Proteomics Core Lab

Committee members:

Institute of Plant and Microbial Biology

Assistant Research Specialist:

Research Assistant:

  • Chin-Wen Chen
  • Hsiao-Jung Yen

Contact phone number:

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



  • A227, Agricultural Technology Building


The Proteomics Core Laboratory(Institute of Plant and Microbial Biology/Agricultural Biotechnology Research Center) provides LC-MS/MS based proteome qualitative and quantitative analyses by using shotgun approach, including protein identification, post-translation modification analysis, and isobaric tagging of tryptic peptides for quantitative proteome analysis. The core laboratory also keeps and maintains required equipment and software for protein 2-dimensional gel electrophoresis and 2-D protein gel image analysis. The core laboratory also intends to establish and develop new proteomic methods, such as techniques for quantitative proteomics, multidimensional LC, phosphopeptide enrichment, phosphorylation site analysis, and target protein analysis and quantification, to provide more advanced techniques for our colleagues in proteomics studies. The laboratory provides a good resource of training and consultation of modern proteomic techniques for our colleagues.


  • nLC-nESI-MS/MS system (Thermo Q Exactive MS, Dionex nanoUHPLC)
  • High performance liquid chromatography (HPLC, Agilent 1200)
  • 2-dimensional PAGE system (Ettan IPGphor 3 for IEF, Protean II XL Multi-Cell and Ettan DALTsix Electrophoresis Unit for SDS-PAGE)
  • Gel image scanner (Typhoon 9400 Scanner, ImageScanner III)
  • Software for 2-D gel analysis (ImageMaster 2-D Platinum v.7.0, PDQuest, v.7.3)
  • Software for 2-D DIGE analysis (DeCyder 2-D differential Analysis v. 5.0)
  • Software for MS data analysis and protein identification (Mascot Server v.2.5, Proteome Discoverer v.2.1)

Selected Publications

Lan P, Li W, Wen TN, and Schmidt W. (2012) Quantitative phosphoproteome profiling of iron-deficient Arabidopsis roots. Plant Physiol. 159:403-417.

Hsu CA, Wen TN, Su YC, Jiang ZB, Chen CW, and Shyur LF. (2012) Biological degradation of anthroquinone and Azo dyes by a novel laccase from Lentinus sp. Environ Sci Technol 46:5109-5117.

Lo YS, Cheng N, Hsiao LJ, Annamalai A, Jauh GY, Wen TN, Dai H, and Chiang KS. (2011) Actin in mung bean mitochondria and implications for its function. Plant Cell 23:3727-3744.

Lan P, Li W, Wen TN, Shiau JY, Wu YC, Lin W, and Schmidt W. (2011) iTRAQ protein profile analysis of Arabidopsis roots reveals new aspects critical for iron homeostasis. Plant Physiology. 155:821–834.

Lee WL, Wen TN, Shiau JY, and Shyur LF. (2010) Differential Proteomic Profiling Identifies Novel Molecular Targets of Paclitaxel and Phytoagent Deoxyelephantopin against Mammary Adenocarcinoma Cells. Journal of Proteome Research. 9:237–253.