Duke Proteomics Core Facility
The School of Medicine, the Institute for Genome Sciences & Policy, and the Duke Comprehensive Cancer Center have collaboratively created a Proteomics Core Facility to provide protein characterization resources for the Duke Research Community. These services include protein identification and protein quantitation from a wide variety of sample types from simple mixtures (gel spots and bands) to complex mixtures (protein complexes, cell lysates, and plasma). The facility is located in room B02 (basement) of the Levine Science Research Center.
The Duke Proteomics Core Facility uses mass spectrometry as the key technology for the qualitative and quantitative characterization of proteins. Our principal approach for the analysis of proteins is 'bottom-up' proteomics, where all proteins are proteolytically digested, producing peptide surrogates (signature peptides) of the original proteins.
Protein identifications are made using state-of-the-art database search engines running on a dedicated high speed Blade cluster, with the capability of searching standard or custom protein databases.
Protein quantitation can be accomplished using a 'gel free, label-free' technology which provides both relative quantitation (test vs. control) and absolute quantitation (nanograms protein). Alternatively, isotope-coded (labeled) samples can be analyzed to provide relative quantitation information.
Proteomics capabilities currently offered
- open (unbiased) qualitative and quantitative analyses using high resolution, accurate mass data for high confidence identifications and good quantitative reproducibility
- preferred tool for differential protein expression & biomarker discovery
- performed on hybrid quadrupole/time-of-flight tandem mass spectrometers coupled with ultra-performance nanoscale capillary liquid chromatographs (LC/ESI/MS/MS)
- targeted protein quantitation for high sensitivity, high specificity and excellent quantitative reproducibility
- preferred tool for protein expression verification
- performed using LC/ESI/MS/MS with multiple reaction monitoring (MRM) on a triple quadrupole tandem mass spectrometer
- characterization of post-translational modifications, including phosphorylation
- multidimensional characterization of gas-phase structures of peptides, intact proteins and protein complexes based on mass, size, shape, and charge
- performed on a hybrid quadrupole/traveling wave ion-mobility/time-of-flight tandem mass spectrometer (LC/ESI/MS/IMS/MS)