The School of Medicine, the Center for Genomics and Computational Biology (GCB), and the Duke Cancer Institute have collaborated with the Proteomics and Metabolomics Core Facility to provide protein characterization resources for the Duke research community. We provide protein identification an quantitation from a wide variety of sample types, from simple mixtures like gel spots and bands to complex mixtures like protein complexes, cell lysates, and plasma. 

We use mass spectrometry as the key technology for qualitative and quantitative protein characterization. Our principal approach for protein analysis is 'bottom-up' proteomics, where all proteins are proteolytically digested, producing peptide surrogates (signature peptides) of the original proteins.

We identify proteins 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.

To quantify proteins, we can use a "gel free, label-free" technology that 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 and 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 quadropole 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)

If you have questions about specific ongoing projects, please contact your project lead:

Proteomics Project Leads:

Metabolomics Project Lead:


Interested in applying for a voucher? Visit the Core Facility Voucher Program to apply.


For all publications that include data generated in the Proteomics and Metabolomics Shared Resource, we kindly request that you acknowledge this support:

We thank the Duke University School of Medicine for the use of the Proteomics and Metabolomics Shared Resource, which provided _________ service.