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陳怡婷(Yi-Ting Chen)

Yi-Ting Chen


Assistant Professor


Ph.D. in Chemistry, National Tsing Hua University, Taiwan


Lab Tel





Biological Mass Spectrometry and Translational Proteomics Laboratory


Biological Mass Spectrometry, Translational Proteomics, Metabolomics, Urologic Oncology

Lab & Research Interest

The major topics of our research group are to develop methods and strategies, primarily based on mass spectrometry (MS), for the detection and quantification of biological molecules, including peptides, proteins, and metabolites. There approaches have been applied to study real-world biological systems including cells, tissues, and body fluids. Our research goals are focused on understanding the basis of molecular oncology of urological system by applying our specialties, including proteomics, metabolomics, biological mass spectrometry, and analytical biochemistry, through independent research ability and international collaboration.

Interest in exploring human proteome has broadened the search for new biomarkers, as well as disease etiology studies. Biomarker discovery in body fluid recently has gained prominence, and numerous investigations have found that levels of specific proteins increase or decrease during disease. One of the main challenges in biomarker discovery is high biological variation between individuals. Therefore, after the discovery phase, potential biomarkers must be verified in a large number of samples. Accurate quantitation of proteins in each sample is part of this verification phase. However, absolute quantitation of numerous proteins in body fluids has not been systematically performed, and their roles as useful “biosignatures” are unknown. This study thus focuses on developing the SISCAP (stable isotope standards and capture by anti-peptide antibodies, namely immuno-MRM-MS) platform to quantitate proteins and peptides in biological specimens. Our lab is responsible for setting up the MRM-MS assay for biomarker verification in a large number of clinical specimens. Using data generated from various techniques of the individual patient combined with large scale modeling of the network of cancer relevant pathways in the individual tumor, a relevant prediction can be deduced towards an individualized therapy for cancer.

Our current research projects include the following topics:

1. Using a Systems Approach to Discover and Assess Urological Cancer Biomarkers.

System approaches for biomarker discovery and mechanism study of urological cancer

2. Targeted and Multiplexed Quantitation of Proteins for Verification of Biomarker Panels using Multiple-Reaction-Monitoring MS (MRM-MS) and immune MRM-MS. (Collaboration with Prof. Christoph Borchers, the Director of the University of Victoria Genome BC Proteomics Centre, Canada; and clinical teams in Chang Gang Memorial Hospital)

Development of MRM-MS assays for protein biomarker verification.

3. Development and Applications of Targeted Proteomic and Metabolomic Approaches in Cancer Biology to study Urological Oncology. (Collaboration with Prof. Liang Li, Department of Chemistry, University of Alberta, Canada).



  1. “MALDI-TOF MS”Yi-Ting ChenY. C. Ling, Instruments Today, 19, 60-70, 1997.
  2. Y. C. Ling, L. Lin and Y. T. Chen, ²Quantitative Analysis of Antibiotics by Matrix-assisted Laser Desorption/Ionization Time-of-flight Mass Spectrometry², Rapid Commun. Mass Spectrometry. 12, 317-327, 1998 (SCI).
  3. Y. T. Chen and Y. C. Ling, ²An Overview of Supercritical Fluid Extraction in Chinese Herbal Medicine:from Preparation to Analysis², Journal of Food and Drug Analysis, Special Issue on Chinese Herbal Medicines, 8, 235-247, 2000 (SCI).
  4. Y. T. Chen and Y. C. Ling, ²Detection of Water-soluble Vitamins by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry using Porphyrin Matrices², J. Mass. Sepctrom. 37, 716-730, 2002 (SCI).
  5. Y. T Chen, C. Y. Tsao, J. M Li, C. Y. Tsai, S. F. Chiu, T. L. Tseng*, ² Large-scale Protein Identification of Human Urine Proteome by Multi-dimensional Liquid Chromatography and Tandem Mass Spectrometry ², Proteomics Clin. Appl. 1, 577-587, 2007 (SCI).
  6. Hui-Chu Hsieh, Yi-Ting Chen, Jen-Ming Li, Ting-Yu Chou, Ming-Fong Chang, See-Chang Huang, Tzu-Ling Tseng, Chung-Cheng Liu, and Sung-Fang Chen*, “Protein Profilings in Mouse Liver Regeneration after Partial Hepatectomy using iTRAQ Technology”. J. Proteome Res. 8, 1004-1043, 2009 (SCI).
  7. Yi-Ting Chen*, Chien-Lun Chen, Hsiao-Wei Chen, Ting Chung, Chih-Ching Wu, Chi-De Chen, Chia-Wei Hsu, Meng-Chieh Chen, Ke-Hung Tsui, Phei-Lang Chang, Yu-Sun Chang, Jau-Song Yu*, ² Discovery of Novel Bladder Cancer Biomarkers by Comparative Urine Proteomics Using iTRAQ Technology ², J. Proteome Research. 9, 5803-5815, 2010 (SCI).
  8. Shih-Yuan Chen, Yi-Ting Chen, Jey-Jau Lee, Soofin Cheng*, Tuning Pore Diameter of Platelet SBA-15 Materials for Enzyme Adsorption, J. Mater. Chem. 21, 5693-5703. 2011 (SCI).
  9. Yi-Ting Chen, Hsiao-Wei Chen, Derek Smith, Kung-Hao Liang, Ting Chung, Chien-Lun Chen, Yu-Sun Chang, Christoph Borchers,* Jau-Song Yu.* Multiplexed quantification of 63 proteins in human urine by multiple reaction monitoring-based mass spectrometry for discovery of potential bladder cancer biomarkers. J. Proteomics. 75, 3529-3545, 2012 (SCI).
  10. Yi-Ting Chen*, Fu-Shing Wang, Zhendong Li, Liang Li*, Yong-Chien Ling*. Development of a Matrix-assisted Laser Desorption Ionization Mass Spectrometric Method for Rapid Process-Monitoring of Phthalocyanine Compounds. Analytica Chimica Acta. 736, 69–77, 2012. (SCI)
  11. Chien-Lun Chen, Yue-Fan Lai,, Kun-Yi Chien, Jau-Song Yu, Hsiao-Wei Chen, Petrus Tang, Chia-Wei Hsu, Chi-De Chen, Yu-Sun Chang, Phei-Lang Chang, Yi-Ting Chen*, Comparative and Targeted Proteomic Analyses of Urinary Exosomes from Bladder Cancer and Hernia Patients. J. Proteome Research. 11, 5611−5629, 2012. (SCI)
  12. Yen-Heng Lin*, Ying-Ju Chen, Chao-Sung Lai*, Yi-Ting Chen, Chien-Lun Chen, Jau-Song Yu, and Yu-Sun Chang, A negative-pressure-driven microfluidic chip for the rapid detection of a bladder cancer biomarker in urine using bead-based enzyme-linked immunosorbent assay. Biomicrofluidics 7, 024103, 2013. (SCI)
  13. Chien-Lun Chen, Tsung-Shih, Lin, Cheng-Han, Tsai, Chih-Ching Wu, Ting Chung,  Kun-Yi Chien, Maureen Wu, Yu-Sun Chang, Jau-Song Yu*, Yi-Ting Chen*, Identification of Potential Bladder Cancer Markers in Urine by Abundant-Protein Depletion Coupled with Quantitative Proteomics. J. Proteomics. 85, 28-43, 2013. (SCI)
  14. Chi-De Chen, Chih-Liang Wang, Chia-Jung Yu, Kun-Yi Chien, Yi-Ting Chen, Min-Chi Chen, Yu-Sun Chang, Chin-Ching Wu*, Jau-Song Yu*. Targeted Proteomics Pipeline Reveals Potential Biomarkers forthe Diagnosis of Metastatic Lung Cancer in Pleural Effusion. J. Proteome Research. 13(6):2818-29, 2014.
  15. Jun Peng, Yi-Ting Chen, Chien-Lun Chen and Liang Li, Development of a Universal Metabolome-Standard Method for Long-term LC-MS Metabolome Profiling and Its Application for Bladder Cancer Urine-Metabolite-Biomarker Discovery. Anal. Chem. 86(13):6540-7, 2014.
  16. Chiun-Gung Juo*, Chien-Lun Chen, Shiang-Ting Lin, Shu-Hsuan Fu, Yi-Ting Chen, Yu-Sun Chang and Jau-Song Yu. Mass accuracy improvement of ESI-RPLC-MS based urinary metabolomic analysis by post-run calibration using sodium formate cluster ions. Rapid Commun. Mass Spectrom. 28, 1813-1820, 2014.
  17. Hsiao-Chien Chen, Yi-Ting Chen, Rung-Ywan Tsai, Min-Cheng Chen, Shi-Liang Chen, Min-Cong Xiao, Chien-Lun Chen, Mu-Yi Hua*. A sensitive and selective magnetic graphene composite-modified polycrystalline-silicon nanowire field-effect transistor for bladder cancer diagnosis. Biosensors and Bioelectronics. 66, 198–207, 2015 . (Co-first author)
  18. Yi-Ting Chen, Li-Ping Tuan, Hsiao-Wei Chen, I-An Wei, Min-Yuan Chou, Han-Min Chen,  Yu-Chang Tyan, Sung-Fang Chen*. Quantitative analysis of prostate specific antigen isoforms using immunoprecipitation and isotope dilution mass spectrometry. Anal. Chem. 2015, 87(1):545-53. (Co-first author)
  19. Chien-Lun Chen, Ting Chung, Chih-Ching Wu, Kwai-Fong Ng, Jau-Song Yu, Cheng-Han Tsai, Yu-Sun Chang, Ying Liang, Yi-Ting Chen*. Comparative tissue proteomics of microdissected specimens reveals novel biomarkers of bladder cancer. Mol. Cell Proteomics. 2015. 14(9), 2466-2478. (Co-first and corresponding author)
  20. Chih-Hsiang Chang, Chia-Hung Yang, Huang-Yu Yang, Tien-Hsing Chen, Chan-Yu Lin, Su-Wei Chang, Yi-Ting Chen, Cheng-Chieh Hung, Ji-Tseng Fang, Chih-Wei Yang, Yung-Chang Chen*. Urinary Biomarkers Improve the Diagnosis of Intrinsic Acute Kidney Injury in Coronary Care units. Medicine. 2015 Oct;94(40):e1703.
  21. Chih-Hsiang Chang, Pei-Chun Fan, Chan-Yu Lin, Chia-Hung Yang, Yi-Ting Chen, Su-Wei Chang, Huang-Yu Yang, Chang-Chyi Jenq, Cheng-Chieh Hung, Chih-Wei Yang, and Yung-Chang Chen. Elevation of Interleukin-18 Correlates with Cardiovascular, Cerebrovascular, and Peripheral Vascular Events: A Cohort Study of Hemodialysis Patients. Medicine. 2015 Oct;94(42):e1836.
  22. Cheng-Hung Lee , Kuo-Sheng Liu , Shang-Hung Chang , Wei-Jan Chen , Kuo-Chun Hung , Shih-Jung Liu* , Jong-Hwei S. Pang , Jyuhn-Huarng Juang , Chou Chung-Chuan , Po-Cheng Chang , Yi-Ting Chen , Fu-Shing Wang. Promoting Diabetic Wound Therapy Using Biodegradable rhPDGF-loaded Nanofibrous Membranes: CONSORT-Compliant Article. Medicine. 2015 Nov;94(47):e1873.
  23. Chia-Hung Yang, Chih-Hsiang Chang, Tien-Hsing Chen, Pei-Chun Fan, Su-Wei Chang, Chun-Chi Chen, Pao-Hsien Chu, Yi-Ting Chen, Huang-Yu Yang, Chih-Wei Yang, Yung-Chang Chen. Combination of Urinary Biomarkers Improve Early Detection of Acute Kidney Injury in Patients with Heart Failure. Circulation Journal, Accepted, 2016.

Book Chapter

  1. Yi-Ting Chen, Carol E. Parker, Hsiao-Wei Chen, Chien-Lun Chen, Dominik Domanski, Derek S. Smith, Chih-Ching Wu, Ting Chung, Kung-Hao Liang, Min-Chi Chen, Yu-Sun Chang, Christoph H. Borchers, and Jau-Song Yu. " Comprehensive Biomarker Discovery and Validation for Clinical Application- A Pipeline that Integrates the Discovery and Verification Studies of Urinary Protein Biomarkers Reveals Candidate Markers for Bladder Cancer". Royal Society of Chemistry (RSC). 2013,0, 271-314. ISBN: 978-1-84973-422-6.


Patent title


Patent No.










Urine and serum biomarkers associated with diabetic nephropathy




Urine and serum biomarkers associated with diabetic nephropathy




Biomarkers associated with nephropathy


US 8,470,547






Urine and serum biomarkers associated with diabetic nephropothy




Biomarkers associated with nephropathy














ZL 2010 8 0005751.2