The School of Medicine and the Duke Cancer Institute have collaborated with the Proteomics and Metabolomics Core Facility to provide protein and small molecule identification and quantification resources for the Duke research community. We provide protein identification and 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.

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Proteomics Capabilities Currently Offered

  • Non-targeted (unbiased) qualitative and quantitative protein analyses using high resolution, accurate mass (HR/AM) instrumentation for high confidence identifications and excellent quantitative accuracy and precision
    • preferred tool for differential protein expression and biomarker discovery
    • performed on Thermo Orbitrap Fusion Lumos or Thermo Exploris 480 mass spectrometers coupled with ultra-performance liquid chromatography (LC/ESI/MS/MS)
    • nanoscale chromatography used for sample-limited and most protein, cell- and tissue-based studies; microscale chromatography used for biofluids, including plasma/serum, whole blood, urine, saliva, CSF and bronchoalveolar lavage fluid
  • Targeted protein quantitation for high sensitivity, high specificity and excellent quantitative reproducibility
    • preferred tool for validation of non-targeted, discovery-based studies and pharmacokinetics of antibody-based therapeutics
    • utilizes stable isotope-labeled internal standards
    • performed using LC/ESI/MS/MS with multiple reaction monitoring (MRM) on a triple quadrupole tandem mass spectrometer or parallel reaction monitoring (PRM) on a HR/AM instrument
  • Qualitative identification and quantification of post-translational modifications, including phosphorylation, ubiquitination, acetylation and S-acylation

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

Proteomics Project Leads:

Metabolomics Capabilities Currently Offered

We can qualitatively and quantitatively measure a large variety of metabolites from various sample origins (tissue, cell, cell media, blood, serum, plasma, urine, feces, etc.). Some established assays include, but are not limited to

  • Q500 and p180 panel (Biocrates)
  • Bile acids (Biocrates)
  • Eicosanoids/oxylipins
  • Hydroxycholesterols
  • Long-chain fatty acids
  • Short-chain fatty acids
  • Neurotransmitters
  • Sphingosines

We are capable of and have been developing the customized assay based on the metabolomics needs from PIs and researchers. Please contact us for any emerging interest.

Metabolomics Project Lead:


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

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