4th Annual Workshop on Metabolomics

Sunday, July 17th - Thursday July 21st, 2016

Welcome to the 4th Annual Workshop on Metabolomics. The course is jointly sponsored by the National Institute of General Medical Sciences (NIGMS) as part of the NIH Common Fund Metabolomics Initiative, and the Departments of Chemistry and Pharmacology and Toxicology at UAB.




The themes in this fourth year of the workshop are:

  1. Design of a metabolomics experiment
  2. Sample stability and extraction methods
  3. Analytical systems (nuclear magnetic resonance and gas- and liquid chromatography-mass spectrometry)
    1. Targeted metabolomics
    2. Untargeted metabolomics
    3. Quantitative metabolomics
  4. Pre-processing of analytical data (Mzmine 2 and XCMSonline and Chenomx)
  5. Statistical analysis of the data (MetaboAnalyst, Simca, SAS)
  6. Metabolite databases (METLIN, HMDB, LIPIDMAPS, PubChem, ChemSpider)
  7. Identification of metabolites (MetaboSearch, MSMS analysis)
  8. Metabolite pathway analysis (Mummichog, KEGG, GeneGo, Ingenuity)
  9. Advanced elective sessions (Imaging mass spectrometry, isotope ratio analysis, Ion mobility, Command line and R programs)
  10. Electives will allow attendees to fine tune their training experience

Tentative Agenda

Sunday, July 17

Time Topics & Speakers
5- 8 pm Social at Double Tree Hotel

Monday, July 18

Time Topics & Speakers Resources
7:30 am Breakfast, VH 302
8:00 - 8:15 am Introductions (Steve Barnes/Hemant Tiwari) - VH 302  
8:15 - 8:20 am Richard Marchase, PhD, Vice-President Research - VH 302
Welcome to UAB
8:20 - 8:35 am Richard Okita, PhD, NIH/NIGMS - VH 302
The NIH Common Fund Program in Metabolomics
8:35 - 9:10 am Stephen Barnes, PhD, UAB - VH 302
How metabolism became metabolomics
9:10 - 9:15 am Questions  
9:15 - 9:55 am Xiangqin Cui, PhD, UAB - VH 302
Designing a metabolomics experiment
9:55 - 10:00 am Questions  
10:00 - 10:20 am Coffee Break  
10:20 - 10:45 am Pamela Bounelis, PhD, UAB - VH 302
Integrity in research
10:50 - 11:25 am Andrew Patterson, PhD, Penn State University - VH 302
Recovering metabolites from biological fluids and tissues
11:25 - 11:30 am Questions  
11:30 - 11:55 am Stephen Barnes, PhD, UAB - VH 302
Choosing the analysis platform
11:55 - 12 noon Questions  
12 noon Lunch  
12:25 - 12:55 Susan Sumner, PhD
Regional Comprehensive Metabolomic Research Centers: the RTI experience
1:15 - 3:00 pm Group 1 – proceed to McCallum for MS training
Group 2 – proceed to Chemistry for NMR training
3:15 - 5:00 pm Group 1 – proceed to Chemistry for NMR training
Group 2 – proceed to McCallum for MS training
Evening On your own  

Tuesday, July 19

Time Topics & Speakers Resources
7:30 am Breakfast
8:00 - 8:15 am Questions  
8:15 - 9:05 am Wimal Pathmasiri, PhD/Rod Snyder - VH 302
NMR data pre-processing
9:30 - 10:20 am James Kinross, MD, Imperial College - Spain auditorium
The iKnife: Tanslational metabolic phenotyping for precision surgery
10:20 - 10:30 am Questions  
10:45 - 11:10 am Xiuxia Du, PhD, UNC-Charlotte - VH 302
MS data pre-processing
11:10 - 11:15 am Questions  
11:15 - 12 noon Xiuxia Du, PhD/Stephen Barnes, PhD - VH 302
Hands-on data analysis with mzmine 2:20
(need write up on downloading mzmine)
12 noon Lunch - VH 302  
12:20 - 1:00 pm TBD - VH 302
Open forum
1:00 - 1:55 pm Wimal Pathmasiri, PhD/Rod Snyder - VH 302
Introductions to NMR data analysis
1:55 - 2:00 pm Questions  
2:00 - 2:25 pm Paul Benton, PhD, Scripps Research Institute - VH 302
Introduction to XCMS
2:25 - 2:30 pm Questions  
2:30 - 2:55 pm Paul Benton, PhD - VH 302
Uploading data to XCMSonline
2:55 - 3:00 pm Questions  
3:00 pm Coffee break  
3:20 - 3:45 pm Paul Benton, PhD - VH 302
“The cloud plot”
3:45 - 3:50 pm Questions  
3:50 - 4:20 pm Paul Benton, PhD - VH 302
Online XCMS analysis and using your iPhone
4:20 - 4:25 pm Questions  
4:30 - 4:55 pm Stephen Barnes, PhD - VH 302
Preparing data for Metaboanalyst
6:30 - 8:30 pm Workshop dinner
Speaker: Gary Patti, PhD –"MythBusters: The Metabolomics Edition"

Wednesday, July 20

Time Topics & Speakers Resources
7:30 am Breakfast
8:00 - 8:15 am Questions  
8:15 - 8:55 am Xiangqin Cui, PhD - VH 302
Statistical analysis – Metaboanalyst
8:55 - 9:00 am Questions  
9:00 - 9:25 am Xiuxia Du, PhD/Stephen Barnes, PhD - VH 302
Metabolite databases
9:25 - 9:30 am Questions  
9:30-9:55 am Gary Patti, PhD - VH 302
Bar coding tandem mass spectral data for metabolite identification
9:55-10:00 am Questions  
10:00-10:20 am Coffee  
10:20-11:00 am Shuzhao Li, PhD, Emory U - VH 302
Pathway analysis using mummichog
11:00-11:05 am Questions  
11:05-11:25 Stephen Barnes, PhD - VH 302
Pathway analysis using Metaboanalyst
11:25 - 11:30 Questions  
11:30 - 11:55 pm Chris Beecher, PhD, IROA Technologies - VH 302
Isotopic signatures and identifying real metabolites
11:55 - 12 noon Questions  
12 noon Lunch  
12:20 - 12:55 pm Matthew Skaley, SCIEX - VH 302
OMICS and Precision Medicine - Full Workflows for Lipidomic and Metabolic Profiling
12:55 - 1:00 pm Questions  
  Workshop hands-on electives 1:15-3:00 pm and 3:15-5:00 pm
1:15 - 3:00 pm
3:15 - 5:00 pm
  1. Using R in data analysis – up to 10 participants (both sessions) – Xiuxia Du - VH 302
  2. Mummichog software – up to 10 participants (both sessions) – Shuzhao Li - RLC
  3. IROA analysis – up to five participants (both sessions) – Chris Beecher - McCallum
  4. Differential Ion mobility – up to five participants (both sessions) – TMPL staff/Jeff Miller - McCallum 427
  5. Imaging metabolomics – preparation and data acquisition (up to five participants) – Janusz Kabarowski/Kelly Walters – Bevill 334 and Chemistry (this demo will last the whole afternoon)
  6. Advanced NMR – up to five participants (both sessions) - Wimal Patmasiri, Rod Snyder - Chemistry
Evening On your own
Birmingham Barons play Montgomery at Regions Field at 7:05 pm

Thursday, July 21

Time Topics & Speakers Resources
7:30 am Breakfast
8:00 - 8:15 am Questions  
8:15 - 9:00 am Adam Wende, PhD, UAB - VH 302
Metabolomics in diabetes
9:00 - 9:05 am Questions  
9:05 - 9:55 am Karan Uppal, PhD, Emory U - VH 302
Integrating –omics data
9:55 - 10:00 am Questions  
10:00 - 10:20 am Coffee  
10:20 - 10:55 am Hui Wu, PhD, UAB - VH 302
The role of the microbiome in metabolomics
10:55 – 11:00 am Questions  
11:00 - 12 noon Workshop attendee presentations - VH 302  
12 noon Lunch  
12:20 - 12:55 pm Norton Kitagawa, PhD, Agilent - VH 302
An Integrated Workflow for Qualitative Flux Analysis by Accurate Mass LC/MS.
12:55 - 1:00 pm Questions  
1:00 - 1:40 pm Tom Beaty, Waters - VH 302  
1:45 - 1:50 pm Questions  
1:50 - 2:25 pm Stephen Barnes, PhD - VH 302
Future in metabolomics
2:25 - 2:30 pm Questions  
2:30 - 3:00 pm Open forum - Chemistry (this demo will last the whole afternoon)  
3:00 - 5:00 pm Consulting with Workshop team  

Workshop Faculty

The bios are drafts.

Stephen Barnes, PhD

Dr. Barnes, Director of the Metabolomics Workshop, is Professor of Pharmacology and Toxicology and has secondary appointments in five other departments.  He started his research career in the laboratory of A. T. (Tony) James, co-inventor of gas-liquid chromatography, studying fatty metabolism in green algae and did his PhD on the carbohydrate metabolism of the acellular slime mold Physarum polycephalum at Imperial College, University of London under the tutelage of Sir Ernst Boris Chain, 1945 Nobel Laureate for the discovery of penicillin. He began his long-standing interest in bile acid metabolism at the Royal Free Hospital with Dame Sheila Sherlock and Barbara Billing. After the winter of 1975 in Alan Hofmann’s lab at the Mayo Clinic in Rochester, he took up an offer to come to the University of Alabama at Birmingham (UAB) in 1977 where he has remained ever since. In the early 1980s he applied high field NMR using superconducting magnets to unravel the proton NMR spectrum of bile acids as well as to use pulse sequences to greatly simplify the process. In 1992 he took over the development of LC-mass spectrometry in biomedical research at UAB and was the Director of the UAB Comprehensive Cancer Center Mass Spectrometry Shared Facility from 1992 to 2009. In 2009 he was appointed as the Director of the Targeted Metabolomics and Proteomics Laboratory (TMPL).  He also was the Associate Director of the Purdue-UAB Botanicals Center for Age-related Disease from 2000-2011 and the Director of the UAB Center for Nutrient-Gene Interaction from 2002-2010. These latter roles provided critical experience in experimental design, statistical analysis of –Omics data and the important role of the diet in determining the outcome of experimental models of chronic diseases.

More details about TMPL can be obtained at http://tmpl.uab.edu

Tom Beaty


Chris Beecher

IROA Technologies

Paul Benton, PhD

Dr. Benton started working with metabolomics datasets in 2006 when he joined Prof. Gary Siuzdak’s lab as a Research Tech. Working with XCMS and METLIN, he developed and published a tandem mass spectra extension to XCMS called XCMS2. He gained a valuable understanding of mass spectrometry methods and the need for computational developments in the field. Working with Dr. Timothy MD Ebbels & Prof. Jeremy Nicholson while studying for his Ph.D at Imperial College London, he developed methods to increase the reproducibility of metabolic profiling experiments and two novel methods for temporal metabolite profiling. Since receiving his Ph. D in August 2013 he has returned to Prof. Siuzdak’s lab at The Scripps Research Institute to develop Online XCMS and the labs many other metabolomics toolset.

Pamela Bounelis, PhD


Xiangqin Cui, PhD

I was initially trained as a lab/field geneticist and later on moved into statistical genetics through my postdoctoral training. After joining the UAB Department of Biostatistics, I have been conducting research in genome-wide studies, such as gene expression (both arrays and next-generation sequencing), next generation sequencing, DNA methylation, metabolomics, and microbiome with more than 50 publications in these areas. I have served as a Co-investigator/Biostatistician for statistical data analyses in multiple funded grants involving omics studies. RNAseq analysis specifically, I have published several papers listed below and taught this topic in national short courses many times. The current application is well-suited to my background and I am enthusiastic to help.


Xiuxia Du, PhD

Dr. Du is an Associate Professor of Bioinformatics at the Department of Bioinformatics and Genomics, University of North Carolina at Charlotte. She received her Ph.D. in Systems Science and Mathematics from Washington University in St. Louis. Subsequently, she did a postdoc at the Pacific Northwest National Laboratory. She joined the University of North Carolina at Charlotte in 2008 as an assistant professor. The research of her group has been focusing on the development of computational algorithms for mass spectrometry-based proteomics and metabolomics research.

Web Site: http://www.du-lab.org

James Kinross, MD

Imperial College


Norton Kitagawa, PhD


Shuzhao Li, PhD

Assistant Professor, Associate Director of Clinical Biomarkers Laboratory, Department of Medicine, Emory University

Dr. Li was trained in bioinformatics, and he has been combining computational developments with metabolomics and systems biology. His work in human immunology applied large-scale data integration and network modeling to delineate transcriptomic programs for antibody response induced by several vaccines. These are early steps towards quantitative and systems modeling of human immunity, which is an integral part of most human diseases. His mummichog software brought genome-scale metabolic models into the field of high throughput metabolomics, and enabled pathway/network analysis for untargeted metabolomics. He strives to bring these scientific developments to personalized and precision medicine.


Jeff Miller


Richard (Dick) Okita



Wimal Pathmasiri, PhD

Wimal Pathmasiri, PhD, is currently a research biochemist in the Systems and Translational Sciences Center at RTI International. Dr. Pathmasiri is a team member of the NIH Eastern Regional Comprehensive Metabolomics Resource Core (RTI RCMRC). His experience includes high-resolution nuclear magnetic resonance (NMR) spectroscopy, gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), medicinal chemistry, structural biology, and molecular biological and bio analytical methods.

Dr. Pathmasiri has expertise in metabolomics in a wide range of research areas including cancer research, disease phenotypes, drug-induced liver injury, energy metabolism, gut microbiome, toxicology, environmental exposure, and immune response to vaccines involving analysis of cells, biological fluids and tissue extracts obtained from animal models and human subjects studies. He has provided leadership for NMR and GC-MS core activities in the RTI RCMRC by optimizing the NMR and GCMS metabolomics pipeline, developing quality control procedures, evaluating software, and setting up center specific protocols for sample preparation, data acquisition, and data analysis.

RTI Intl Regional Comprehensive Metabolomics Research Center


Andrew Patterson, PhD

Penn State University


Gary Patti, PhD

Jeevan Prasain, PhD

Dr. Prasain is an Assistant Professor of Pharmacology and Toxicology at UAB. He received his undergraduate and master’s training (Chemistry) at Tribhuvan University, Nepal and his Ph.D. at Toyama Medical & Pharmaceutical University, Japan. His expertise is in the use of NMR and LC-MS for the discovery and identification of natural products. He will be demonstrating the use of LC-MS methods for the analysis of metabolite classes.

Website: http://www.uab.edu/proteomics/massspec/personnel/prasain.php

Rodney Snyder, MS

Rodney Snyder is a research chemist in Discovery Sciences Division at RTI. He has conducted studies involving metabolism, pharmacokinetics, and adduct analysis. Mr. Snyder's experience includes all aspects of conducting absorption, distribution, metabolism, and excretion (ADME) studies in rodents using oral, dermal, and intravenous exposure routes. He has 20 years of experience in conducting ADME and pharmacokinetic studies. Mr. Snyder has worked extensively on the development of high-performance liquid chromatography (HPLC) and HPLC-mass spectrometry methods for the identification and quantitation of xenobiotics and their metabolites in biological media and the analysis of hemoglobin and DNA adducts. Much of his research has involved the conduct of studies to help understand metabolism, and the effects of dose and exposure route, and extrapolation between species. Mr. Snyder has also developed methods to conduct metabolomics analysis of endogenous metabolites in biofluids, as well as using innovative software tools to interpret the data. Mr. Snyder is also part of the RTI Regional Comprehensive Metabolomics Resource Core (RCMRC) directed by Susan Sumner which is one of three Cooperative Agreement centers that are funded to work in a U24 consortium to establish our national standards for metabolomics research and reporting, to facilitate translational and clinical research using metabolomics, and to train and educate future researchers.

RTI Intl Regional Comprehensive Metabolomics Research Center

Susan Sumner, PhD

RTI International


Hemant Tiwari, PhD

Dr. Tiwari is the Co-Director of the Metabolomics Workshop. He received his Ph.D. in mathematics from the University of Notre Dame, South Bend, Indiana. While being a faculty at the University of Maine, he got interested in statistical genetics, and completed a post-doctoral fellowship in Statistical Genetics under Prof. Robert Elston in the Department of Biometry and Genetics at Louisiana State University Medical Center, New Orleans and at the Case Western Reserve University in Cleveland. Subsequently, he worked as a faculty member in the Department of Epidemiology and Biostatistics at Case Western Reserve University. In January 2002, he joined UAB as a faculty in the Department of Biostatistics (Section on Statistical Genetics). His research interests include Genetic Linkage Analysis, Disequilibrium Mapping, Population Genetics, Molecular Evolution, Bioinformatics, and Genetics of Infectious Diseases. Currently, he is involved in gene mapping studies of epilepsy, SLE, phonological disorders, and dental traits. He is the Head of the Section on Statistical Genetics, the William “Student” Sealy Gosset Professor, Director of the Biostatistics Pre-Doctoral NHLBI Training Program and Director of the Post-Doctoral NHLBI Training Program in Statistical Genetics. He also is the Director of the NIGMS-funded National Short Course in Statistical Genetics and Genomics.

Website: http://www.soph.uab.edu/ssg/people/tiwari

Karan Uppal, PhD

My research focuses on computational metabolomics, integrative -omics, and development of machine learning techniques for analyzing and extracting knowledge and information from “BIG” omics data, clinical text, and biomedical literature. I have a formal training in Bioinformatics with a focus on the development and application of statistical and machine learning techniques for analyzing high-throughput -omics data and biomedical/clinical text. I have experience in analyzing and developing computational pipelines for metabolomics, epigenomics, proteomics, and transcriptomics data. I also have experience in developing tools (https://sourceforge.net/u/kuppal2/profile/) and algorithms for network based annotation of high-resolution mass spectrometry data, predicting protein-protein interactions, and integrative analysis of –omics data. I developed xMSanalyzer that optimizes the performance of existing LC/MS data processing software such as apLCMS and XCMS for improved feature detection. The software allows detection of quantitatively reliable low abundance and variable chemicals and chemicals that are present in only small subset of samples. I have developed MetabNet for metabolome-wide association studies and algorithms for computational prediction of metabolite identity. I have also developed R packages for supervised and unsupervised analysis of metabolomics data and for identifying metabolic biomarkers using univariate and multivariate feature selection techniques such as PLSDA. I also have the expertise to integrate heterogeneous data (metabolomics and gene expression; metabolomics and proteomics) and identify the network structure or modules of co-regulating metabolites, which would assist in characterizing the association of the unknown chemicals with respect to diseases, clinical traits, and biological pathways. I have experience in developing literature mining tools and algorithms for automated summarization and knowledge discovery from clinical and biomedical text. I am proficient in R, Java, Perl, Python, C++, Flex, PHP, ActionScript, JavaScript, MySQL, and database and web-application development.

Adam Wende, PhD

In August of 2013 I started my independent laboratory at the University of Alabama at Birmingham, and have focused my training and research for the past 16 years to expand our understanding of the molecular pathways in control of mitochondrial function of striated muscle. During my thesis training I focused on how exercise alters skeletal muscle metabolism and glycogen turnover through the regulation of gene expression by the transcriptional co-activator PGC-1α. My postdoctoral training expanded these interests to include studies of how heart function, directly related to diabetic complications versus exercise, is influenced by insulin signaling and glucose utilization. By combining the gained expertise in transcriptional biology and cellular signaling I have concentrated on a mission to decipher the cardiometabolic regulation of cellular function in normal physiology and disease. This work has two primary goals: 1) to determine the role of metabolic substrate switching in heart disease, and 2) to define the posttranslational regulation of mitochondrial enzyme activity and epigenetic regulation of gene expression that together may lead to the development of muscular energetic dysfunction. I have begun to explore multiple aspects of metabolic control in a systems biology approach. Current animal model work in the laboratory, supported by an NIH R00 Pathway to Independence award (R00 HL111322), is focused on changes in DNA methylation and protein O-GlcNAcylation that may impact gene expression, protein function, and mitochondrial capacity in the hearts of diabetics. One of my primary reasons for starting my independent career at UAB is the strength of their Center for Free Radical Biology, Comprehensive Cardiovascular Center, and Diabetes Research Center. As an investigator at the intersection of these various fields the environment is perfect. In my short time at UAB I have contributed to collaborations while increasing the funding for my independent work. Specifically, as a collaboration we have obtained NIH funding to explore the role of circadian rhythm in regulating insulin signaling with Dr. Martin Young (R01 HL123574) and relevant to my participation of this workshop is an Administrative Supplement to examine metabolomics in the diabetic mouse heart (R00 HL111322-04S1). Most recently I have expanded this animal model studies to examine DNA methylation and RNA-sequencing in diabetic human heart failure samples (U24 DK076169; CHAAMPS; and CCTS). I have found my participation in this workshop to be both educational and critical to integrating different omics data with the focus on understanding diabetic complications and potential molecular mechanisms to treat them.



Hotel options will be distributed to attendees once they have been selected to attend the workshop.

Additional Lodging Options:

Apply (2016 Workshop)

To apply, please perform the following tasks.

  1. Complete on-line application form at http://goo.gl/forms/DHLelzRnyO. Only fully completed application form will be considered.
  2. Send your current curriculum vitae to mammadu@uab.edu.
  3. Send letters of recommendation (minimum of two) to mammadu@uab.edu.
  4. Send a proposal to mammadu@uab.edu. Using a one-page proposal, describe why learning about metabolomics and its methodology would help your current research and/or influence your research career plans. If you have questions about the proposal, please contact Dr. Stephen Barnes – sbarnes@uab.edu

Attendance is limited to 40 for this course. Please apply prior to Friday, April 29, 2016. Accepted applicants will be notified by Friday, May 12th, with registration fee due by May 26th.

Women, members of under-represented minority groups, and individuals with disabilities are strongly encouraged to apply.

There will be 20 fellowships for graduate students and postdoctoral fellows attending the workshop. The fellowships will provide up to $1200 of travel and hotel expenses. Selection will be based on information provided by the applicants.

Upon Acceptance, the fee for attendees is:
$300 – for graduate students and postdoctoral fellows
$750 – for faculty at academic, government, and non-profit organizations
$1,500 – for-profit organizations

The fee includes course tuition and syllabus, breakfast, lunch and refreshment breaks and the Workshop dinner. Hotel accommodation and travel will be the attendees’ responsibility.

The fee will be payable upon acceptance into the course.

Need more information? Contact Lynn Waddell at 205 934-4579/mammadu@uab.edu

Refund and Cancellation Policy: Attendee substitutions are allowed, but notification must be made in writing by Friday, May 26th and sent to mammadu@uab.edu or by fax at 205.934.8240. After this date no substitutions will be granted. UAB reserves the right to cancel this conference, in which case a full refund of your registration fee will be provided. We are unable to refund any travel costs (flight, hotel, etc.) in the case of UAB’s cancellation.

Recording and Photography Clause: UAB reserves exclusive rights to record (audio and video) and/or photograph all conference proceedings for use in marketing materials, presentations and course content sales.

The fee will be payable upon acceptance into the course.

Need more information?  Contact Lynn Waddell at 205 934-4579/mammadu@uab.edu

For enquiries please contact

Stephen Barnes
Lynn Waddell


Volker Hall - 1670 University Blvd‎

Chemistry Building - 901 14th Street South

McCallum Basic Health Sciences Bldg - 1918 University Blvd

LRC - 1714 9th Avenue South

Bevill Biomedical Ssciences - 845 19th Street South


Many thanks to

  1. NIH Common Fund R25 GM103798-03
  2. Mary-Ann Bjornsti, PhD (Chair, Pharmacology & Toxicology)
  3. Richard A Dluhy, PhD (Chair Department of Chemistry)
  4. UAB School of Medicine
  5. Comprehensive Cancer Center
  6. Comprehensive Cardiovascular Center (CCVC)
  7. Office of the UAB Vice-President for Research
  8. UAB-UCSD O’Brien Acute Kidney Injury Center
  9. Diabetes Research Center & Comprehensive Diabetes Center
  10. Center for Free Radical Biology
  11. Agilent, Sciex and Waters



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