Proteomics and Metabolics Core Facility Mass spectrometry based high-throughput proteomics and metabolomics, a part of system biology, is foundational for a full understanding of a biological system including a metabolic process or disease state, and has received considerable attention since the sequencing of the human genome. Oxidative/nitrosative damage by reactive radical species appears to be central to the pathogenesis of many human diseases including cancer and is central to a broad range of biotic and abiotic stress and physiological responses in microorganisms, plants and other animals. Specific modified proteins or metabolites are generated following stressing insults and accumulate in different degenerated tissues and fluids, determining altered organ functionalities. Mass spectrometry based technologies have been propitious to the development of molecular medicine, especially in the discovery of diagnostic biomarkers of oxidative and nitrosative stress enabling early detection of diseases such as lung cancer from these biological fluids. Although Redox Proteomics and Metabolomics is currently a nascent field of research, the opportunities for mass spectrometry based biomarker discovery involved in disease strictly linked to oxidative/nitrosative stress are clear and compelling. Clinical research also hopes to benefit from proteomics and metabolomics by both the identification of new drug targets and the development of new diagnostic markers Nature (422, 115-116; 2003). Proteomics and Metabolomics Core The Laboratory for Proteomics and Metabolomics analysis at the Redox Biology Center (RBC) supports scientists within the RBC and the University of Nebraska. The Core provides all the tools of modern functional proteomics and metabolomics. Equipped with cutting edge mass spectrometry based state-of-the-art technologies for proteomics and metabolomics; protein and metabolite profiling, protein identification, protein and peptide fractionation and quantitation, differential expression analysis, shot gun proteomics, personalized experimental design consultation and comprehensive individualized bioinformatics support. This laboratory also provides mass spectrometry services for proteomic analysis including protein sequencing and identification, mapping protein-protein interactions, and characterization of protein modifications such as phosphorylation, oxidation, and glycosylation, etc along with analysis of metabolites, either in context of metabolomics or metabolite profiling. We recently introduced shot gun quantitative proteomics based protein expression difference analysis using MudPIT (Multidimensional Protein Identification Technology) and multiplexed proteome analysis from complex biological samples. We are very interested in collaborations with scientists at UNL and UNMC in studying systems of biomedical importance such as redox proteomics and metabolomics, biomarker discovery from complex biological samples, and microbial proteomics. Instruments: |
We
recently acquired the LCQ Fleet LC-MS system with PQD that
provides rapid and confident sample analysis for routine proteomics
and metabolomics applications. This ion trap mass spectrometer
provides maximum information in minimum time with low levels
of sample consumption. Designed to perform with high sensitivity
and specificity, the LCQ Fleet is capable of producing accurate
results at low detection levels with high throughput particularly
when used in combination with Thermo- Accela high-speed LC
system. Intelligent data dependent acquisition of the LCQ Fleet
enables rapid compound screening for maximum structural information.
The advancement of proteomics analysis requires high accuracy
and more productivity the LCQ Fleet routinely delivers excellent
results for complex proteomics study. It has several features
that make it well-suited for these applications: e.g. Fast
scanning resolves co-eluting peptides often present in complex
protein digests during real time, online LC/MS proteomics analysis
and high sensitivity enables the detection of trace compounds
in a complex mixture and high quality MS spectra provides routine
peptide identification with high correlation scores for confident
sequence identification. Pulsed Q Dissociation (PQD) can be
used for the detection of low mass fragments for iTRAQ™ analysis
during protein quantitation analysis.
We
also acquired the Thermo Scientific Accela™ high-speed chromatographic
system provides fast, efficient chromatographic separations
over an expansive range of flow rates and pressures. Accela
optimizes the performance of sub-two micron particle
columns, providing seamless operation spanning conventional
LC pressures from short LC columns, up to 15,000 psi for long-column
separations of complex bio mixtures and Accela UPLC system
for the fast separation of metabolites.
