The Southeast Resource Center for Integrated Metabolomics (SECIM) integrates existing strengths to create a comprehensive resource for basic and clinical scientists to obtain state-of-the-art metabolomics data and analyses. Bioinformatics (Core 4) is directed by Prof. Lauren Mclntyre, with assistance from the SECIM Program Coordinator, Dr. Eric Milgram, who will be responsible for developing the SECIM pipeline and implementing QA/QC on all analytical platforms in collaboration with technical core leaders. This core will provide robust and automated analysis tools in a Galaxy interface that will allow users to interactively analyze processed SECIM analytical data. This interface will be organized into a series of workflows that will be available through an Analysis Dashboard, which will provide basic statistical tools and automatic data reformatting. One ofthe primary goals ofthe Bioinformatics Core is to provide the foundation (e.g., data processing, normalization, scaling, reformatting, etc.) that is needed by most studies, freeing them to devote their efforts to answering specific scientific questions. Prof. Peihua Qiu, UF Chair of Biostatistics, will be a critical interface between the Bioinformatics Core and outside projects with biostatistics components. The Bioinformatics Core will also work with select exemplar projects to develop novel analytical approaches. The projects will be chosen for their potential for impact and overall importance to the field. Examples will include projects such as efficient correlation of LC-MS and NMR data, which will be conducted in collaboration with the SECIM technical cores and the Nicholson group at Imperial College London;and new approaches to isotopic ratio outlier analysis (IROA) that expand the capabilities beyond 2-group studies and integrate 13C NMR for efficient biomarker identification in collaboration with SECIM consultant Dr. Chris Beecher. As these advanced tools are developed, they will be deployed on the Galaxy interface and made available to SECIM users and other academic investigators. Finally, the Bioinformatics Core will provide a critical interface to the Promotion and Outreach Core by helping to identify the needs of individual projects that utilize SECIM and to develop instructional modules that will be offered through our annual Metabolomics Workshops.

Public Health Relevance

The major goal of metabolomics is the measurement and characterization of metabolites from living organisms, including people. Small molecule metabolites are sensitive to disease, treatment, and many environmental factors, and they can be used as indicators of disease in diagnosis or as markers to assess the outcome of treatment.

Project Start
Project End
Budget Start
2014-09-01
Budget End
2015-08-31
Support Year
2
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of Florida
Department
Type
DUNS #
City
Gainesville
State
FL
Country
United States
Zip Code
32611
Hattori, Ayuna; Tsunoda, Makoto; Konuma, Takaaki et al. (2017) Cancer progression by reprogrammed BCAA metabolism in myeloid leukaemia. Nature 545:500-504
Le Guennec, Adrien; Tayyari, Fariba; Edison, Arthur S (2017) Alternatives to Nuclear Overhauser Enhancement Spectroscopy Presat and Carr-Purcell-Meiboom-Gill Presat for NMR-Based Metabolomics. Anal Chem 89:8582-8588
Ulmer, Candice Z; Koelmel, Jeremy P; Ragland, Jared M et al. (2017) LipidPioneer : A Comprehensive User-Generated Exact Mass Template for Lipidomics. J Am Soc Mass Spectrom 28:562-565
Markley, John L; Br├╝schweiler, Rafael; Edison, Arthur S et al. (2017) The future of NMR-based metabolomics. Curr Opin Biotechnol 43:34-40
Reed, Laura K; Baer, Charles F; Edison, Arthur S (2017) Considerations when choosing a genetic model organism for metabolomics studies. Curr Opin Chem Biol 36:7-14
Liu, Haiyan; Garrett, Timothy J; Su, Zhihua et al. (2017) UHPLC-Q-Orbitrap-HRMS-based global metabolomics reveal metabolome modifications in plasma of young women after cranberry juice consumption. J Nutr Biochem 45:67-76
DeRatt, Barbara N; Ralat, Maria A; Lysne, Vegard et al. (2017) Metabolomic Evaluation of the Consequences of Plasma Cystathionine Elevation in Adults with Stable Angina Pectoris. J Nutr 147:1658-1668
Koelmel, Jeremy P; Kroeger, Nicholas M; Gill, Emily L et al. (2017) Expanding Lipidome Coverage Using LC-MS/MS Data-Dependent Acquisition with Automated Exclusion List Generation. J Am Soc Mass Spectrom 28:908-917
Koelmel, Jeremy P; Ulmer, Candice Z; Jones, Christina M et al. (2017) Common cases of improper lipid annotation using high-resolution tandem mass spectrometry data and corresponding limitations in biological interpretation. Biochim Biophys Acta 1862:766-770
Wang, Cheng; He, Lidong; Li, Da-Wei et al. (2017) Accurate Identification of Unknown and Known Metabolic Mixture Components by Combining 3D NMR with Fourier Transform Ion Cyclotron Resonance Tandem Mass Spectrometry. J Proteome Res 16:3774-3786

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