Proteomics Core Lab

Committee members:

Institute of Plant and Microbial Biology

Assistant Research Specialist:

Research Assistant:

  • Chin-Wen Chen
  • Ying-Mi Lai
  • Pei-Yi Lin

Contact phone number:

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



  • A227, Agricultural Technology Building

Targeted peptide (SRM/PRM)

Targeted Proteomics analyzes specific peptides of an interested protein in a complex proteome. The purpose is to determine whether the targeted protein is presented (if it is above our detection limit) in your sample and the relative and/or absolute quantity in one sample or across multiple samples.

Targeted Proteomics analysis is a mass spectrometer version of a western blot, but this approach is not only far more accurate but also antibody-free. Data is acquired through Parallel Reaction Monitoring (PRM) technology which is integrated in our mass spectrometer. PRM approach firstly selects the peptides which are digested from your interested protein and then fragments them to generate fragmented product ions. The characteristic fragmented ions of interested peptides are selected as spectral library, so it requires preliminary runs to optimize and to build the library.

Here are some examples that you would utilize PRM method:

  • Verify your knockdown target is actually knocked down.
  • Quantify the expression level of a specific protein across samples or a time course experiment.
  • Detect different protein isoforms.
  • Validate DDA results for abundance changes.

The targeted peptide services include:

  • Enzymatic digestion (trypsin or other proteases available)
  • Peptide purification and concentration (C18 desalting)
  • Build the spectral library (fragmented ions intensities and retention time)
  • A quality control run (digested BSA or Hela cells)
  • LC-MS/MS analysis (PRM method)
  • Database search (Proteome Discoverer and Mascot)
  • Data analysis (Skyline software)
  • Results returned via Excel and PPT files