Enhanced inflammation and suppressed adaptive immunity in COVID-19 with prolonged RNA shedding
Xiaohua Tang#, Rui Sun#, Weigang Ge#, Tingting Mao#, Liujia Qian#, Chongquan Huang#, Zhouyang Kang#, Qi Xiao, Meng Luo, Qiushi Zhang, Sainan Li, Hao Chen, Wei Liu, Bingjie Wang, Shufei Li, Xiaoling Lin, Xueqin Xu, Huanzheng Li, Lianpeng Wu, Jianyi Dai, Huanhuan Gao, Lu Li, Tian Lu, Xiao Liang, Xue Cai, Guan Ruan, Fei Xu, Yan Li, Yi Zhu*, Ziqing Kong*, Jianping Huang* & Tiannan Guo*
Cell Discovery volume 8, Article number: 70 (2022)
Proteotypic Differences of Follicular-Patterned Thyroid Neoplasms
Dongdong Huang, Huifang Zhang, Lu Li, Weigang Ge, Wei Liu, Zhen Dong, Jinlong Gao, Nan Yao, Wenxin Fu, Lingling Huang, Tiannan Guo, Yaoting Sun* and Xiaodong Teng*
Front. Endocrinol., 06 July 2022, doi.org/10.3389/fendo.2022.854611
Optimization of Microflow LC Coupled with Scanning SWATH and Its Application in Hepatocellular Carcinoma Tissues
Huanhuan Gao, Youqi Liu, Vadim Demichev, Stephen Tate, Chen Chen, Jiang Zhu, Cong Lu, Markus Ralser, Tiannan Guo*, and Yi Zhu*
J. Proteome Res, 2 June 2022, doi.org/10.1021/acs.jproteome.2c00078
Molecular Subgroups of Intrahepatic Cholangiocarcinoma Discovered by Single-Cell RNA Sequencing-Assisted Multi-Omics Analysis
Xuanwen Bao#, Qiong Li#, Jinzhang Chen#, Diyu Chen#, Chanqi Ye#, Xiaomeng Dai, Yanfang Wang, Xin Li, Xiaoxiang Rong, Fei Cheng, Ming Jiang, Zheng Zhu, Yongfeng Ding, Rui Sun, Chuan Liu, Lingling Huang, Yuzhi Jin, Bin Li, Juan Lu, Wei Wu, Yixuan Guo, Wenguang Fu, Sarah Raye Langley, Vincent Tano, Weijia Fang, Tiannan Guo*, Jianpeng Sheng*, Peng Zhao*, Jian Ruan*
Cancer Immunol Res canimm, 20 May 2022, doi.org/10.1158/2326-6066.CIR-21-1101
Proteomic characterization of Omicron SARS-CoV-2 host response
Jianfeng Bao#, Rui Sun#, Jingwen Ai#, Liujia Qian#, Fang Liu#, Hongyu Wang#, Lingling Tan, Xue Cai, Yingqiu Shi, Xiao Liang, Weigang Ge, Jing Wu, Chen Chen, Wenhong Zhang*, Jinsong Huang* & Tiannan Guo*
Cell Discovery, 18 May 2022, doi.org/10.1038/s41421-022-00418-x
An open invitation to the Understudied Proteins Initiative
Georg Kustatscher*, Tom Collins, Anne-Claude Gingras, Tiannan Guo, Henning Hermjakob, Trey Ideker, Kathryn S. Lilley, Emma Lundberg, Edward M. Marcotte, Markus Ralser & Juri Rappsilber*
Nature Biotechnology, May 09, 2022, https://doi.org/10.1038/s41587-022-01316-z
Understudied proteins: opportunities and challenges for functional proteomics
Georg Kustatscher*, Tom Collins, Anne-Claude Gingras, Tiannan Guo, Henning Hermjakob, Trey Ideker, Kathryn S. Lilley, Emma Lundberg, Edward M. Marcotte, Markus Ralser & Juri Rappsilber*
Nat Methods, May 09, 2022, https://doi.org/10.1038/s41592-022-01454-x
RAB2A promotes cervical cancer progression as revealed by comprehensive analysis of HPV integration and proteome in longitudinal cervical samples
Yifan Meng#*, Shitong Lin#, Yi Zhou#, Xiao Yi#, Ping Wu, Qing Zhang, Weigang Ge, Canhui Cao, Peipei Gao, Wenhua Zhi, Ting Peng, Juncheng Wei, Wencheng Ding, Ding Ma, Guoliang Li, Qin Yang*, Tiannan Guo*, Xi Zeng*, Peng Wu*
Clinical Translational Medicine, March 28th, 2022. doi.org/10.1002/ctm2.767
Multi-omics in COVID-19: Seeing the unseen but overlooked in the clinic
Tian Lu, Yingrui Wang, Tiannan Guo*
Cell Reports Medicine, March 15 2022, doi.org/10.1016/j.xcrm.2022.100580
Stratification of follicular thyroid tumours using data-independent acquisition proteomics and a comprehensive thyroid tissue spectral library
Yaoting Sun*, Lu Li, Yan Zhou, Weigang Ge, He Wang, Runxin Wu, Wei Liu, Hao Chen, Qi Xiao, Xue Cai, Zhen Dong, Fangfei Zhang, Junhong Xiao, Guangzhi Wang, Yi He, Jinlong Gao, Oi Lian Kon, Narayanan Gopalakrishna Iyer, Haixia Guan, Xiaodong Teng, Yi Zhu*, Yongfu Zhao*, Tiannan Guo*
Molecular Oncology, 23 February 2022, doi.org/10.1002/1878-0261.13198
Circulating proteome and progression of type 2 diabetes
Wanglong Gou, MSc#, Liang Yue, BSc#, Xin-yi Tang, MPH, Yan-yan Wu, MPH, Xue Cai, MSc, Menglei Shuai, BSc, Zelei Miao, MPH, Yuanqing Fu, PhD, Hao Chen, BSc, Zengliang Jiang, PhD, Jiali Wang, MPH, Yunyi Tian, MPH, Congmei Xiao, MSc, Nan Xiang, BSc, Zhen Wu, PhD, Yu-ming Chen, PhD*, Tiannan Guo, PhD*, Ju-Sheng Zheng, PhD*
The Journal of Clinical Endocrinology & Metabolism, dgac098, https://doi.org/10.1210/clinem/dgac098
sRAGE alleviates SARS-CoV-2-induced pneumonia in hamster
Xiuqin Zhang#, Dan Li#, Rui Sun#, Xinli Hu#, Zhiqi Song#, Xiaotian Ni, Hua Zhu, Tiannan Guo*, Chuan Qin*& Rui-Ping Xiao*
Sig Transduct Target Ther 7, 36 (2022). https://doi.org/10.1038/s41392-022-00883-6
PROTREC: A probability-based approach for recovering missing proteins based on biological networks
Weijia Kong, Bertrand Jern Han Wong, Huanhuan Gao, Tiannan Guo, Xianming Liu, Xiaoxian Du, Limsoon Wong*, Wilson Wen Bin Goh*
Journal of Proteomics. 6 January 2022. doi.org/10.1016/j.jprot.2021.104392
DIA-based Proteomics Identifies IDH2 as a Targetable Regulator of Acquired Drug Resistance in Chronic Myeloid Leukemia
Wei Liu, Yaoting Sun, Weigang Ge, Fangfei Zhang, Lin Gan, Yi Zhu, Tiannan Guo*, Kexin Liu*
Mol Cell Preteomics. DOI:https://doi.org/10.1016/j.mcpro.2021.100187
Proteomic datasets of HeLa and SiHa cell lines acquired by DDA-PASEF and diaPASEF
Zelu Huang, WeijiaKong, Bertrand Jernhan Wong, Huanhuan Gao, Tiannan Guo, Xianming Liu, Xiaoxian Du, Limsoon Wong*, Wilson Wen Bin Goh*
Data in Brief, Volume 41, 2022, doi.org/10.1016/j.dib.2022.107919
Proteomic and metabolomic profiling of urine uncovers immune responses in patients with COVID-19
Xiaojie Bi#, Wei Liu#, Xuan Ding#, Shuang Liang#, Yufen Zheng#, Xiaoli Zhu#, Sheng Quan#, Xiao Yi, Nan Xiang, Juping Du, Haiyan Lyu, Die Yu, Chao Zhang, Luang Xu, Weigang Ge, Xinke Zhan, Jiale He, Zi Xiong, Shun Zhang, Yanchang Li, Ping Xu, Guangjun Zhu, Donglian Wang, Hongguo Zhu, Shiyong Chen, Jun Li, Haihong Zhao, Yi Zhu*, Huafen Liu*, Jiaqin Xu*, Bo Shen*, Tiannan Guo*
Cell Reports. December 27,2021 doi.org/10.1016/j.celrep.2021.110271
Proteomics profiling of colorectal cancer progression identifies PLOD2 as a potential therapeutic target
Yingkuan Shao#, Kailun Xu#, Xi Zheng, Biting Zhou, Xiuli Zhang, Lin Wang, Yaoting Sun, Dan Li, Ting Chen, Jian Wang, Shaojun Yu, Lifeng Sun, Xiaoming Xu, Shaozhi Dai, Huanhuan Gao, Guan Ruan, Wei Liu, Xue Cai, Tiansheng Zhu, Lina Qi, Jiani Chen, Wangxiong Hu, Xingyue Weng, Yi Zhu, Xueping Xiang, Zhiyuan Hu, Jinfan Li, Lirong Chen, Jimin Shao*, Shu Zheng*, Tiannan Guo*
Cancer Communications. 04 December 2021 doi.org/10.1002/cac2.12240
A prostate cancer tissue specific spectral library for targeted proteomic analysis
Rui Sun, Mengge Lyu, Shuang Liang, Weigang Ge, Yingrui Wang, Xuan Ding, Cheng Zhang, Yan Zhou, Shanjun Chen, Lirong Chen, Tiannan Guo*
Proteomics. 20 November 2021 httpsdoi.org/10.1002/pmic.202100147
Potential Use of Serum Proteomics for Monitoring COVID-19 Progression to Complement RT-PCR Detection
Ying Zhang#, Xue Cai#, Weigang Ge#, Donglian Wang#, Guangjun Zhu#, Liujia Qian#, Nan Xiang, Liang Yue, Shuang Liang, Fangfei Zhang, Jing Wang, Kai Zhou, Yufen Zheng, Minjie Lin, Tong Sun, Ruyue Lu, Chao Zhang, Luang Xu, Yaoting Sun, Xiaoxu Zhou, Jing Yu, Mengge Lyu, Bo Shen, Hongguo Zhu*, Jiaqin Xu*, Yi Zhu*, and Tiannan Guo*
J. Proteome Res. November 16, 2021 doi.org/10.1021/acs.jproteome.1c00525
Novel deep learning radiomics model for preoperative evaluation of hepatocellular carcinoma differentiation based on computed tomography data
Yong Ding#, Shijian Ruan#, Yubizhuo Wang#, Jiayuan Shao#, Rui Sun, Wuwei Tian, Nan Xiang, Weigang Ge, Xiuming Zhang, Kunkai Su, Jingwen Xia, Qiang Huang, Weihai Liu, Qinxue Sun, Haibo Dong*, Mylène C. Q. Farias, Tiannan Guo*, Andrey S. Krylov, Wenjie Liang*, Wenbo Xiao, Xueli Bai, Tingbo Liang*
Clin. Transl. Med. 2021;11:e570. doi.org/10.1002/ctm2.570
Computational Optimization of Spectral Library Size Improves DIA-MS Proteome Coverage and Applications to 15 Tumors
Weigang Ge#, Xiao Liang#, Fangfei Zhang#, Yifan Hu#, Luang Xu, Nan Xiang, Rui Sun, Wei Liu, Zhangzhi Xue, Xiao Yi, Yaoting Sun, Bo Wang, Jiang Zhu, Cong Lu, Xiaolu Zhan, Lirong Chen, Yan Wu, Zhiguo Zheng, Wangang Gong, Qijun Wu, Jiekai Yu, Zhaoming Ye, Xiaodong Teng, Shiang Huang, Shu Zheng, Tong Liu*, Chunhui Yuan*, Tiannan Guo*
J. Proteome Res. 2021, 20, 12, 5392–5401。 doi.org/10.1021/acs.jproteome.1c00640
SnapShot: Clinical proteomics
Yi Zhu, Ruedi Aebersold, Matthias Mann, Tiannan Guo
Cell. 2021. 184(18):4840-4840 el. doi:10.1016/j.cell.2021.08.015
Gut microbiota may underlie the predisposition of healthy individuals to COVID-19
Wanglong Gou#, Yuanqing Fu#, Liang Yue#, Geng-dong Chen#, Xue Cai#, Menglei Shuai#, Fengzhe Xu#, Xiao Yi, Hao Chen, Yi Zhu, Mian-li Xiao, Zengliang Jiang, Zelei Miao, Congmei Xiao, Bo Shen, Xiaomai Wu, Haihong Zhao, Wenhua Ling, Jun Wang, Yu-ming Chen*, Tiannan Guo*, Ju-Sheng Zheng*
Journal of Genetics and Genomics
Volume 48, Issue 9, 20 September 2021, Pages 792-802
https://doi.org/10.1016/j.jgg.2021.04.002
Phenotypic characterization of two novel cell line models of castration resistant prostate cancer
Michael C Haffner*, Akshay Bhamidipati, Harrison K Tsai, David M Esopi, Ajay M Vaghasia, Jin-Yih Low, Radhika A Patel, Gunes Guner, Minh-Tam Pham, Nicole Castagna, Jessica Hicks, Nicolas Wyhs, Ruedi Aebersold, Angelo M De Marzo, William G Nelson, Tiannan Guo, Srinivasan Yegnasubramanian*
Prostate. 2021 Aug 16. doi: 10.1002/pros.24210
METTL9 mediated N1-histidine methylation of zinc transporters is required for tumor growth
Mengyue Lv#, Dan Cao#*, Liwen Zhang, Chi Hu, Shukai Li, Panrui Zhang, Lianbang Zhu, Xiao Yi, Chaoliang Li, Alin Yang, Zhentao Yang, Yi Zhu, Kaiguang Zhang & Wen Pan*
Protein Cell 12, 965–970 (2021). https://doi.org/10.1007/s13238-021-00857-4
On the feasibility of deep learning applications using raw mass spectrometry data
Joris Cadow*, Matteo Manica, Roland Mathis, Tiannan Guo, Ruedi Aebersold, María Rodríguez Martínez*
Bioinformatics. 2021.37(Suppl_1):i245-i253.10.1093/bioinformatics/btab311
High-Throughput Proteomics and AI for Cancer Biomarker Discovery
Qi Xiao, Fangfei Zhang, Luang Xu, Liang Yue, Oi Lian Kon, Yi Zhu*, Tiannan Guo*
Advanced Drug Delivery Reviews. 25 June,2021,10.1016/j.addr.2021.113844
Eleven routine clinical features predict COVID-19 severity uncovered by machine learning of longitudinal measurements
Kai Zhou#, Yaoting Sun#, Lu Li#, Zelin Zang#, Jing Wang#, Jun Li#, Junbo Liang#, Fangfei Zhang, Qiushi Zhang, Weigang Ge, Hao Chen, Xindong Sun, Liang Yue, Xiaomai Wu, Bo Shen, Jiaqin Xu, Hongguo Zhu, Shiyong Chen, Hai Yang, Shigao Huang, Minfei Peng, Dongqing Lv, Chao Zhang, Haihong Zhao, Luxiao Hong, Zhehan Zhou, Haixiao Chen, Xuejun Dong, Chunyu Tu, Minghui Li, Yi Zhu*, Baofu Chen*, Stan Z. Li*, Tiannan Guo*
Computational and Structural Biotechnology Journal. 2021. 19: 3640-3649. doi: 10.1016/2021.06.22
The Hippo-TAZ axis mediate vascular endothelial growth factor C in glioblastoma-derived exosomes to promote angiogenesis
Zhengmin Wang#, Yifan Yuan#, Xiong Ji#, Xing Xiao#, Zhujun Li, Xiao Yi, Yi Zhu, Tiannan Guo, Yin Wang, Liang Chen*, Ying Liu*
Cancer letters. Volume 513, 10 August 2021, Pages 1-13.doi.org/10.1016/j.canlet.2021.05.002
Immunometabolism the CyTOF way
Liujia Qian, Tiannan Guo*
Immunity. Preview. 13 April 2021 10.1016/j.immuni.2021.03.019
Multi-organ Proteomic Landscape of COVID-19 Autopsies
Xiu Nie#, Liujia Qian#, Rui Sun#, Bo Huang#, Xiaochuan Dong#, Qi Xiao#, Qiushi Zhang#, Tian Lu, Liang Yue, Shuo Chen, Xiang Li, Yaoting Sun, Li Lu, Luang Xu, Li Yan, Ming Yang, Zhangzhi Xue, Shuang Liang, Xuan Ding, Chunhui Yuan, Li Peng, Wei Liu, Xiao Yi, Mengge Lyu, Guixiang Xiao, Xia Xu, Weigang Ge, Jiale He, Jun Fan, Junhua Wu, Meng Luo, Xiaona Chang, Huaxiong Pan, Xue Cai, Junjie Zhou, Jing Yu, Huanhuan Gao, Mingxing Xie, Sihua Wang, Guan Ruan, Hao Chen, Hua Su, Heng Mei, Danju Luo, Dashi Zhao, Fei Xu, Yan Li, Yi Zhu*, Jiahong Xia*, Yu Hu*, Tiannan Guo*
Cell. 2021. 184(3): 775-791. doi: 10.1016/j.cell.2021.01.004
Proteomic and metabolomic investigation of serum lactate dehydrogenase elevation in COVID-19 patients
Haixi Yan#, Xiao Liang#, Juping Du#, Zebao He#, Yu Wang, Mengge Lyu ,Liang Yue, Fangfei Zhang, Zhangzhi Xue, Luang Xu, Guan Ruan, Jun Li, Hongguo Zhu, Jiaqin Xu, Shiyong Chen, Chao Zhang, Dongqing Lv ,Zongmei Lin, Bo Shen, Yi Zhu*, Biyun Qian*, Haixiao Chen*, Tiannan Guo*
Proteomics. 13 May 2021. doi.org/10.1002/pmic.202100002
ProteomeExpert: A Docker image based web-server for exploring, modeling, vis-ualizing, and mining quantitative proteomic data sets
Tiansheng Zhu, Hao Chen, Xishan Yan, Zhicheng Wu, Xiaoxu Zhou, Qi Xiao, Weigang Ge, Qiushi Zhang, Chao Xu, Luang Xu, Guan Ruan, Zhangzhi Xue, Chunhui Yuan*, Guo-Bo Chen* and Tiannan Guo*
Bioinformatics. January 08, 2021 doi.org/10.1093/bioinformatics/btaa1088
BatchServer: a web server for batch effect evaluation, visualization and correction
Zhu, Tiansheng; Sun, Rui; Zhang, Fangfei; Chen, Guo-Bo; Yi, Xiao; Ruan, Guan; Yuan, Chunhui; Zhou, Shuigeng*; Guo, Tiannan*
Journal of Proteome Research. December 18, 2020 10.1021/acs.jproteome.0c00488
Convergent network effects along the axis of gene expression during prostate cancer progression
Konstantina Charmpi#, Tiannan Guo*#, Qing Zhong#, Ulrich Wagner#, Rui Sun, Nora C Toussaint, Christine Fritz, Chunhui Yuan, Hao Chen, Niels J Rupp, Ailsa Christiansen, Dorothea Rutishauser, Jan H Ruschoff, Christian Fankhauser, Karim Saba, Cedric Poyet, Thomas Hermanns, Kathrin Oehl, Ariane Leoni Moore, Christian Beisel, Laurence Calzone, Loredana Martignetti, Qiushi Zhang, Yi Judy Zhu, Maria Rodriguez Martinez, Matteo Manica, Michael C Haffner, Ruedi Aebersold*, Peter J Wild*, Andreas Beyer*
Genome Biology. 14 Dec. 2020,21(302) 10.1186/s13059-020-02188-9
Phenotype Classification using Proteome Data in a Data-Independent Acquisition Tensor Format
Fangfei Zhang#, Shaoyang Yu#, Lirong Wu#, Zelin Zang, Xiao Yi, Jiang Zhu, Cong Lu, Ping Sun, Yaoting Sun, Sathiyamoorthy Selvarajan, Lirong Chen, Xiaodong Teng, Yongfu Zhao, Guangzhi Wang, Junhong Xiao, Shiang Huang, Oi Lian Kon, Gopalakrishna N. Iyer, Stan Z. Li*, Zhongzhi Luan*, Tiannan Guo*
Journal of American Society of Mass Spectrometry. (2020) 10.1021/jasms.0c00254
PulseDIA: Data-Independent Acquisition Mass Spectrometry Using Multi-Injection Pulsed Gas-Phase Fractionation
Cai, Xue#; Ge, Weigang#; Yi, Xiao; Sun, Rui; Zhu, Jiang; Lu, Cong; Sun, Ping; Zhu, Tiansheng; Yuan, Chunhui; Ruan, Guan; Liang, Shuang; Lyu, Mengge; Huang, Shiang; Zhu, Yi*; Guo, Tiannan*
Journal of Proteome Research. 10.1021/acs.jproteome.0c00381 Online. 25th Sept 2020
Generating Proteomic Big Data for Precision Medicine
Liang Yue#, Fangfei Zhang#, Rui Sun, Yaoting Sun, Chunhui Yuan, Yi Zhu, Tiannan Guo*
Proteomics. Invited. Online: 29 July 2020 10.1002/pmic.201900358
DPHL: A DIA pan-human protein mass spectrometry library for robust biomarker discovery
Tiansheng Zhu#, Yi Zhu#*, Yue Xuan#, Huanhuan Gao, Xue Cai, Sander R. Piersma, Thang V. Pham, Tim Schelfhorst, Irene Bijnsdorp, Rui Sun, Liang Yue, GuanRuan, Qiushi Zhang, Mo Hu, Yue Zhou, Winan J. Van Houdt, T.Y.S Lelarge, J. Cloos, Anna Wojtuszkiewicz, Danijela Koppers-Lalic, F. Baettger, ChantalScheepbouwer, R.H Brakenhoff, G.J.L.H. van Leenders, Jan N.M. Ijzermans, J.W.M. Martens, R.D.M. Steenbergen, N.C. Grieken, Sathiyamoorthy Selvarajan, Sangeeta Mantoo, Sze Sing Lee, Serene Jie Yi Yeow, Syed Muhammad Fahmy Alkaff, Nan Xiang, Yaoting Sun, Xiao Yi, Shaozheng Dai, Wei Liu, Tian Lu, ZhichengWu, Xiao Liang, Man Wang, Yingkuan Shao, Xi Zheng, Kailun Xu, Qin Yang, Yifan Meng, Cong Lu, Jiang Zhu, Jin’e Zheng, Bo Wang, Sai Lou, Yibei Dai, Chao Xu,Chenhuan Yu, Huazhong Ying, Tony Kiat-hon Lim, Jianmin Wu, Xiaofei Gao, Zhongzhi Luan, Xiaodong Teng, Peng Wu, Shi’ang Huang, Zhihua Tao, N.Gopalakrishna Iyer, Shuigeng Zhou, Wenguang Shao, Henry Lam, Ding Ma, Jiafu Ji , Oi Lian Kon, Shu Zheng, Ruedi Aebersold, Connie R. Jimenez, Tiannan Guo*
Genomics, Proteomics and Bioinformatics. online 2020 Aug 12 10.1016/j.gpb.2019.11.008
Proteomic and Metabolomic Characterization of COVID-19 Patient Sera
Bo Shen#, Xiao Yi#, Yaoting Sun#, Xiaojie Bi#, Juping Du#, Chao Zhang#, Sheng Quan#, Fangfei Zhang, Rui Sun, Liujia Qian, Weigang Ge, Wei Liu, Shuang Liang, Hao Chen, Ying Zhang, Jun Li, Jiaqin Xu, Zebao He, Baofu Chen, Jing Wang, Haixi Yan, Yufen Zheng, Donglian Wang, Jiansheng Zhu, Ziqing Kong, Zhouyang Kang, Xiao Liang, Xuan Ding, Guan Ruan, Nan Xiang, Xue Cai, Huanhuan Gao, Lu Li, Sainan Li, Qi Xiao, Tian Lu, Yi Judy Zhu*, Huafen Liu*, Haixiao Chen*, Tiannan Guo*
Cell. 2020. 182(1): 59-72. doi:10.1016/j.cell.2020.05.032
Data-Independent Acquisition Mass Spectrometry and Software Tools: a Glimpse in 2020
Fangfei Zhang, Weigang Ge, Guan Ruan, Xue Cai, Tiannan Guo*
Proteomics 2020, e1900276. Invited Review 10.1002/pmic.201900276
A circulating exosomes-based novel screening tool for colorectal cancer revealed by Shotgun and Data Independent Acquisition mass spectrometry
Xi Zheng#, Kailun Xu#, Biting Zhou#, Ting Chen, Yanqin Huang, Qilong Li, Fei Wen, Weiting Ge, Jian Wang, Shaojun Yu, Liang Zhu, Liang Yue, Xue Cai, Qiushi Zhang, Guan Ruan, Tiansheng Zhu, Zhicheng Wu, Yi Zhu, Yingkuan Shao*, Tiannan Guo*, Shu Zheng*
Journal of Extracellular Vesicles. 2020, 9(1) 1750202. 10.1080/20013078.2020.1750202
Accelerated Lysis and Proteolytic Digestion of Biopsy-level Fresh Frozen and FFPE Tissue Samples Using Pressure Cycling Technology
Gao, Huanhuan; Zhang, Fangfei; Liang, Shuang; Zhang, Qiushi; Lyu, Mengge; Qian, Liujia; Liu, Wei; Ge, Weigang; Chen, Chen; Liu, Kexing; Yi, Xiao; Zhu, Jiang; Lu, Cong; Sun, Ping; Zhu, Yi*; Guo, Tiannan*
Journal of Proteome Research. 2020, 19(5), 1982-1990. 10.1021/acs.jproteome.9b00790
Accelerated Protein Biomarker Discovery from FFPE Tissue Samples using Single-shot, Short Gradient Microflow SWATH MS
Rui Sun#, Christie Hunter*#, Chen Chen, Weigang Ge, Nick Morrice, Qiushi Zhang, Xue Cai, Bo Wang, Xiaoyan Yu, Xiaodong Teng, Lirong Chen, Shaozheng Dai, Jian Song, Zhongzhi Luan, Changbin Yu, Ruedi Aebersold, Yi Zhu*, Tiannan Guo*
Journal of Proteome Research. 2020, 19(7), 2732-2741. 10.1021/acs.jproteome.9b00671
Quantitative proteome landscape of the NCI-60 cancer cell lines
Tiannan Guo*#, Augustin Luna#, Ching Chiek Koh#, Vinodh Rajapakse#, Zhicheng Wu, Michael Patrick Menden, Wei Liu, Yaoting Sun, Yongran Cheng, Laurence Calzone, Loredana Martignetti, Alessandro Ori, Murat Iskar, Ludovic Gillet, Qing Zhong, Sudhir Varma, Uwe Schmitt, Peng Qiu, Yi Zhu, Kexin Liu, Peter Wild, Garnett Mathew, Peer Bork, Martin Beck, Julio Saez-Rodriguez, William Reinhold, Chris Sander, Yves Pommier*, Ruedi Aebersold*
iScience. 2019, 21:664-680. 10.1016/j.isci.2019.10.059
Arabidopsis Proteome and the Mass Spectral Assay Library
Huoming Zhang, Pei Liu, Tiannan Guo, Huayan Zhao, Dalila Bensaddek, Ruedi Aebersold, Liming Xiong
Scientific Data. 6, Article number: 278 (2019) 10.1038/s41597-019-0294-0
High-throughput Proteomics analysis of FFPE tissue samples facilitates tumor stratification
Yi Zhu#, Tobias Weiss#, Qiushi Zhang, Qing Zhong, Zhicheng Wu, Tiansheng Zhu, Chao Xu, Sai Lou, Bo Wang, Xiaoyan Yu, Ludovic Gillet, Peter Blattmann, Rui Sun, Xiao Yi, Ailsa Christiansen, Karim Saba, Dorothea Rutishauser, Jelena Ljubicic, Christian D. Fankhauser, Michael B. Schmid, Christine Fritz, Niels J. Rupp, Cedric Poyet, Elisabeth Rushing, Michael Weller, Patrick Roth, Eugenia Haralambieva, Silvia Hofer, Chen Chen, Wolfram Jochum, Xiaofei Gao, Lirong Chen, Peter J. Wild*, Ruedi Aebersold*, Tiannan Guo*
Molecular Oncology. 2019. 13 (11) :2305-2328. 10.1002/1878-0261.12570
Proteomic investigation of intra-tumor heterogeneity using network-based contextualization
Goh, Wilson; Zhao, Yaxing; Sue, Andrew; Guo, Tiannan; Wong, Limsoon
Journal of Proteomics. 2019 Jul 16;206:103446. 10.1016/j.jprot.2019.103446
Comparative analysis of mRNA degradation and protein degradation in 68 pairs of adjacent prostate tissue samples indicates high stability of proteins
Wenguang Shao#, Tiannan Guo#*, Nora C Toussaint, Ulrich Wagner, Li Li, Konstantina Charmpi, Yi Zhu, Rui Sun, Dorothea Rutishauser, Thomas Hermanns, Christian Daniel Fankhauser, Cedric Poyet, Jelena Ljubicic, Niels Rupp, Jan H. Rüschoff, Qing Zhong, Andreas Beyer, Yansheng Liu, Gunnar Rätsch, Peter J. Wild*, Ruedi Aebersold*
Nature Communications 10, Article number: 2524, 2019. 10.1038/s41467-019-10513-5
In-depth Serum Proteomics Reveals Biomarkers of Psoriasis Severity and Response to Traditional Chinese Medicine
Meng Xu#, Jingwen Deng#, Kaikun Xu#, Tiansheng Zhu#, Ling Han, Wang Dan, Yaoting Sun, Cheng Chang, Xiaomei Zhang, Jiayu Dai, Liang Yue, Qiushi Zhang, Xue Cai, Yi Zhu, Hu Duan, Yuan Liu, Dong Li, Yunping Zhu, Timothy R. D. J. Radstake, Deepak M.W. Balak, Danke Xu*, Tiannan Guo*, Chuanjian Lu* and Xiaobo Yu*
Theranostics. 2019; 9(9):2475-2488. 10.7150/thno.31144
Identification of protein abundance changes in biopsy-level hepatocellular carcinoma tissues using PCT-SWATH
Yi Zhu#, Jiang Zhu#, Cong Lu, Ping Sun, Wei Xie, Qiushi Zhang, Liang Yue, Tiansheng Zhu, Guan Ruan, Ruedi Aebersold*, Shiang Huang*, Tiannan Guo*
Proteomics Clinical Applications. 2019 Jan;13(1):e1700179. 10.1002/prca.201700179
Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers
Tiannan Guo#, Li Li#, Qing Zhong*, Niels J Rupp, Konstantina Charmpi, Christie E Wong, Ulrich Wagner, Jan H Rueschoff, Wolfram Jochum, Christian Fankhauser, Karim Saba, Cedric Poyet, Peter J Wild*, Ruedi Aebersold*, Andreas Beyer*
Life Science Alliance. 29 May 2018. 1(2) 10.26508/lsa.201800042
High-Throughput Proteomic Analysis of Fresh-Frozen Biopsy Tissue Samples Using Pressure Cycling Technology Coupled with SWATH Mass Spectrometry
Yi Zhu, Tiannan Guo *
Methods Mol Biol. 2017 Oct 26. Invited contribution. 10.1007/7651_2017_87
Towards a one-stop solution for large-scale proteomics data analysis
Yi Zhu, Tiannan Guo*
Sci China Life Sci. 2018 Mar;61(3):351-354. Invited contribution. 10.1007/s11427-017-9113-5
Application of Nanosecond Laser Photolysis Protein Footprinting to Study EGFR Activation by EGF in Cells
Yi Zhu, Aida Serra, Tiannan Guo, Jung Eun Park, Qing Zhong, and Siu Kwan Sze
J Proteome Res. 2017 Jun 2;16(6):2282-2293. 10.1021/acs.jproteome.7b00154
A curated collection of tissue microarray images and clinical outcome data of prostate cancer patients
Qing Zhong #, Tiannan Guo #, Markus Rechsteiner, Jan H Rüschoff, Niels Rupp, Christian Fankhauser, Karim Saba, Ashkan Mortezavi, Cédric Poyet, Thomas Hermanns, Yi Zhu, Holger Moch, Ruedi Aebersold, Peter J. Wild
Scientific Data. 2017. 10.1038/sdata.2017.14
Phosphatase POPX2 exhibits dual regulatory functions in cancer metastasis
Songjing Zhang, Ting Weng, Cheruba, Elsie, Tiannan Guo, Hei Chan, Siu Kwan Sze, and Cheng-Gee Koh
J Proteome Res. 2016 Dec 15. 10.1021/acs.jproteome.6b00748
TRIM24 is an oncogenic transcriptional activator in prostate cancer
Anna C. Groner, Laura Cato, Jonas de Tribolet-Hardy, Tiziano Bernasocchi, Hana Janouskova , Diana Melchers, René Houtman, Andrew C. B. Cato, Patrick Tschopp, Lei Gu, Andrea Corsinotti, Qing Zhong, Christian Fankhauser, Christine Fritz, Cédric Poyet, Ulrich Wagner, Tiannan Guo, Ruedi Aebersold, Levi A. Garraway, Peter J. Wild, Jean-Philippe Theurillat, Myles Brown
Cancer Cell. Published online 24 May 2016. 10.1016/j.ccell.2016.04.012
Reproducible Tissue Homogenization and Protein Extraction for Quantitative Proteomics Using MicroPestle-Assisted Pressure-Cycling Technology
Shao S, Guo T, Gross V, Lazarev A, Koh CC, Gillessen S, Joerger M, Jochum W, Aebersold R
J Proteome Res. 2016 May 10. 10.1021/acs.jproteome.5b01136
Image-based computational quantification and visualization of genetic alterations and tumour heterogeneity
Qing Zhong, Jan H Rüschoff, Tiannan Guo, Maria Gabrani, Peter J Schüffler, Markus Rechsteiner, Yansheng Liu, Thomas J Fuchs, Niels J Rupp, Christian Fankhauser, Joachim M Buhmann, Sven Perner, Cédric Poyet, Miriam Blattner, Davide Soldini, Holger Moch, Mark A Rubin, Aurelia Noske, Josef Rüschoff, Michael C Haffner, Wolfram Jochum, Peter J Wild
Scientific Reports. 6, Article number: 24146 (2016). 10.1038/srep24146
Quantitative proteomics signature profiling based on network contextualization
Goh WW, Guo T, Aebersold R, Wong L
Biol Direct. 2015 Dec 15;10:71. 10.1186/s13062-015-0098-x
Minimal sample requirement for highly multiplexed protein quantification in cell lines and tissues by PCT-SWATH mass spectrometry
Shao S, Guo T, Koh CC, Gillessen S, Joerger M, Jochum W, Aebersold R
Proteomics. 2015 Nov;15(21):3711-21. 10.1002/pmic.201500161
Global Metabonomic and Proteomic Analysis of Human Conjunctival Epithelial Cells (IOBA-NHC) in Response to Hyperosmotic Stress
Chen L, Li J, Guo T, Ghosh S, Koh SK, Tian D, Zhang L, Jia D, Beuerman RW, Aebersold R, Chan EC, Zhou L
J Proteome Res. 2015 Sep 4;14(9):3982-95. 10.1021/acs.jproteome.5b00443
Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps
Tiannan Guo, Petri Kouvonen, Ching Chiek Koh, Ludovic C Gillet, Witold E Wolski, Hannes L Röst, George Rosenberger, Ben C Collins, Lorenz C Blum, SilkeGillessen, Markus Joerger, Wolfram Jochum, Ruedi Aebersold*
Nature Medicine. 2015. 21, 407-413. 10.1038/nm.3807
The methyltransferase Ezh2 controls cell adhesion and migration through direct methylation of the extranuclear regulatory protein talin
Gunawan M, Venkatesan N, Loh JT, Wong JF, Berger H, Neo WH, Li LY, La Win MK, Yau YH, Guo T, See PC, Yamazaki S3, Chin KC4, Gingras AR5, Shochat SG, Ng LG, Sze SK, Ginhoux F, Su IH
Nature Immunology. 2015 May;16(5):505-16. 10.1038/ni.3125
Mass spectrometry-based proteomic quest for diabetes biomarkers
Shao S, Guo T, Aebersold R
Biochim Biophys Acta — Proteins and Proteomics. 2015 Jun;1854(6):519-27. 10.1016/j.bbapap.2014.12.012
A repository of assays to quantify 10,000 human proteins by SWATH-MS
Rosenberger G, Koh CC, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, Lam H, Bader SL, Campbell DS, Deutsch EW, Moritz RL, Tate S, Aebersold R
Scientific Data. 2014 Sep 16;1:140031. 10.1038/sdata.2014.31
LEO1 is regulated by PRL-3 and mediates its oncogenic properties in Acute Myeloid Leukemia
Zhu J, Zhang H, Chong PS, Zhou J, Cheong LL, Liu SC, Qian J, Guo T, Sze SK, Zeng Q, Chng WJ
Cancer Research. 2014 Jun 1;74(11):3043-53. 10.1158/0008-5472.CAN-13-2321
An Integrative Transcriptome and Proteome Study to Identify the Signaling Network Regulated by POPX2 Phosphatase
Zhang S, Guo T, Chan H, Sze SK, Koh CG
Journal of Proteome Research, 2013. 12(6):2525-36. 10.1021/pr301113c
Multidimensional identification of tissue biomarkers of gastric cancer
Tiannan Guo, Lingling Fan, Wai Har Ng, Yi Zhu, Mengfatt Ho, Wei Keat Wan, Kiat Hon Lim, Whee Sze Ong, Sze Sing Lee, Shiang Huang Oi Lian Kon*, and Siu Kwan Sze*
Journal of Proteome Research. 2012 Jun 1;11(6):3405 10.1021/pr300212g
Elucidating Structural Dynamics of Integral Membrane Proteins on Native Cell Surface by Hydroxyl Radical Footprinting and Nano LC-MS/MS
Zhu Y, Guo T, Sze SK
Methods in Molecular Biology 2011, Volume 790, Part 5, 287-303. 10.1007/978-1-61779-319-6_22
Investigation of POPX2 Phosphatase Functions by Comparative Phosphoproteomic Analysis
Singh P, Gan CS, Guo T, Phang HQ, Sze SK, Koh CG
Proteomics. 2011. 11:2891-2900. 10.1002/pmic.201100044
Simultaneous Analysis of Proteome, Phospho- and Glycoproteome of Rat Kidney Tissue with Electrostatic Repulsion Hydrophilic Interaction Chromatography
Hao P, Guo T, Sze SK
PLoS ONE 2011. 6(2): e16884. 10.1371/journal.pone.0016884
Global molecular dysfunctions in gastric cancer revealed by an integrated analysis of the phosphoproteome and transcriptome
Tiannan Guo, Sze Sing Lee, Wai Har Ng, Yi Zhu, Chee Sian Gan, Jiang Zhu, Haixia Wang, Shiang Huang, Siu Kwan Sze* and Oi Lian Kon*
Cellular and Molecular Life Sciences 2011. 68(11):1983-2002. 10.1007/s00018-010-0545-x
Quantitative Proteomics Discloses MET Expression in Mitochondria as a Direct Target of MET Kinase Inhibitor in Cancer Cells
Guo T, Zhu Y, Gan CS, Lee SS, Zhu J, Wang H, Li X, Christensen J, Huang S, Kon OL, Sze SK
Molecular & Cellular Proteomics. 2010. 9(12):2629-41. 10.1074/mcp.M110.001776
Novel Application of Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) in Shotgun Proteomics: Comprehensive Profiling of Rat Kidney Proteome
Hao P, Guo T, Li X, Adav SS, Yang J, Wei M, Sze SK
Journal of Proteome Research. 2010, 9 (7), 3520-3526. 10.1021/pr100037h
Simultaneous characterization of glyco- and phospho-proteomes of mouse brain membrane proteome with electrostatic repulsion hydrophilic interaction chromatography (ERLIC)
Zhang H, Guo T, Li X, Datta A, Park JE, Yang J, Lim SK, Tam JP, Sze SK
Molecular & Cellular Proteomics. 2010. Apr;9(4):635-47. 10.1074/mcp.M900314-MCP200
Elucidating in vivo structural dynamics in integral membrane protein by hydroxyl radical footprinting
Zhu Y, Guo T, Park JE, Li X, Meng W, Datta A, Bern M, Lim SK, Sze SK
Molecular & Cellular Proteomics. 2009. 8:1999-2010. 10.1074/mcp.M900081-MCP200
Elucidating the structure of cyclotide by partial acid hydrolysis and LC-MS/MS analysis
Sze SK*, Wang W, Meng W, Yuan R, Guo T, Zhu Y, Tam JP*.
Analytical Chemistry. 2009. 81(3):1079-88. (*corresponding authors) 10.1021/ac802175r
One-step procedure for peptide extraction from in-gel digestion sample for mass spectrometric analysis
Meng W, Zhang H, Guo T, Pandey C, Zhu Y, Kon OL, Sze SK.
Analytical Chemistry, 2008. 80(24): 9797-9805. 10.1021/ac801344z
Hybridization of Pulsed-Q Dissociation and Collision-Activated Dissociation in Linear Ion Trap Mass Spectrometer for iTRAQ Quantitation
Guo T, Gan CS, Zhang H, Zhu Y, Kon OL, Sze SK
Journal of Proteome Research, 2008, 7(11):4831-4840. 10.1021/pr800403z
A Comparative Study of Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) versus SCX-IMAC-Based Methods for PhosphopeptideIsolation/Enrichment
Gan CS, Guo T, Zhang H, Lim SK, Sze SK.
Journal of Proteome Research, 2008. 7(11): 4869-4877. 10.1021/pr800473j
