Proteomics Core Lab

Committee members:

Institute of Plant and Microbial Biology

Assistant Research Specialist:

Research Assistant:

  • Chin-Wen Chen
  • Ying-Mi Lai
  • Pei-Yi Lin

Contact phone number:

  • 02-27871157 (Chuan-Chih)
  • 02-27871030 (Lab)



  • A227, Agricultural Technology Building

Welcome to the web home of the Proteomics Core Laboratory (PCL) in the Institute of Plant and Microbial Biology. The Proteomics Core provides state-of-the-art liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomic services to researchers throughout Institute of Plant and Microbial Biology (IPMB) and Agricultural Biotechnology Research Center (ABRC).  The Proteomics Core offers a variety of services including protein identification, quantifying protein expression levels, identifying post-translational modifications, protein interactome mapping, large-scale (phospho)proteomics profiling, targeted proteomics analysis, and sample preparation from a broad range of organisms such as plants, bacteria, and fungi. Currently the Proteomics Core has three well-trained scientists and in operation a Q-Exactive mass spectrometer. We have various proteomics software resources including Mascot Server, Proteome Discoverer, MaxQuant, and Skyline.

Our mission is to use cutting-edge proteomics technologies to reveal a deeper understanding of plant and microbial biology. Our discovery and targeted proteomics will assist researchers to accelerate their research timelines and to provide the key insights they need to move forwards. We are interested in developing new proteomic approaches and implementing these methods to study unique scientific projects. We also provide user training and consultation of modern proteomic techniques for our colleagues.


Discovery Proteomics

Targeted Proteomics

Service Rates

  • IPMB and ABRC users
  • External users please discuss with Chuan-Chih Hsu for more detailed information

Sample Analysis Workflow

  • Project Set-up
    1. Researcher meets with PCL scientists to discuss the project objective
    2. PCL scientists determine the most suitable strategies to analyze samples
  • Project Execution
    1. Researcher submits the form and brings samples to PCL
    2. PCL completes sample preparation and LC-MS/MS analysis
  • Project Reporting and billing
    1. PCL sends data report to researchers upon project completion
    2. PCL sends bills to researchers and researchers pay the bills

Sample Submission Form


Useful Links/Tools

Selected Publications

  • Publications from the PCL users
  1. Wong MM, Bhaskara GB, Wen TN, Lin WD, Nguyen TT, Chong GL, Verslues PE. (2020) Phosphoproteomics of Arabidopsis Highly ABA-Induced1 identifies AT-Hook-Like10 phosphorylation required for stress growth regulation. Proc Natl Acad Sci U.S.A. 116(6):2354-2363.
  2. Kanno T, Venhuizen P, Wen TN, Lin WD, Chiou P, Kalyna M, Matzke AJM, Matzke M. (2018) PRP4KA, a Putative Spliceosomal Protein Kinase, Is Important for Alternative Splicing and Development in Arabidopsis thaliana. Genetics. 210(4):1267-1285.
  3. Bhaskara GB, Wen TN, Nguyen TT, Verslues PE. (2017) Protein Phosphatase 2Cs and Microtubule-Associated Stress Protein 1 Control Microtubule Stability, Plant Growth, and Drought Response. Plant Cell 29(1):169-191.
  4. Rodríguez-Celma J, Tsai YH, Wen TN, Wu YC, Curie C, Schmidt W. (2016) Systems-wide analysis of manganese deficiency-induced changes in gene activity of Arabidopsis roots. Sci. Rep. 6:35846.
  5. Cho HY, Wen TN, Wang YT, Shih MC. (2016) Quantitative phosphoproteomics of protein kinase SnRK1 regulated protein phosphorylation in Arabidopsis under submergence. J. Exp. Bot. 67(9):2745-60.
  • Publications from Chuan-Chih
  1. Wang, P.*; Hsu, C.-C.*; Du, Y.; Zhu, P.; Zhao, C.; Fu, X.; Zhang, C.; Paez, J. S.; Macho, A. P.; Tao, W. A.; Zhu, J.-K. (2020) Mapping proteome-wide targets of protein kinases in plant stress responses. Natl. Acad. Sci. U.S.A. 117 (6), 3270-3280.
  2. Hsu, C.-C.; Tsai, C.-F.; Tao; W. A.; Wang, P. (2020) Phosphoproteomic Strategy for Profiling Osmotic Stress Signaling in Arabidopsis J. Vis. Exp. 160, e61489.
  3. Kim, T.-W.*; Park, C. H.*; Hsu, C.-C.*; Zhu, J.-Y.; Hsiao, Y.; Branon, T.; Xu, S.-L.; Ting, A. Y.; Wang, Z.-Y. (2019) Application of Turbo-ID-mediated proximity labeling for mapping a GSK3 kinase signaling network in Arabidopsis. bioRxiv,
  4. Hsu, C.-C.; Zhu, Y.; Arrington, J. V.; Paez, J. S.; Wang, P.; Zhu, P.; Chen, I.-H.; Zhu, J.-K.; Tao, W. A. (2018) Universal plant phosphoproteomics workflow and its application to tomato signaling in response to cold stress. Mol. Cell. Proteomics 17(10), 2068-2080.
  5. Wang, P.*; Zhao, Y.*; Li, Z.*; Hsu, C.-C.*; Liu, X.; Fu, L.; Hou, Y.-J.; Du, Y.; Xie, S.; Zhang, C.; Gao, M.; Cao, M.; Huang, X.; Zhu, Y.; Tang, K.; Wang, X.; Tao, W. A.; Xiong, Y.; Zhu, J.-K. (2018) Reciprocal regulation of the TOR kinase and ABA receptor balances plant growth and stress response. Mol. Cell 69(1), 100-112.