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Department of Chemistry



Professor (joint appointment)
Room B209, Institute of Chemis
Fax: +886-2-2783-1237
Research Interest

  • Advanced bioinformatics-assisted mass spectrometry methods for comprehensive signatures of membrane sub-proteome and its downstream phosphoproteome and S-nitrosoproteome associated with disease.

  • Surface functionalized nanoprobe-based affinity mass spectrometry for multiplexed quantitation of disease-associated protein markers, discovery of post-translational modification in disease and epitope mapping for drug-interacting protein.

Career and Service Experiences

  • B.S., 1992, National Taiwan University.

  • Ph.D., 1997, Iowa State University.

  • Postdoctoral Research Fellow, 1997, Ames Laboratory; 1998-1999, National Tsing-Hua University.

  • Assistant Research Fellow, 1999-2005; Associate Research Fellow, 2005-2010; Research Fellow, 2010-2019; Distinguished Research Fellow, 2019-present; Director, 2013-2019, Institute of Chemistry; Acting Director, 2019-present, Institute of Chemistry; Adjunct Research Fellow, 2004-present, Genomic Research Center, Academia Sinica.

  • President, 2009-2011, Taiwan Proteomics Society.

  • Editorial Board Member, 2008-present, European Journal of Mass Spectrometry.

  • Council Member, 2009-present, AOHUPO.

Honors and Awards

  • Young Chemists Award, The Chinese Chemical Society, 2006.

  • Distinguished Young Chemist Award, Federation of Asian Chemical Societies, 2007.

  • Junior Research Investigators Award, Academia Sinica, 2008.

  • Ta-You Wu Memorial Award, National Science Council, 2008.

  • Outstanding Scholar Award, Taiwan Society for Mass Spectrometry, 2012.

  • Outstanding Research Award, National Science Council, 2012.

Selected Publications

  • Tsai, C.-F.; Hsu, C.-C.; Hung, J.-N.; Wang, Y.-T.; Choong, W.-K.; Zeng, M.-Y.; Lin, P.-Y.; Hong, R.-W.; Sun, T.-Y.; Chen, Y.-J.* “Sequential Phosphoproteomic Enrichment through Complementary Metal-Directed Immobilized Metal Ion Affinity Chromatography” Anal. Chem.201486, 685–693.

  • Lu, Y.-W.; Chien, C.-W.; Lin, P.-C.; Huang, L.-D.; Chen, C.-Y.; Wu, S.-W.; Han, C.-L.; Khoo, K.-H.; Lin, C.-C.*; Chen, Y.-J.* “BAD-Lectins: Boronic Acid-Decorated Lectins with Enhanced Binding Affinity for the Selective Enrichment of Glycoproteins” Anal. Chem. 201385, 8268–8276.

  • Han, C.-L.; Chen, J.-S.; Chan, E.-C.; Wu, C.-P.; Yu, K.-H.*; Chen K.-T.; Tsou, C.-C.; Tsai,C.-F.; Chien, C.-W.; Kuo, Y.-B.; Lin, P.-Y.; Yu, J.-S.; Chen, M.-C.; Chan, C.-C.; Chang, Y.-S.; Chen, Y.-J* “An Informatics-Assisted Label-Free Approach for Personalized Tissue Membrane Proteomics: Case Study on Colorectal Cancer” Mol. Cell. Proteomics 201110, 003087.

  • Obena, R. P.; Lin, P.-C; Lu, Y.-W.; Li, I.-C.; del Mundo, F.; dR Acro, S.; Nuesca, G. M.; Lin, C.-C.; Chen, Y.-J.* ”Iron Oxide Nanomatrix Facilitating Metal Ionization in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry” Anal. Chem. 201183, 9337–9343.

  • Chen, Y.-J.; Ku, W.-C.; Lin, P.-Y.; Chou, H.-C.; Khoo, K.-H.; Chen, Y.-J.* “S-Alkylating Labeling Strategy for Site-Specific Identification of the S-Nitrosoproteome” J. Proteome Res. 20109, 6417–6439.

  • Wang, Y.-T.; Tsai, C.-F.; Hong, T.-C.; Tsou, C.-C.; Lin, P.-Y.; Pan, S.-H.; Hong,T.-M.; Yang, P.-C.; Sung, T.-Y.; Hsu, W.-L.; Chen, Y.-J.* “An Informatics-Assisted Label-Free Quantitation Strategy That Depicts Phosphoproteomic Profiles in Lung Cancer Cell Invasion” J. Proteome Res. 20109, 5582–5597.

  • Ku, W.-C.; Chiu, S.-K.; Chen, Y.-J.; Huang, H.-H.; Wu, W. G.; Chen, Y.-J.* “Complementary Quantitative Proteomics Reveals that Transcription Factor AP-4 Mediates E-box-dependent Complex Formation for Transcriptional Repression of HDM2” Mol. Cell. Proteomics20098, 2034–2050.

  • Lin, P.-C.; Chen, S.-H.; Wang, K.-Y.; Chen, M.-L.; Adak, A.-K.; Hwu, J.-R.; Chen, Y.-J.*; Lin, C.-C.* “Fabrication of Oriented Antibody-Conjugated Magnetic Nanoprobes and Their Immunoaffinity Application” Anal. Chem. 200981, 8774–8782.

  • Chen, Y.-J.; Ku, W.-C.; Feng, L.-T.; Tsai, M.-L.; Hsieh, C.-H.; Hsu, W.-H.; Liaw, W.-F.; Hung, C.-H.*; Chen, Y.-J.* “Nitric Oxide Physiological Responses and Delivery Mechanisms Probed by Water-Soluble Roussin’s Red Ester and {Fe(NO)2}10 DNIC” J. Am. Chem. Soc. 2008130, 10929–10938.

  • Han, C.-L.; Chien, C.-W.; Chen, W.-C.; Chen, Y.-R.; Wu, C.-P.; Chen, Y.-J.* “A Multiplexed Quantitative Strategy for Membrane Proteomics: Opportunities for Mining Therapeutic Targets for Autosomal-Dominant Polycystic Kidney Disease” Mol. Cell. Proteomics 20087, 1983–1997.

Update: 2021-11-15