Protein Quantification

Process At A Glance

  • Discuss experiment with Proteomics staff
  • Prepare sample
  • Complete services request via iLab
  • Submit samples and form
  • Proteomics runs sample
  • Results sent to investigator

Location: Thomas Building, DE-352
Contact phone: (206) 667-1051
(206) 667-2872
Contact e-mail:

Mass spectrometer outputTechniques such as SILAC, iTRAQ, ICAT, and AQUA are available for quantifying proteins and peptides by mass spectrometry. All of the techniques include some form of stable isotope (e.g. carbon-13) incorporation into proteins that is detected by the mass spectrometer and used for quantification. Each quantification technique has its own strengths, limitations and requirements. The Proteomics Facility should be consulted during the design of proteomics experiments to ensure the appropriate technique is selected.

Sample Preparation

A number of methods are possible for preparing samples for quantitative analysis. Solution digestions followed by chromatographic fractionation and gel slice digestion are the most typical methods. Investigators can take their samples through the complete preparation, or the proteomics staff can assist with some steps. If you choose to prepare your own gel samples, see our Tips for SDS-PAGE Gel Handling

Sample Submission

Complete your service request form through iLab or the button link in the right side panel. Submit a copy of your service request with your samples. If you don’t have an account in iLab, you can register for one on the link.

Analysis of Results

Data generated within the resource are analyzed by the software Proteome Discoverer or Protein Pilot.  Viewers for these softwares can be downloaded from the manufacturers.  See “Data Analysis” in the left-hand task bar for more information.