Yu-Ju Chen, Ph.D. Stem Cell Proteomics

Yu-Ju Chen, Ph.D.
Stem Cell Proteomics 
 Email: yjchen@chem.sinica.edu.tw
 Related Links:

 Lab Web Site at Academia Sinica

 Selected Publications 

 Recent advancements in quantitative proteomics hold promise to facilitate system-wide delineation of stem cells. In this sub-project, we developed new strategies for quantitative profiling of membrane proteome and phosphoproteome. The current progress included (1) a new label-free methodology (2) phosphoproteomics study on neural stem cell differentiation.

  1. We developed a simple and robust “SEMI label-free strategy” that integrates our recently published gel-assisted digestion, a highly specific and reproducible automatic pH/acid controlled IMAC and LC-MS/MS analysis. Without isotope labeling, the multiplexed quantitation platform demonstrated 4000-fold dynamic range, better than 20% of accuracy and precision in the proteome scale; more than 500 phosphoproteins can be simultaneously quantified in single LC-MS/MS. 
  2. To understand the selection of cell fates by pathway signaling and transcriptional mechanisms in neuron differentiation, we analyzed the phosphoproteome of human embryonal carcinoma NTera-2 cells upon Oct-4 silencing and astrocytic differentiation. The preliminary data quantified 646 phosphoproteins/ 1231 phosphopeptides; more than 50 % phosphorylation sites have differential levels after OCT4 stimulation. Many of these differentially phosphorylated proteins are associated with function in neuron differentiation, cell differentiation and transcription regulation, which remain further validation in the future. 

Associate Research Fellow, 
Institute of Chemistry 
Education and Positions 

  • B.S., National Taiwan University
  • Ph.D., Iowa State University, USA 
  • Postdoctoral Research Associate, Ames Laboratory, U.S.A.
  • Postdoctoral Research Associate, National Tsing Hua University 

Honors and Awards 

  • Outstanding Young Investigator Award, Chemical Society Located in Taipei (2006); 
  • Distinguished Young Chemist Award, Federation of Asian Chemical Societies (2007). 
  • Research Award for Junior Research Investigators, Academia Sinica, 2008
  • Wu Ta-You memorial award, National Science Council, 2008.