Proteomics

The Barnett Institute provides a vibrant, collaborative environment for research in a broad range of areas and programs. The research groups of Profs. Karger and Hancock are internationally recognized for their contributions to proteomic analysis; professors Engen and Zhou complement this expertise with new methods of targeted protein analysis using HX-exchange and biochemical assays.  Work in varied collaborations has been fruitful in optimizing all steps of the proteomic workflow, including significant advances in the software for analyzing LC-MS data sets.  In the key area of LC-MS analysis, the use of ultra-narrow bore monolithic capillary columns and porous-layer open tubular (PLOT) columns with nanospray ESI has dramatically inproved sensitivity and resolution.

Dr. Hancock’s Multiple Lectin Affinity Chromatography can select glycoproteins, a highly promising class of serum proteins for biomarker discovery.  Biomarkers for cervical cancer have been discovered in collaboration with Cytyc Corp; collaborations are active in many other cancers.  Extended Range Proteomic Analysis (ERPA) takes more full advantage of the capabilities of the new hybrid FTMS-linear ion trap mass spectrometers in comprehensive characterization of a targeted protein.  Comprehensive protein analysis has revealed significant differences between bona-fide and generic protein therapeutics

Metabolomics

The NanoSplitter developed in Paul Vouros’ group provides the advantages of nanoelectrospray mass spectrometry with LC methods developed on traditional 4 mm columns. 100-improvement in S/N while permitting 99% of the eluant to be directed to fraction collection or other methods of detection, such as UV,  radiometric detection or  Coulometric Arrays.   Micro-NMR methods, have reduced the sample mass to obtain interpretable NMR spectra down to the mid-nanogram level.  When used to load LC-MS fraction collected using the NanoSpltter, this system provides an exquisitely sensitive and practical LC-MS-NMR platform.  Differential Ion Mobility (DMS) has proven invaluable as a front-end to MS, to disrupt or filter cluster ions.  An LC-MS method for profiling 15 conjugated lipid hormones in a single run was developed in Vouros’ group, using single reaction monitoring among other innovations, in a collaborative program with the Center for Drug Discovery.

Chemical Biology

The Graham Jones research group is dedicated to the application of synthetic organic chemistry to the development of diagnostic and therapeutic agents. Since the mid-90’s the program has produced over 120 original research publications and attracted over $8 million in research funding. In most cases projects represent joint efforts between our NU program (housed in the Bioorganic & Medicinal Chemistry Laboratory) and collaborators at the nearby Harvard Medical School.

The Environmental Cancer Research Program

“The mission of the Environmental Cancer Research Program (ECRP) is to help defeat cancer by fighting environmental carcinogens. To fight carcinogens we first need to identify them and learn their origins. Much remains to be learned about the carcinogens to which humans are exposed. The ECRP seeks to develop and apply tests that discover, measure and characterize carcinogens, including the pathways for their toxicity. The tests will find carcinogens no matter where they are, but will especially look for them in the worst place, which is on the DNA of people. Human DNA is the ultimate target in the body for carcinogens. Damage to DNA is the basis of all cancer. Defeating carcinogens is an important way to prevent cancer. The Environmental Cancer Research Program is part of the prevention war against cancer.”

Drs Giese and Vouros have been developing better assays for DNA adducts including a novel mass tag with high sensitivity, a study on exposure of hospital workers to the sterilization gas ethylene oxide, and CEC and CE assays for biomarkers of carcingens from grilled meats or cigarette smoke.  A new program by Dr. Vouros in collaborations with Helmut Zarbl of the Fred Hutchinson cancer center is investigating the relationship between DNA adduct formation and toxicogenomic processes.

Current Research Areas:

Comprehensive Characterization of Proteins:

  • Variation in glycosylation and phosphorylation
  • Variation in amino acid sequence
  • Levels of degradation, glycation
  • Disulphide bonding
  • Process Analytical Technology (PAT)

Proteomic Analysis

  • Biomarker Discovery – Clinical Proteomics
  • Glycoproteomic Analysis
  • Pharmacokinetics of Therapeutic Antibodies
  • Metabolic Pathway Analysis

Complex Samples

  • Identification of Natural Products from Bioactive Crude Extracts
  • Trace-level LC-MS-NMR
  • Metabolomic Analysis of Blood and Tissue

Protein Solution Structure and Dynamics using Hydrogen-Deuterium Exchange MS
Epigenetic Modifications of DNA
Bio-organic Chemistry: Synthesis of Prodrugs and Imaging Agents
DNA Damage Caused by Environmental Effects – DNA Adduct Detection