Proteomics Facility
Biological Mass Spectrometry, Separation Science, Platform Development, and Applied Chemistry:
Basic and Applied Research for Clinical Proteomics, Metabolomics,
Systems Biology, and Personalized Medicine
The proteomics and mass spectrometry core facility is dedicated to the identification and quantification of components associated with complex biological matrices and less complex mixtures of synthetic molecules. In the scope of Drug Discovery and Innovation, mass spectrometry may be used to characterize and quantitate the composition of metabolites and proteins in a single yet multitier experiment. The main overall goal of clinical proteomics is to describe the difference between normal and abnormal [metabolome]+[proteome] expression states. This expression state can be any disease such as Cancer, Alzheimer, Diabetes, Microbe Infection, etc. Identifying and quantifying changes in the molecules that cause disease leads toward drug discovery and clinical trials. Thus, the broad field of clinical proteomics leads towards systems biology and eventually an understanding and implementation of personalized medicine.
One of the goals of the proteomics and mass spectrometry core is to facilitate basic and applied research for clinical proteomics. Thus, our lab supports both the basic research and the clinical proteomics aspects of systems biology by collecting data on the states of different biological systems. Specifically, proteomics is the measurement of all proteins at a given time (including PTM's, isoforms, etc.) for an expression state. With sophisticated sample preparation, separations, mass spectrometry, and informatics, we are able to provide information that drives drug discovery for personalized medicine. Our mass spectrometry platforms are currently well suited for simple (protein identification from SDS-PAGE) to complex sample types (posttranslational modification characterization and relative quantitation of proteins from multiple sample types).
A second goal is to facilitate the development of robust metabolomic mass spectrometry based platforms. Metabolomics refers mostly to the small molecule metabolites; however, we extend the definition to such classes as sterols, fat-soluble vitamins, etc. Currently, we are developing and applying discovery and targeted small molecule characterization workflows. Further, our current platforms in the Chemistry Mass Spectrometry Facility are well suited for synthetic molecule characterization, as well as more complex mixtures.
The basic research aspect of our lab is rooted in the selection of classes of molecules from a variety of different biological systems. Each sample type — microorganisms, algae, cultured mammalian cells, mammalian tissue, etc. — require different techniques to analyze a specific molecule class. The clinical proteomics aspect includes robust high-throughput liquid chromatograph mass spectrometry. The synergy between correct sample preparation and robust mass spectrometry yield relevant information for Drug Discovery and Innovation.
Current Institutes and Departments Working with the Proteomics and Mass Spectrometry Core Facility
USF - College of Arts and Sciences - Cell Biology, Microbiology, and Molecular Biology (Proteomics)
USF - College of Arts and Sciences - Chemistry Department (Synthetic Molecules, Metabolomics, and Proteomics)
USF College of Behavior and Community Sciences - Communication Science and Disorders (Targeted Metabolomics)
USF Health - Center of Excellence for Aging and Brain Repair (Targeted Metabolomics)
USF Health - Morsani College of Medicine - Department of Molecular Medicine (Proteomics)
USF Health - Morsani College of Medicine - Department of Obstetrics and Gynecology (Proteomics)
USF Health - College of Public Health - Department of Global Health (Proteomics)
University of Florida - Department of Ophthalmology (Proteomics)
University of Florida - Department of Psychiatry - Division of Addiction Medicine (Proteomics)
University of North Texas - Department of Biology (Proteomics)
Intezyne Technologies Inc. (Intact Protein Analysis and Proteomics)
Novozymes Technologies Inc. (Proteomics)
CDDI core laboratories are equipped with the following instrumentation:
LC-MS Platforms - General Descriptions - Please contact the Core Facility for more information.
Instruments at the CDDI Proteomics Core Facility
Hybrid linear ion trap-Orbitrap (LTQ Orbitrap XL, Thermo) nLC/MS - High-Throughput Proteomics Platform
- Relative Quantitation with iTRAQ and SILAC
- Posttranslational Modification Characterization
- Recombinant Protein Molecular Weight Determination
- Large Scale Proteomic Experiments
Linear ion trap (LTQ XL, Thermo) nLC/MS - High-Throughput Proteomics Platform
- Gel-Band Protein Identification
- Spectral Counting Relative Quantitation
- Project Development Samples
- Discovery Type Proteomic Experiments
Triple quadrupole (TSQ Quantum Ultra, Thermo) nLC or LC/MS - High-Throughput Targeted MS Experiments
- Targeted “high-flow” quantitation of small molecules (or metabolites)
- Targeted nLC quantitation of diagnostic proteins/peptides
Protein Informatics Software
- MASCOT - Bioworks - MaxQuant -Scaffold 3.3 - Scaffold PTM - ProteoIQ - Ingenuity Pathway Analysis
Instruments at the Chemistry Mass Spectrometry Core Facility
Triple quadrupole (Agilent 6140 QqQ) - High-Throughput Targeted MS Experiments - Installed Jan 2012
- Targeted “high-flow” quantitation of small molecules (or metabolites)
- Developing new project related to small molecule analysis
Quadrupole-TOF (Agilent 6500 Q-TOF LC/MS)
- High-mass accuracy mass measurement
- Developing new project related to small molecule analysis
Ancillary protein characterization equipment:
- ChemiDoc XRS and Pharos FX imagers (Bio-Rad)
- DF Pathfinder 20 FPLC system (Bio-Rad)
- Surveyor Plus HPLC system (Thermo)
Jeremiah D. Tipton, Ph.D.
Director of Proteomics and Mass Spectrometry, CDDI
Bio & Profile
Lab Location:
3720 Spectrum Blvd., Suite 311
IDR Building
Tampa, Florida 33612
Telephone:
(813) 974-8049
Questions or Comments:
cddi@usf.edu
