Protein Modification (PTM) Analysis

Process At A Glance

  • Discuss experiment with Proteomics staff
  • Prepare sample
  • Complete service 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: proteomics@fredhutch.org

Loading Appartus for Mass SpectrometryProtein modifications that result in mass increases or losses to proteins are readily detectable by mass spectrometry. The facility has extensive experience with characterizing acetylation, methylation, and phosphorylation modifications. Since there are over 300 known protein modifications, the Proteomics Facility should be consulted during the design-phase of experiments in order to develop the appropriate strategy for mass spectrometric analysis of the modification.

Sample Preparation

A number of sample preparation approaches are used for PTM analysis. Peptide mapping to locate protein modification sites (e.g. in vitro kinase experiments) often involves cutting purified/enriched bands from SDS-PAGE gels, proteolytic digestion, and sample desalting. For large-scale PTM analysis (e.g., phosphoproteomics), solution digestion, chromatographic fractionation, PTM enrichment, and desalting are typically required. 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.