y*. High accuracy mass measurement of peptides with internal calibration using a dual electrospray ionization sprayer system for protein identification. Rapid Communications in Mass Spectrometry 2002, 16, 505-511.

2001

1. Lu Y, Zhou F, Shui W, Bian L, Guo Y, Yang, P*. Pulsed electrospray for mass spectrometry. Analytical Chemistry 2001, 73, 4748-4753.