Proteomics Core Lab

Committee members:

Institute of Plant and Microbial Biology

Assistant Research Specialist:

Research Assistant:

  • Chin-Wen Chen
  • Pei-Yi Lin
  • Ting-An Chen

Contact phone number:

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



  • A227, Agricultural Technology Building

Protein identification

A bottom-up method using mass spectrometry to identify the amino acid sequences of interested proteins. Samples from solution, IP beads, or polyacrylamide gels are digested using different proteases (Lys-C, trypsin, Glu-C, or chymotrypsin) into peptides. Digested peptides are concentrated, purified using C18 StageTip, and analyzed using nano liquid chromatography tandem mass spectrometry (nano LC-MS/MS). For solution samples, samples with detergents such as NP-40, Triton-X, and PEG are not MS-compatible.  Samples containing these detergents have to be run in a polyacrylamide gel to eliminate the interferences. We can work with SDS-containing samples, please contact the core for more detailed information. The MS analysis time and loading amount can be adjusted according to sample complexity. The identified peptides are reassembling into proteins by proteomics search engine, and the results are returned to the users via Excel file.

The protein ID services include:

  • Enzymatic digestion (in solution or in gel digestion)
  • Peptide purification and concentration (C18 desalting)
  • A quality control run (digested BSA or Hela cells)
  • LC-MS/MS analysis (DDA mode)
  • Database search (Proteome Discoverer and Mascot)
  • Results returned via Excel file