62

Bioinformatics. 2021.37(Suppl_1):i245-i253.10.1093/bioinformatics/btab311.

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*

61

Advanced Drug Delivery Reviews. 25 June 2021 10.1016/j.addr.2021.113844

High-Throughput Proteomics and AI for Cancer Biomarker Discovery.

Qi Xiao, Fangfei Zhang, Luang Xu, Liang Yue, Oi Lian Kon, Yi Zhu*,Tiannan Guo*

60

Cancer letters. Accepted:10.1016/j.canlet.2021.05.002

The Hippo-TAZ axis mediate vascular endothelial growth factor C in glioblastoma-derived exosomes to promote angiogenesis.

Zhengmin Wang#, Yifan Yuan, Xiong Ji, Xing Xia, Zhujun Li, Xiao Yi, Yi Zhu, Tiannan Guo, Yin Wang, Liang Chen*, Ying Liu*

59

BioRxived: April 09, 2021 10.1101/2021.04.08.438976

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*

57 COVID-19 Research

Proteomics. Accepted 10.1002/pmic.202100002

Proteomic and Metabolomic Investigation of COVID-19 Patients with Elevated Serum Lactate Dehydrogenase.

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*

56

Bioinformatics. 2021.37(2):273-275.10.1093/bioinformatics/btaa1088

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*

55

BioRxived: Nov 25, 2020 10.1101/2020.11.24.395426

Optimization of Spectral Library Size Improves DIA-MS Proteome Coverage.

Weigang Ge #, Xiao Liang #, Fangfei Zhang #, Luang Xu, Nan Xiang, Rui Sun, Wei Liu, Zhangzhi Xue, Xiao Yi, 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*

54 COVID-19 Research

Cell. 2021. 184(3): 775-791. doi: 10.1016/j.cell.2021.01.004

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*

53 COVID-19 Research

Computational and Structural Biotechnology Journal. 2021. 19: 3640-3649. doi: 10.1016/2021.06.22.

Eleven Routine Clinical Features Predict COVID-19 Severity.

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*

52 COVID-19 Research

MedRxived: June 17, 2020 10.1101/2020.06.14.20131078

Proteomics Uncovers Immunosuppression in COVID-19 Patients with Long Disease Course.

Shaohua Tang#, Rui Sun#, Qi Xiao#, Tingting Mao#, Weigang Ge#, Chongquan Huang#, Meng Luo, Liujia Qian, Hao Chen, Qiushi Zhang, Sainan Li, Wei Liu, Shufen Li, Xueqin Xu, Huangzheng Li, Lianpeng Wu, Jianyi Dai, Huanhuan Gao, Lu Li, Tian Lu, Xiao Liang, Xue Cai, Guan Ruan, Kexin Liu, Fei Xu, Yan Li, Yi Zhu*, Jianping Huang*, Tiannan Guo*

51 COVID-19 Research

Journal of Genetics and Genomics. Accepted. 10.1101/2020.04.22.20076091

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*

50 Representative Publication

MedRxived: April 14, 2020 10.1101/2020.04.09.20059741

Protein Classifier for Thyroid Nodules Learned from Rapidly Acquired Proteotypes.

Yaoting Sun#, Sathiyamoorthy Selvarajan#, Zelin Zang#, Wei Liu#, Yi Zhu#, Hao Zhang#, Hao Chen, Xue Cai, Huanhuan Gao, Zhicheng Wu, Lirong Chen, Xiaodong Teng, Yongfu Zhao, Sangeeta Mantoo, Tony Kiat-Hon Lim, Bhuvaneswari Hariraman, Serene Yeow, Syed Muhammad Fahmy Syed Abdillah, Sze Sing Lee, Guan Ruan, Qiushi Zhang, Tiansheng Zhu, Weibin Wang, Guangzhi Wang, Junhong Xiao, Yi He, Zhihong Wang, Wei Sun, Yuan Qin, Qi Xiao, Xu Zheng, Linyan Wang, Xi Zheng, Kailun Xu, Yingkuan Shao, Kexin Liu, Shu Zheng, Ruedi Aebersold, Stan Z. Li*, Oi Lian Kon*, N. Gopalakrishna Iyer*, Tiannan Guo*.

49 COVID-19 Research

Cell. 2020. 182(1): 59-72. doi:10.1016/j.cell.2020.05.032

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 *.

48

Journal of Proteome Research. December 18, 2020 10.1021/acs.jproteome.0c00488

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 *.

47

Genome Biology. 14 Dec. 2020,21(302) 10.1186/s13059-020-02188-9

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, View ORCID ProfileYi Judy Zhu, Maria Rodriguez Martinez, Matteo Manica, Michael C Haffner, Ruedi Aebersold*, Peter J Wild*, Andreas Beyer*.

46 Representative Publication

Journal of American Society of Mass Spectrometry. (2020) 10.1021/jasms.0c00254

Phenotype Prediction using a Tensor Representation and Deep Learning from Data Independent Acquisition Mass Spectrometry.

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 *.

45

Proteomics. Invited. Online: 29 July 2020 10.1002/pmic.201900358

Generating Proteomic Big Data for Precision Medicine.

Liang Yue #, Fangfei Zhang #, Rui Sun, Yaoting Sun, Chunhui Yuan, Yi Zhu, Tiannan Guo*.

44 Review Highlight

Proteomics 2020, e1900276. Invited Review 10.1002/pmic.201900276

Data-Independent Acquisition Mass Spectrometry and Software Tools: a Glimpse in 2020.

Fangfei Zhang, Weigang Ge, Guan Ruan, Xue Cai,Tiannan Guo*.

43 Technological Highlight

Journal of Proteome Research. 10.1021/acs.jproteome.0c00381 Online. 25th Sept 2020

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 *.

42

Journal of Proteome Research. 2020, 19(7), 2732-2741. 10.1021/acs.jproteome.9b00671

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 *.

41 Technological Highlight

Journal of Proteome Research. 2020, 19(5), 1982-1990. 10.1021/acs.jproteome.9b00790

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 *.

40

Journal of Extracellular Vesicles. 2020, 9(1) 1750202. 10.1080/20013078.2020.1750202

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*.

39 Technological Highlight

Genomics, Proteomics and Bioinformatics. online 2020 Aug 12 10.1016/j.gpb.2019.11.008

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 *.

38

iScience. 2019, 21:664-680. 10.1016/j.isci.2019.10.059

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 *.

37

Scientific Data. 6, Article number: 278 (2019) 10.1038/s41597-019-0294-0

Arabidopsis Proteome and the Mass Spectral Assay Library.

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

36 Representative Publication

Molecular Oncology. 2019. 13 (11) :2305-2328. 10.1002/1878-0261.12570

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 *.

35

Journal of Proteomics. 2019 Jul 16;206:103446. 10.1016/j.jprot.2019.103446

Proteomic investigation of intra-tumor heterogeneity using network-based contextualization.

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

34

Nature Communications 10, Article number: 2524, 2019. 10.1038/s41467-019-10513-5

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 *.

33

Theranostics. 2019; 9(9):2475-2488. 10.7150/thno.31144

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 *.

32

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

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 *.

31

Life Science Alliance. 29 May 2018. 1(2) 10.26508/lsa.201800042

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 *.

30

Sci China Life Sci. 2018 Mar;61(3):351-354. Invited contribution. 10.1007/s11427-017-9113-5

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

Yi Zhu, Tiannan Guo *.

29

Methods Mol Biol. 2017 Oct 26. Invited contribution. 10.1007/7651_2017_87

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

Yi Zhu, Tiannan Guo *.

28

J Proteome Res. 2017 Jun 2;16(6):2282-2293. 10.1021/acs.jproteome.7b00154

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

27 Representative Publication

Nature Medicine. 2015. 21, 407-413. 10.1038/nm.3807

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.

26

Scientific Data. 2017. 10.1038/sdata.2017.14

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.

25

Cancer Cell. Published online 24 May 2016. 10.1016/j.ccell.2016.04.012

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.

24

J Proteome Res. 2016 May 10. 10.1021/acs.jproteome.5b01136

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.

23

J Proteome Res. 2016 Dec 15. 10.1021/acs.jproteome.6b00748

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.

22

Scientific Reports. 6, Article number: 24146 (2016). 10.1038/srep24146

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.

21

Nature Immunology. 2015 May;16(5):505-16. 10.1038/ni.3125

Ezh2 Controls Cell Adhesion and Migration through Direct Methylation of Extra-Nuclear 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.

20

Proteomics. 2015 Nov;15(21):3711-21. 10.1002/pmic.201500161

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.

19

Biol Direct. 2015 Dec 15;10:71. 10.1186/s13062-015-0098-x

Quantitative proteomics signature profiling based on network contextualization.

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

18

J Proteome Res. 2015 Sep 4;14(9):3982-95. 10.1021/acs.jproteome.5b00443

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.

17

Biochim Biophys Acta -- Proteins and Proteomics. 2015 Jun;1854(6):519-27. 10.1016/j.bbapap.2014.12.012

Mass spectrometry-based proteomic quest for diabetes biomarkers.

Shao S, Guo T, Aebersold R.

16

Scientific Data. 2014 Sep 16;1:140031. 10.1038/sdata.2014.31

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.

15

Journal of Proteome Research. 2012 Jun 1;11(6):3405 10.1021/pr300212g

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 *.

14

Cellular and Molecular Life Sciences 2011. 68(11):1983-2002. 10.1007/s00018-010-0545-x

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 *.

13

Molecular & Cellular Proteomics. 2010. 9(12):2629-41. 10.1074/mcp.M110.001776

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.

12

Journal of Proteome Research, 2008, 7(11):4831-4840. 10.1021/pr800403z

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.

11

Cancer Research. 2014 Jun 1;74(11):3043-53. 10.1158/0008-5472.CAN-13-2321

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.

10

Journal of Proteome Research, 2013. 12(6):2525-36. 10.1021/pr301113c

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.

9

Proteomics. 2011. 11:2891-2900. 10.1002/pmic.201100044

Investigation of POPX2 Phosphatase Functions by Comparative Phosphoproteomic Analysis.

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

8

PLoS ONE 2011. 6(2): e16884. 10.1371/journal.pone.0016884

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

Hao P, Guo T, Sze SK.

7

Methods in Molecular Biology 2011, Volume 790, Part 5, 287-303. 10.1007/978-1-61779-319-6_22

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.

6

Molecular & Cellular Proteomics. 2010. Apr;9(4):635-47. 10.1007/978-1-61779-319-6_22

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.

5

Molecular & Cellular Proteomics. 2009. 8:1999-2010. 10.1074/mcp.M900081-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.

4

Journal of Proteome Research. 2010, 9 (7), 3520-3526. 10.1021/pr100037h

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.

3

Analytical Chemistry. 2009. 81(3):1079-88. (*corresponding authors) 10.1021/ac802175r

Elucidating 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*.

2

Journal of Proteome Research, 2008. 7(11): 4869-4877. 10.1021/pr800473j

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.

1

Analytical Chemistry, 2008. 80(24): 9797-9805. 10.1021/ac801344z

A 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.