PUBLICATIONS

Note: *, co-corresponding; #, co-first author.

Full list of publications:
42

A circulating extracellular vesicles-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 Apr 14;9(1):1750202. doi: 10.1080/20013078.2020.1750202. PMID: 32363013.

41

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; Yi, Xiao; Zhu, Jiang; Lu, Cong; Sun, Ping; Liu, Kexing; Zhu, Yi *; Guo, Tiannan *.

Journal of Proteome Research. 2020 Jul 2;19(7):2907. PMID: 32182071. PMID: 32182071.

40

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 May 1;19(5):1982-1990. doi: 10.1021/acs.jproteome.9b00790. PMID: 32053377.

39

Quantitative proteome landscape of the NCI-60 cancer cell lines

Tiannan Guo*#, Augustin Luna#, Vinodh Rajapakse#, Ching Chiek Koh#, Zhicheng Wu, Wei Liu, Yaoting Sun, Huanhuan Gao, Michael Patrick Menden, Chao Xu, Laurence Calzone, Loredana Martignetti, Chiara Auwerx, Marija Buljan, Amir Banaei-Esfahani, Alessandro Ori, Murat Iskar, Ludovic Gillet, Ran Bi, Jiangnan Zhang, Huanhuan Zhang, Chenhuan Yu, Qing Zhong, Sudhir Varma, Uwe Schmitt, Peng Qiu, Qiushi Zhang, Yi Zhu, Peter J. Wild, Mathew J. Garnett, Peer Bork, Martin Beck, Kexin Liu, Julio Saez-Rodriguez, Fathi Elloumi, William C. Reinhold, Chris Sander, Yves Pommier*, Ruedi Aebersold*.

iScience. 2019 Nov 22;21:664-680. doi: 10.1016/j.isci.2019.10.059. PMID: 31733513.

38

Arabidopsis Proteome and the Mass Spectral Assay Library

Huoming Zhang*#, Pei Liu#, Tiannan Guo#, Huayan Zhao, Dalila Bensaddek, Ruedi Aebersold, Liming Xiong.

Scientific Data. 2019 Nov 22;6(1):278. doi: 10.1038/s41597-019-0294-0. PMID: 31757973.

37

High-throughput Proteomic analysis of FFPE tissue samples facilitates tumor stratification

Yi Zhu#, Tobias Weiss#, Qiushi Zhang, Rui Sun, Bo Wang, Xiao Yi, Zhicheng Wu, Huanhuan Gao, Xue Cai, Guan Ruan, Tiansheng Zhu, Chao Xu, Sai Lou, Xiaoyan Yu, Ludovic Gillet, Peter Blattmann, Karim Saba, Christian D. Fankhauser, Michael B. Schmid, Dorothea Rutishauser, Jelena Ljubicic, Ailsa Christiansen, 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, Qing Zhong, Peter J. Wild*, Ruedi Aebersold*, Tiannan Guo*.

Molecular Oncology. 2019 Sep;13(11): 2305-2328. doi: 10.1002/1878-0261.12570. PMID: 31495056.

36

Proteomic investigation of intra-tumor heterogeneity using network-based contextualization — A case study on prostate cancer

Goh, Wilson*#; Zhao, Yaxing#; Sue, Andrew; Guo, Tiannan; Wong, Limsoon*.

Journal of Proteomics. 2019 Aug 30;206:103446. doi: 10.1016/j.jprot.2019.103446. PMID: 31323421.

35

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, Peng Xue, Ulrich Wagner, Li Li, Konstantina Charmpi, Yi Zhu, Jianmin Wu, Maria Buljan, Rui Sun, Dorothea Rutishauser, Thomas Hermanns, Christian Daniel Fankhauser, Cedric Poyet, Jelena Ljubicic, Niels Rupp, Jan H. Rüschoff, Qing Zhong, Andreas Beyer, Jaifu Ji, Ben C. Collins, Yansheng Liu, Gunnar Rätsch, Peter J. Wild*, Ruedi Aebersold*.

Nature Communications. 2019 Jun 7;10(1):2524. doi: 10.1038/s41467-019-10513-5. PMID: 31175306.

34

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, Yuhong Yan, Danni Yao, Hao Deng, Dan Wang, 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 Apr 13;9(9):2475-2488. doi: 10.7150/thno.31144. PMID: 31131048.

33  Wiley Top Downloaded Paper 2018-2019

Identification of protein abundance changes in biopsy-level hepatocellular carcinoma tissues using PCT-SWATH

Yi Zhu#, Jiang Zhu#, Cong Lu, Qiushi Zhang, Wei Xie, Ping Sun, Xiaochuan Dong, Liang Yue, Yaoting Sun, Xiao YI, Tiansheng Zhu, Guan Ruan, Ruedi Aebersold*, Shi’ang Huang*, Tiannan Guo*.

Proteomics Clinical Applications. 2019 Jan.13(1): e1700179. doi: 10.1002/prca.201700179. PMID: 30365225.

32

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. 2018 May 29;1(2):e201800042. doi: 10.26508/lsa.201800042. PMID: 30090875.

31 (invited book chapter)

High-Throughput Proteomic Analysis of Fresh-Frozen Biopsy Tissue Samples Using Pressure Cycling Technology Coupled with SWATH Mass Spectrometry

Yi Zhu, Tiannan Guo*.

Methods in Molecular Biology. 1788: 279-287. doi: 10.1007/7651_2017_87. PMID: 29071490.

30

Towards a one-stop solution for large-scale proteomics data analysis

Yi Zhu, Tiannan Guo*.

Science China Life Sciences. 2018 Mar;61(3):351-354. doi: 10.1007/s11427-017-9113-5. PMID: 28801860.

29

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*.

Journal of Proteome Research. 2017 Jun 2;16(6):2282-2293. doi: 10.1021/acs.jproteome.7b00154. Epub 2017 May 8. PMID: 28452222.

28

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 Mar 14;4:170014. doi: 10.1038/sdata.2017.14. PMID: 28291248.

27

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*.

Journal of Proteome Research. 2017 Feb 3;16(2):698-711. doi: 10.1021/acs.jproteome.6b00748. PMID: 27976581.

26

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. 2016 Jun 13;29(6):846-858. doi: 10.1016/j.ccell.2016.04.012. PMID: 27238081.

25

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*.

Journal of Proteome Research. 2016 Jun 3;15(6):1821-9. doi: 10.1021/acs.jproteome.5b01136. PMID: 27098501.

24

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. 2016 Apr 7;6:24146. doi: 10.1038/srep24146. PMID: 27052161.

23

Quantitative proteomics signature profiling based on network contextualization

Goh WW*, Guo T, Aebersold R, Wong L.

Biology Direct. 2015 Dec 15;10:71. doi: 10.1186/s13062-015-0098-x. PMID: 26666224.

22

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. doi: 10.1002/pmic.201500161. PMID: 26287124.

21

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*.

Journal of Proteome Research. 2015 Sep 4;14(9):3982-95. doi: 10.1021/acs.jproteome.5b00443. PMID: 26260330.

20

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, Silke Gillessen, Markus Joerger, Wolfram Jochum, Ruedi Aebersold*.

Nature Medicine. 2015 Apr;21(4):407-13. doi: 10.1038/nm.3807. PMID: 25730263.

19

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. doi: 10.1038/ni.3125. PMID: 25751747.

18

Mass spectrometry-based proteomic quest for diabetes biomarkers

Shiying Shao*, Tiannan Guo, Ruedi Aebersold*.

Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics. 2015 Jun;1854(6):519-27. doi: 10.1016/j.bbapap.2014.12.012. PMID: 25556002.

17

Quantitative proteomics reveals differential biologicalprocesses in healthy neonatal cord neutrophils and adultneutrophils

Jiang Zhu#, Huoming Zhang*#, Tiannan Guo, Wenying Li, Huiyu Li,YiZhu and Shi’ang Huang*

Proteomics. 2014 Jul;14(13-14):1688-97. doi: 10.1002/pmic.201400009. PMID: 24782442.

16

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. doi: 10.1038/sdata.2014.31. PMID: 25977788.

15

LEO1 is regulated by PRL-3 and mediates its oncogenic properties in Acute Myeloid Leukemia

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. doi: 10.1158/0008-5472.CAN-13-2321. PMID: 24686170.

14

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 Jun 7;12(6):2525-36. doi: 10.1021/pr301113c. PMID: 23621870.

13

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):3405-13. doi: 10.1021/pr300212g. PMID: 22533479.

12

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. 790(5): 287-303. doi: 10.1007/978-1-61779-319-6_22. PMID: 21948423.

11

Investigation of POPX2 Phosphatase Functions by Comparative Phosphoproteomic Analysis

Singh P, Gan CS, Guo T, Phang HQ, Sze SK, Koh CG*.

Proteomics. 2011 Jul;11(14):2891-900. doi: 10.1002/pmic.201100044. PMID: 21656682.

10

Simultaneous Analysis of Proteome, Phospho- and Glycoproteome of Rat Kidney Tissue with Electrostatic Repulsion Hydrophilic Interaction Chromatography

Piliang Hao, Tiannan Guo, Siu Kwan Sze*

PloS One. 2011 Feb 23;6(2):e16884. doi: 10.1371/journal.pone.0016884. PMID: 21373199.

09

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 Jun;68(11):1983-2002. doi: 10.1007/s00018-010-0545-x. PMID: 20953656.

08

Quantitative Proteomics Discloses MET Expression in Mitochondria as a Direct Target of MET Kinase Inhibitor in Cancer Cells

Tiannan Guo, Yi Zhu, Chee Sian Gan, Sze Sing Lee, JiangZhu, Haixia Wang, Xin Li, James Christensen, Shiang Huang, Oi Lian Kon*, Siu Kwan Sze*.

Molecular & Cellular Proteomics. 2010 Dec;9(12):2629-41. doi: 10.1074/mcp.M110.001776. PMID: 20713453.

07

Novel Application of Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) in Shotgun Proteomics: Comprehensive Profiling of Rat Kidney Proteome

Piliang Hao, Tiannan Guo, Xin Li, Sunil S. Adav, Jie Yang, Meng Wei, and Siu Kwan Sze*

Journal of Proteome Research. 2010 Jul 2;9(7):3520-6. doi: 10.1021/pr100037h. PMID: 20450224.

06

Simultaneous characterization of glyco- and phospho-proteomes of mouse brain membrane proteome with electrostatic repulsion hydrophilic interaction chromatography (ERLIC)

Huoming Zhang, Tiannan Guo, Xin Li, Arnab Datta, Jung Eun Park, Jie Yang, Sai Kiang Lim, James P. Tam, Siu Kwan Sze*.

Molecular & Cellular Proteomics. 2010 Apr;9(4):635-47. doi: 10.1074/mcp.M900314-MCP200. PMID: 20047950.

05

Elucidating in vivo structural dynamics in integral membrane protein by hydroxyl radical footprinting

Yi Zhu, Tiannan Guo, Jung Eun Park, Xin Li, Wei Meng, Arnab Datta, Marshall Bern, Sai Kiang Lim, Siu Kwan Sze*.

Molecular & Cellular Proteomics. 2009 Aug;8(8):1999-2010. doi: 10.1074/mcp.M900081-MCP200. PMID: 19473960.

04

Elucidating the structure of cyclotide by partial acid hydrolysis and LC-MS/MS analysis

Siu Kwan Sze*, Wei Wang, Wei Meng, Randong Yuan, Tiannan Guo, Yi Zhu, James P. Tam*.

Analytical Chemistry. 2009 Feb 1;81(3):1079-88. doi: 10.1021/ac802175r. PMID: 19178340.

03

One-step procedure for peptide extraction from in-gel digestion sample for mass spectrometric analysis

Wei Meng, Huoming Zhang, Tiannan Guo, Chhiti Pandey, Yi Zhu, Oi Lian Kon, Siu Kwan Sze*.

Analytical Chemistry. 2008 Dec 15;80(24):9797-805. doi: 10.1021/ac801344z. PMID: 18986172.

02

Hybridization of Pulsed-Q Dissociation and Collision-Activated Dissociation in Linear Ion Trap Mass Spectrometer for iTRAQ Quantitation

Tiannan Guo, Chee Sian Gan, Huoming Zhang, Yi Zhu, Oi Lian Kon, Siu Kwan Sze*.

Journal of Proteome Research. 2008 Nov;7(11):4831-40. doi: 10.1021/pr800403z. PMID: 18837533.

01

A Comparative Study of Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) versus SCX-IMAC-Based Methods for PhosphopeptideIsolation/Enrichment

Chee Sian Gan, Tiannan Guo, Huoming Zhang, Sai Kiang Lim, Siu Kwan Sze*.

Journal of Proteome Research. 2008 Nov;7(11):4869-77. doi: 10.1021/pr800473j. PMID: 18828627.