Proteomics and Metabolomics

Researchers working on equipment used in proteomics and metabolomics

The School of Medicine, the Duke Center for Genomics and Computational Biology (GCB), and the Duke Cancer Institute have collaborated with the Proteomics and Metabolomics Shared Resource 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 like gel spots and bands to complex mixtures like protein complexes, cell lysates, and plasma. The facility is located in room B02 (basement) of the Levine Science Research Center.

The Proteomics and Metabolomics Shared Resource uses 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.

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 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.

Facility News

Duke Translational Research Institute Core Services vouchers are awarded on a quarterly basis. The facility is pleased to announce that proteomics is having an impact in these voucher studies; approximately 50 percent of the 2010 awards have utilized proteomics for their studies.

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

Acknowledging the Input of Core Facilities

A common question of labs when working with core facilities is how best to acknowledge or include as authors the core in the publication of results and interpretation provided by the core. The Association of Biomolecular Resource Facilities (ABRF) has published recommended guidelines for authorship on manuscripts, and we ask our users to consider these guidelines when publishing data generated by the Proteomics and Metabolomics Shared Resource. Ultimately, the decision to include or acknowledge is decided by the senior author (or PI) on the publication. Because a publication record is essential to ensure a high-quality core facility and for the professional development of its staff, we ask our users to carefully consider the input of core members to scientific publications.


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.

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)


September 28, 2016
The School of Medicine departments, institutes and centers oversee a
April 18, 2016

Join GCB's shared resources at the Duke University School of Medicine's first annual Core Day.

March 30, 2016

Applications are due April 15th for the spring cycle of the SOM core facility voucher program.