’Omics

Metabolomics, Proteomics, and Bioinformatics

High-throughput ’omics analysis platforms are the technologies of choice for analyzing complex mixtures derived from biological matrices such as liver, feces, intestine, blood, and urine. Our ’omics core maximizes our capability for deciphering the mechanism and therapy for liver injury, nutrition and gut:liver interactions, and liver:environment/toxin/drug interactions. Our ’omics core is composed of three major components including Metabolomics Core, Proteomics Core, and Bioinformatics.

The overarching goal of the ’omics Core is to support the proposed COBRE research. This goal will be met through application of state-of-the-art separation science and mass spectrometry techniques to analyze research samples containing complex mixtures of metabolites, proteins and protein fragments.

Aims of the Core

  1. Application of LC-MS, comprehensive GCxGC/TOF-MS and integrated LA-ICP-MS platforms for quantitative analysis of metabolites, metal ions, and metal-protein complex in biological samples.
  2. Application of MDLC-MS and affinity enrichment methods for targeted protein quantification.

Core Leaders

Facilities & Instrumentation

The ’omics Core (Core B) is built on a long-standing collaborative effort of the Core PIs (Zhang and Merchant) with the PI and individual members of the COBRE. Dr. Zhang has a 1400 ft² laboratory in chemistry building room 316 equipped for bioanalytical chemistry work. Metabolomics analysis will be performed in CREAM center. The CREAM center is located on the 3ʳᵈ floor of Shumaker Research Building with about 2500 ft² research space. Dr. Merchant has 679 ft² of research space in the in the Donald Baxter Research Building. The Proteomics Laboratories have 1475 ft² of dedicated space in the Donald Baxter Research Building. Adequate power, gas, vacuum, water and safety equipment (e.g., fume hoods) are available in both locations to carry out procedures and accommodate personnel and projects supported by this Core.

Instrumentation for Metabolomics

  • LECO Pegasus III 4D GC×GC/TOF-MS instrument equipped with Gerstel MPS2 autosamplers with capability of online derivatization
  • Thermo LTQ-FT interfaced to a FTICR-MSn with CID, ECD, and IRMPD dissociation modes with sources such as ESI
  • Thermo XSeries II collision-cell ICP-MS with New Wave 213 nm Laser Ablation system with cryostage and ESI microsampler
  • Thermo Delta V Isotope-ratio triple-collector MS with dual-inlets and Isolink liquid introduction/oxidation interface for a dedicated Surveyor micro-LC with auto-sampler system
  • Agilent GS-MS systems equipped with 7820 GC with split/splitless, NIST 2008 MS library and AMDIS programs
  • Agilent 1100 HPLC, Agilent 1200 HPLC with fraction collector, and Dionex UtliMate 3000 LC System

Instrumentation for Proteomics

  • Proxeon EASY nLC 1000 UHPLC-nanospray UHPLC/nanospray/ Thermo Orbitrap Elite mass spectrometer with ETD fragmentation (installed March 2012)
  • Dionex U3000 capHPLC/robotic spotting/ABI 700 Proteomics Analyzer MALDI-TOF/TOF
  • Dionex U3000 capHPLC/nanospray/ Thermo LTQ linear ion trap with MSn capabilities
  • Proxeon EASY nLC 1000 UHPLC-nanospray/TSQ Quantum Discovery MAX triple quadrupole mass spectrometer
  • Nanospray/ABI QStar XL Q-TOF mass spectrometer
  • UHPLC/nanospray/Thermo LTQ Orbitrap XL
  • Micromass capillary LC - Qq-TOF hybrid tandem mass spectrometer
  • Micromass Quattro LC HPLC-electrospray ionization-MS-MS (triple quadrupole) with EI and APC ionization sources
  • ThermoFinnigan Duo ESI-ion trap, equipped with HPLC or capillary electrophoresis sample introduction

Core Services

The ’omics Core will work with investigators to design and perform assays for individual needs.