Xiang Zhang, Ph.D. - US grants

DESCRIPTION (provided by applicant): High-throughput omics analysis platforms provide important new technical capabilities to analyze complex biological fluids for disease markers. A particularly important platform for metabolomics is two-dimensional gas chromatography time-of- flight mass spectrometry (GCxGC/TOF-MS) that provides both high precision and extended capacity for molecular detection. However, data analysis from this platform is not developed for high sample numbers or for detection of the very large numbers of analytes that this technology detects (more than 1500 per biofluid sample). We will develop an informatics platform for accurate and efficient analysis of data generated from GCxGC/TOF-MS analyses through the following specific aims: (1) Mass informatics for differential metabolomics, (2) Interactive visual analysis of metabolite correlation networks, and (3) Informatics analysis tools integration. The biological information that our system will deliver is regulation of altered metabolites that relate to phenotypic differences between groups of samples. This information will enable assessment of human health and wellness, and will have a direct impact on public health. In the context of existing collaborations, our initial large scale application focus will be analyses of metabolomic profiling data from plasma samples of patients with breast and prostate cancer compared with control subjects. Broadly speaking, our informatics tools will facilitate efforts in the metabolomics community to perform comparative metabolite profiling with high precision and high volume on the powerful GCXGC-TOF-MS platform. The project consists of the development of algorithms for assessment of metabolite identification accuracy, alignment of spectra, and normalization of datasets. Separate algorithms will be developed to distinguish specific molecules that are observed to be different between different sample cohorts and to provide a statistical significance context for each differentially expressed molecule. An additional group of algorithms will be developed to enable interactive visual analysis of metabolite correlation networks. Deliverables from this project will include provision of independent software modules that can be remotely invoked via web services and an integrated web-based data analysis pipeline for GCxGC/TOF-MS data. PUBLIC HEALTH RELEVANCE: High-throughput molecular omics analysis platforms provide important new technical capabilities to analyze complex biological fluids for disease markers. A particularly important platform for metabolomics is two-dimensional gas chromatography time-of- flight mass spectrometry (GCxGC/TOF-MS) that provides both high precision and extended capacity for molecular detection. This approach usually uses a short polar column after the main analytical column. Typically, the second column is operated at a higher temperature than the first column. The metabolites co-eluted from the first GC column are further separated in the second column because of the difference of column temperature and the chromatography matrix. The further separated metabolites are directed to a high capacity time-of-flight mass spectrometry system for detection. Two- dimensional gas chromatography offers significant advantages for analysis of complex samples including: an order-of-magnitude increase in separation capacity, significant increase in signal-to-noise ratio and dynamic range, and improvement of mass spectral deconvolution and similarity matches. Since GCWGC/TOF-MS can provide more and accurate information, it represents powerful tool for the analysis of small molecule metabolites in complex biological systems. However, data analysis from this platform is not developed for high sample numbers or for detection of the very large numbers of analytes that this technology detects (more than 1500 per biofluid sample). We will develop a set of computational algorithms for accurate and efficient analysis of data generated from GCxGC/TOF-MS analyses through the following specific aims: (1) Mass informatics for differential metabolomics, (2) Interactive visual analysis of metabolite correlation networks, and (3) Informatics analysis tools integration. The biological information that our system will deliver is regulation of altered metabolites that relate to phenotypic differences between groups of samples. This information will enable assessment of human health and wellness, and will have a direct impact on public health. A direct application of this type of information is metabolite biomarker discovery in clinical biomedical research. In the context of existing collaborations, our initial large scale application focus of the developed mass informatics system will be analyses of metabolomic profiling data from human plasma samples of patients with breast cancer and human multiple myeloma, compared with corresponding control subjects. With the raw instrument data as input information, our informatics tools will perform a series of data mining and discover the metabolites present in the sample and also provide their regulation information. These informatics tools will facilitate efforts in the metabolomics community to perform comparative metabolite profiling with high precision and high volume on the powerful GCXGC-TOF-MS platform. The project consists of the development of algorithms for assessment of metabolite identification accuracy, alignment of spectra, and normalization of datasets. Separate algorithms will be developed to distinguish specific molecules that are observed to be different between different sample cohorts and to provide a statistical significance context for each differentially expressed molecule. An additional group of algorithms will be developed to enable interactive visual analysis of metabolite correlation networks. Deliverables from this project will include provision of independent software modules that can be remotely invoked via web services and an integrated web-based data analysis pipeline for GCxGC/TOF-MS data.

? DESCRIPTION (provided by applicant): This proposal requests funds for acquisition and continuing operation of a two-dimensional ultra performance liquid chromatography coupled with a high resolution and high accuracy mass spectrometer with tandem MS/MS capability (2DLC-MS/MS) for metabolomics. This instrument will be located in the Shumaker Research Building (room 335) at the Center for Regulatory Environmental and Analytical Metabolomics (CREAM), as a part of integrated metabolomics platforms to support the basic, translational and clinical research at the University of Louisville. The proposed instrument will complement and gradually replace our use of the existing hybrid quadrupole linear ion-trap and Fourier transform ion cyclotron resonance mass spectrometry (LTQ- FTICR-MS) instrument. This LTQ-FTICR-MS has been formally designated as in retired status by the manufacturer as of January 2014 and the manufacturer will now only provide preventive maintenance. We are under risk, at any moment, of losing the capability of conducting high resolution high accuracy mass spectrometry-based metabolomics analyses at the CREAM Center. The Specific Aims of this proposal are provision of the following for the University of Louisville biomedical research community: Specific Aim 1: For the established Major Users (78% allotment of time): Provision of increased capacity for identification and quantification of metabolites with complementary analyses of spatial and temporal flux through metabolic pathways. Specific Aim 2: For appropriate Research Centers & Institutes, less frequent (<100 samples / year) Users, and prospective Users of mass spectrometry (17% allotment of time): Vigorous promotion of the use of high accuracy and high resolution mass spectrometry in biomedical research with an education program for research and scientific career development.

Abstract: The primary function of Omics Core is to provide members of the ULARC with the expertise, resources and facilities needed for metabolomic, proteomic and bioinformatic analyses of biological samples collected to study liver injury, nutrition, gut:liver interactions, and liver:environment/toxicant/drug interactions. OMICS Core personnel will assist with the design of sample collection protocols, will drive the development and the execution of novel and robust chromatographic methods for sample separation and mass spectrometric methods for the analysis of proteins, peptides, and metabolites with a goal of providing a greater understanding of the evolution of molecular mechanisms that correlate with or participate in liver dysfunction. The core will ensure uniformity and standardization in sample preparation, method development, instrument performance, data collection, data reporting and data sharing. The Core endeavors to contribute to the overall success and utility of the ULARC and to enhance the infrastructure and the technical and academic capabilities of the institution as a whole. In addition to its function as a service core, we will also promote the education and training of the ULARC members with regards to state-of?the-art Omics and Bioinformatics methods; with particular attention to the ULARC junior investigators.

This award is jointly supported by the Major Research Instrumentation, the Chemistry Research Instrumentation programs, and the Established Program to Stimulate Competitive Research. The University of Louisville is acquiring an upgraded X-band electron paramagnetic resonance (EPR) spectrometer to support the research of Professor Craig Grapperhaus along with colleague Xiang Zhang. This instrument facilitates research in the areas of chemistry, physical chemistry, biology, and biochemistry. An EPR spectrometer yields detailed information on electronic structure and intermolecular interactions by detecting paramagnetic species. Lifetimes of free radicals, which are short-lived, highly reactive species, and transition metal ions can be identified and quantified in a variety of materials. This instrument enhances the educational, research, and teaching efforts of students at all levels in multiple departments within the University of Louisville and at two primarily undergraduate institutions, Indiana University Southeast and Bellarmine University.<br/><br/>The award of the EPR spectrometer is aimed at enhancing research and education at all levels, especially in areas such as carbon-free fuels, electronic and spintronic materials, pharmacological applications, and cellular stress caused by diabetes. Specifically, the instrument enables a wide range of projects including electrocatalysts with redox active ligands for small molecule activation and studies of water-soluble catalysts for green organic synthesis. Other investigations include structural biology studies of higher order DNA that is essential for cell life cycles and transcription regulation elements in gene promotor regions. It also assists in the fundamental investigations of a mitochondrial membrane protein that exhibits catalytic activity and the study of reactive oxygen species inducing cell processes. Additionally, it enables the characterization of the magnetic properties of 2D magnetic materials.<br/><br/>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.