Protein Identification

Location: Thomas Building, DE-352
Contact phone: (206) 667-1051, (206) 667-2872
Contact e-mail: proteomics@fredhutch.org

Proteins are identified through the bottom-up proteomics scheme. Purified proteins or mixtures of proteins in solution or SDS-PAGE gels are digested with a protease, typically trypsin, and the proteolytic peptides are subjected to tandem mass spectrometry (MS/MS). The resulting MS/MS data are compared to protein databases via automated protein database searching to identify the proteins that contain the peptides detected by the mass spectrometer.

The higher the amount of protein available for use the higher the likelihood for successful identification; however, the identification of a single protein at 1-10 ng level is possible.

Sample Preparation

Sample preparation involves cutting bands from SDS-PAGE gels, proteolytic digestion, and sample desalting or proteolytic solution digestions and sample desalting. 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. 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