MetaboNews Masthead

MetaboNews
Issue 23 - July 2013

CONTENTS:


Online version of this newsletter:
http://www.metabonews.ca/Jul2013/MetaboNews_Jul2013.htm

Welcome to the twenty-third issue of MetaboNews, a monthly newsletter for the worldwide metabolomics community. In this issue, we feature a Research Spotlight article on the false positive paradox in metabolomics. In May 2012, we introduced a new section called MetaboInterviews that features interviews with metabolomics experts from around the world. This issue includes an interview with David Wishart, Professor of Biological Sciences & Computing Science at the University of Alberta and Director of The Metabolomics Innovation Centre (TMIC). This newsletter is produced by The Metabolomics Innovation Centre (TMIC, http://www.metabolomicscentre.ca/), and is intended to keep metabolomics researchers and other professionals informed about new technologies, software, databases, events, job postings, conferences, training opportunities, interviews, publications, awards, and other newsworthy items concerning metabolomics. We hope to provide enough useful content to keep you interested and informed and appreciate your feedback on how we can make this newsletter better (metabolomics.innovation@gmail.com).

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 Software Spotlight

1) Research Spotlight

 Metline XCMS Logo

The False Positive Paradox in Metabolomics

Feature article contributed by Caroline Johnson, Winnie Uritboonthai, and Gary Siuzdak,The Scripps Research Institute, La Jolla, California

The False Positive Paradox is defined as a statistical outcome where a false positive is more probable than a true positive. Metabolite identification represents an example of the paradox, especially when accurate mass measurements alone are used for identification. An extreme example would be searching METLIN (metlin.scripps.edu) with a neutral mass of 180.0634 (the mass of glucose), this particular entry produces 24 hits within 2 parts per million (ppm) accuracy. 

Analytical Chemistry recently highlighted an article from our lab that discussed the importance of tandem mass spectrometry analysis (Figure 1, Patti, G.J. et al. Anal. Chem. 2013, 85(2):798-804) in metabolite characterization, as well as the introduction of XCMS Cloud Plots (http://xcmsonline.scripps.edu/). Specifically, this article compared the use of precursor accurate mass measurements by themselves for identifying metabolites versus using precursor and tandem mass spectrometry data. The purpose of the plot was to illustrate the level of false positives that come from using just accurate mass measurements of precursor ions for identification purposes. 

# of metabolite hits generated from the METLIN database as a function of m/z error & m/z error & tandem MS data

Figure 1. The number of metabolite hits generated from the METLIN data base as a function of m/z error (top) and m/z error and tandem mass spectrometry data. Tandem mass spectrometry data offers significantly higher confidence and lower rate of false positives.

It is intuitively obvious that metabolite assignments based on accurate mass measurements alone create a high level of false positive identifications. Two reasons for this redundancy are the existence of isobaric metabolites (compounds with identical mass) and secondly, metabolites that have similar masses that cannot be resolved with the mass accuracy of many mass analyzers. To illustrate this, the number of metabolite hits from the METLIN database was plotted as a function of accurate mass measurements and mass error, and a second superimposed plot calculated the number of hits based on a combination of accurate mass measurements, tandem mass spectrometry (MS/MS) data, and mass error (Figure 1). Using this plot, even at the extreme of accuracy (0.0 ppm error) an average of 4 metabolites were identified based on accurate mass measurements alone, hence the reference to the “paradox”. However when accuracy was combined with tandem mass spectrometry data, the average number of identifications dropped to 1.1.

A specific example of the false positive paradox is shown in Figure 2 with data on three isobaric metabolites that have identical elemental composition and mass, and therefore are indistinguishable based on accurate mass measurements. It is only possible that, at best, one of these three is correct. Fortunately, as shown, the compounds have distinct tandem fragmentation patterns, one of which matched to a key metabolite implicated in neuropathic pain (Patti, G.J. et al., Nat. Chem. Biol. 2012, 8(3):232-4).


Tandem MS data used to distinguish dimethylsphingosine (DMS), sphingosine C-20, & stearoyl acethanolamide

Figure 2. Tandem mass spectrometry data used to distinguish dimethylsphingosine (DMS), sphingosine C-20, and stearoyl ethanolamide, all having the same elemental composition. Each of these metabolites has the exact same molecular weight and are therefore indistinguishable based on accurate mass measurements. The importance of peak intensity should also be noted, for example, using in silico measurements (without accurate experimental intensities), DMS and C-20 would be indistinguishable.

In order to at least minimize the false positive paradox in metabolomics and improve the assignment statistics behind metabolite identification, we've created the METLIN database with over 75,000 molecules and 56,000+ tandem mass spectra. So while with mass spectrometry technology it is possible to observe many peaks (features) corresponding to a wide range of metabolites, given the high redundancy in the mass of metabolites, accurate mass alone is incapable of identifying them. However, tandem mass spectrometry will not completely eliminate false positives especially in cases of stereoisomers, or lipids where the location of double bonds is not well defined, nonetheless it is a step closer to identifying metabolites with a higher level of confidence.  

On a separate yet related note, I would like to acknowledge my gratitude to the companies, institutions, and laboratories that have donated and continue to provide us with compounds that allow us to generate the tandem mass spectrometry data in METLIN. They include SIGMA-Aldrich, Cayman Chemical, ChromaDex, Joint BioEnergy Institute (JBEI), Millenium Laboratories, Genomics Institute of the Novartis Research Foundation (GNF), UCSD (William Gerwick), TSRI (Dale Boger), and the NIH/NCI. We are also open to any new metabolic entities to add to METLIN, whether they are of plant, animal, or micro-organism origin. If you have metabolites that you wish to contribute, please contact us (see the contact information below).


METLIN Contact Information

Please note: If you know of any metabolomics research programs, software, databases, statistical methods, meetings, workshops, or training sessions that we should feature in future issues of this newsletter, please email Ian Forsythe at metabolomics.innovation@gmail.com.

 MetaboInterview Icon

2) MetaboInterviews
MetaboInterviews features interviews with prominent researchers in the field of metabolomics. The aim of these interviews is to shed light on metabolomics researchers around the world and give them an opportunity to share their metabolomics story. In this issue, we feature an interview with David Wishart of the University of Alberta and The Metabolomics Innovation Centre.


David Wishart

 Professor of Biological Sciences & Computing Science at the University of Alberta, Director of The Metabolomics Innovation Centre (TMIC), and Senior Research officer & Director of the Nano Life Science Program at the NRC’s National Institute for Nanotechnology (NINT)
 David Wishart
Biography
Dr. David Wishart (PhD Yale, 1991) has been with the University of Alberta (U of A) since 1995. Dr. Wishart has active research programs in structural biology, nanobiology, synthetic biology, prion biology, bioinformatics, and metabolomics. Some of his lab's most significant contributions have been in the area of protein chemical shift analysis and the prediction of protein structure.

Dr. Wishart has directed a number of core labs at the U of A over the years including the Faculty of Pharmacy's mass spectrometry core (from 1998-2002), the Polyomx bioinformatics core (2001-2004), the PENCE bioinformatics core facility (2002-2005), and the Genome Canada Bioinformatics Help Desk (2003-2011). From 2006-2009, Dr. Wishart led the Human Metabolome Project (HMP), a multi-university, multi-investigator project that catalogued all of the known metabolites in human tissues and biofluids. Using advanced methods in NMR spectroscopy, mass spectrometry, multi-dimensional chromatography, and machine learning, Dr. Wishart and his colleagues identified or found evidence for more than 40,000 endogenous metabolites. This information has been archived on a freely accessible web-resource called the Human Metabolome Database.

The methods and ideas developed for the HMP have helped lay the foundation for a number of other metabolomic databases (DrugBank, T3DB, FooDB) and metabolomic software tools (MSEA, MetaboAnalyst, MetPA, MetaboMiner). They have also led to the development of a number of interesting clinical metabolomics projects and collaborations. These include studies of several cancer biomarkers, the identification of organ transplant biomarkers, and exploring wound healing mechanisms.


Metabolomics Interview (MN, MetaboNews; DW, David Wishart)

MN: How did you get involved in metabolomics?

DW: Back in 1997 I had to teach a class on NMR to undergraduate pharmacy students and needed to come up with examples of how NMR could be useful for analyzing blood and urine for diagnostic purposes. I found a couple of papers that showed interesting results but realized that there wasn’t any kind of software or database to allow people to readily interpret NMR spectra of biofluids, or to rapidly identify and quantify compounds from NMR spectra. So, I became very interested in the computational challenge of deconvoluting NMR spectra—partly because it was very closely related to some other work I was doing in structural biology. I guess it was that challenge, or desire to build software that could rapidly interpret NMR spectra of biofluids, that led me into metabolomics. Shortly after that (1999) we spun off a small metabolomics company (Chenomx) that used some of the ideas I had developed for spectral deconvolution. Of course in those early days, the word “metabolomics” hadn’t been invented and so we struggled to find a name that could describe what we were trying to do. We concatenated the term “chemical genomics”  to come up with “che-nomics”. Obviously that term never caught on. Regardless, my peripheral involvement with Chenomx led to more and more interactions with metabolomics researchers and the eventual realization that the metabolomics community needed some common resources (databases, software, chemical libraries) to move the field further along. One thing led to another and by 2005 my lab at the University of Alberta was awarded a large grant ($7 million) from Genome Canada to characterize the human metabolome. The Human Metabolome Project or HMP, as we called it, really focused my attention on metabolomics and it catalyzed many other developments and exciting changes in my laboratory’s activities. I’m also hoping that some of the outputs from the HMP, like the Human Metabolome Library (HML), HMDB, DrugBank, T3DB, and MetaboAnalyst are also helping other young scientists get involved in metabolomics too.

 MN: What are some of the most exciting aspects of your work in metabolomics?

DW: I am particularly excited about the opportunity to work with clinicians. In my other life as a structural biologist, it’s often frustrating to realize that our best work or most exciting discoveries are often many years removed from any practical applications. But with metabolomics, some of our findings are already finding clinical applications. In other words, we’re starting to have a real and positive impact on human health. So in contrast to structural biology, metabolomics is giving me an opportunity to address relevant medical questions and in some cases, come up with practical or useful diagnostic, prognostic, predictive tests. Metabolomics is still a very young field; as a result, almost anything you try is going to be new or different. So the frequency and relative ease with which new discoveries or unanticipated findings can be made is very exciting and very appealing. Yet another compelling facet to metabolomics is the fact that you often get to work with some really talented people from very diverse backgrounds. These interactions have opened my eyes to many new areas of science and allowed me to learn a whole lot more about analytical chemistry and biochemistry, including mass spectrometry, chromatography, metabolism, statistics, and clinical medicine. With metabolomics you’re always learning and you are constantly struck by the beautiful complexity of living systems.

MN: What key metabolomics initiatives are you pursuing at your research centre or institute?

DW: We are still working on the Human Metabolome Project and we are still maintaining a large collection of databases and chemical libraries to support the metabolomics community. I am also getting more involved with data standardization and the development of data exchange standards, especially for NMR and for data visualization. We are increasingly moving into the development of technologies to create systems for “automated metabolomics” or handheld metabolomics devices using a combination of nanotechnology and microfluidics.

MN: What is happening in your country in terms of metabolomics?

DW: Canada operates a national metabolomics centre called The Metabolomics Innovation Centre or TMIC. I am very fortunate to be the director of TMIC and work with some outstanding individuals such as the co-leader of TMIC Dr. Christoph Borchers, and co-investigators Dr. Liang Li and Dr. James Harynuk—who are located in British Columbia and Alberta. Together we are trying to develop innovative metabolomics techniques and offer useful metabolomics services for Canadian researchers and companies. Several other metabolomics research groups are starting to be established in Ontario (McMaster) and Quebec, especially at McGill. Canada also has a flourishing metabolomics industry with several companies such as Chenomx Inc., Metabolomic Technologies Inc., and Metabolistics Inc. (all based in Edmonton, AB) as well as Phenomenome Discoveries (located in Saskatoon, SK). While there has been a lot of activity in human metabolomics and clinical applications in Canada, there is now a growing interest in metabolomics coming from the agri-food sector and even the oil and gas industry.

MN: How do you see your work in metabolomics being applied today or in the future?

DW: We’re hoping our databases and software servers are still useful and will continue to be useful to the metabolomics community. We will continue to update and upgrade these resources as long as funding permits. We’re hoping the technologies that we are developing will also make metabolomics easier, faster, cheaper for other researchers. We have a very strong emphasis on quantitative metabolomics (i.e., identifying and measuring absolute concentrations) and we hope that this approach will be adopted by more metabolomics laboratories. I believe quantitative metabolomics will encourage greater standardization and more widespread adoption of metabolomics, especially in the biomedical fields. In the future, we would like to see metabolomics be an integral part of clinical medicine and an integral part of food quality and food safety assessments.

MN: As you see it, what are metabolomics' greatest strengths?

DW: Unlike other fields like proteomics or transcriptomics, metabolomics is truly quantitative. This gives it a degree of reproducibility and platform independence that allows the results from metabolomics studies to be easily translated into medical or industrial or environmental practices. I think the other key strength to metabolomics is that it gives a clear, quantitative picture of the interactions between genes and the environment; in particular, metabolomics allows us to measure an organism’s phenotype in ways that were previously not possible.

MN: What do you see as the greatest barriers for metabolomics?

DW: Our obsession with genomics. In the world of “omics” science, metabolomics is like a mouse among elephants. The level of funding it receives from funding agencies and the amount of press it gets is disproportionately small for the size of the community and its overall scientific impact. For instance, nearly every genome sequencing or GWA study gets >$10 million in funding agency support without anyone batting an eye. Since 2006 we’ve spent more than a billion dollars on GWA studies of complex diseases and hundreds of news stories have been released about “new disease genes” being discovered. However many of these “discoveries” are subsequently found to be artefacts and are not reproducible. Despite this huge investment, we’ve only been able to explain about 1-2% of the observed disease risk or incidence for conditions like diabetes, autism, Crohn’s disease, and others. On the other hand, there are now dozens of published metabolomic studies that repeatedly show the same sets of metabolites being highly predictive for a large proportion of these same complex diseases that genomics can’t explain. Unfortunately, no one (in either the funding agencies or the press) is noticing this. Since 1997 the US government has invested more than $50 billion into genomics research but less than $100 million has been invested into metabolomics. In Canada, over the past 12 years, more than $3 billion has been invested into genomics and less than $10 million has been invested into metabolomics. To me this lopsided obsession represents the single greatest barrier to the success and adoption of metabolomics.

Of course, it would certainly help if metabolomics could be as fast, cheap, and as comprehensive as DNA sequencing or if it could be as routinely quantitative as a blood glucose test. The fact that metabolomics has been slow, expensive, non-quantitative and the fact that it offers pretty minimal coverage of most metabolomes is probably another barrier to its widespread adoption.

MN: What improvements, technological or otherwise, need to take place for metabolomics to really take off?

DW: It needs to be much more comprehensive. In other words, thousands of metabolites need to be identified in a single run. It needs to be faster and cheaper so that it can match the throughput of other 'omics' disciplines, like genome sequencing or microarrays. It needs more high profile successes and it needs advocates or lobbyists who are well connected in the news media and who are well entrenched in the government policy and research funding hierarchy.

 MN: How does the future look in terms of funding for metabolomics?

DW: Some countries are making significant new investments into metabolomics and overall things are looking somewhat promising in North America. I am particularly pleased to see the recent investments that the NIH is making into metabolomics. Hopefully Canada will notice what’s being done in the US. I think recent economic conditions in Europe are limiting operating investments or infrastructure support for metabolomics. Asia seems to be an area where metabolomics will experience tremendous growth over the next few years. However, my long term expectation is that metabolomics funding will still only be tiny a fraction of what is routinely provided to other areas of 'omics' science—at least until the metabolomics community does a better job of reaching out, publicizing its successes, and getting heard.

 MN: What role can metabolomics standards play?

DW: Standards are essential to the success of metabolomics. Metabolomics is still lagging behind other 'omics' fields in both the deployment of standards and the adoption of standards. Certainly improved standards and increased expectations regarding the measurement, reporting and deposition of metabolite data would really help the community. We need a “GenBank” for metabolomics. I am hoping the EBI initiative with MetaboLights and other database activities in the US will help. Of course my own group is trying to contribute to the effort through constant standardization upgrades to the HMDB and our other databases and servers.
Biomarker Beacon

3) Biomarker Beacon

Feature article contributed by Ian Forsythe, Editor, MetaboNews, Department of Computing Science, University of Alberta, Edmonton, Canada


Metabolomics is an emerging field that is complementary to other omics sciences and that is gaining increasing interest across all disciplines. Because of metabolomics' unique advantages, it is now being applied in functional genomics, integrative and systems biology, pharmacogenomics, and biomarker discovery for drug development and therapy monitoring. A substantial number of biomarkers are small molecules or metabolites (MW <1500 Da), which can be used for disease testing, drug testing, toxic exposure testing, and food consumption tracking. While standard clinical assays are limited in the number and type of compounds that can be detected, metabolomics measures many more compounds. Since a single compound is not always the best biomarker (diagnostic, prognostic, or predictive), healthcare practitioners can use metabolomic information about multiple compounds to make better medical decisions. Global metabolic profiling is now being used to determine clinical biomarkers in assessing the pathophysiological health status of patients.

In the following two recent studies, metabolomic approaches were used to develop tools for the identification of biomarkers associated with aggressive prostate cancer and colorectal cancer, respectively.
  1. McDunn JE, Li Z, Adam KP, Neri BP, Wolfert RL, Milburn MV, Lotan Y, Wheeler TM. Metabolomic signatures of aggressive prostate cancer. Prostate. 2013 Jul 3. doi: 10.1002/pros.22704. [Epub ahead of print] [PMID: 23824564]

    Although current diagnostic techniques permit the detection of prostate cancer, they fail to stratify patients according to the aggressiveness of the cancer. Increased levels of sarcosine have recently been associated with prostate cancer metastasis. In this paper, the research team sought to identify metabolites associated with aggressive prostate cancer. The investigators analyzed 331 prostate tumour tissue samples and 178 cancer-free tissue samples, using gas chromatography-mass spectrometry and ultrahigh performance liquid chromatography-tandem mass spectrometry followed by statistical analysis. When comparing prostate cancer tissue samples with cancer-free samples, they found altered metabolite profiles for metabolites involved in energetics, stress, cell growth, and loss of prostate-specific biochemical activity. In particular, the researchers found high levels of NAD+ and kynurenine in aggressive prostate tumours. This study adds to our basic understanding of how various metabolites contribute to the aggressiveness of prostate cancer, work that may one day translate into superior clinical diagnostics for this disease.

  1. Tan B, Qiu Y, Zou X, Chen T, Xie G, Cheng Y, Dong T, Zhao L, Feng B, Hu X, Xu LX, Zhao A, Zhang M, Cai G, Cai S, Zhou Z, Zheng M, Zhang Y, Jia W. Metabonomics identifies serum metabolite markers of colorectal cancer. J Proteome Res. 2013 Jun 7;12(6):3000-9. doi: 10.1021/pr400337b. Epub 2013 May 29. [PMID: 23675754]

    Researchers are increasingly looking at metabolite levels in biofluids in hopes that they might discover a molecular signature for the accurate and reliable diagnosis of disease. In this study, the researchers sought to identify metabolites associated with colorectal cancer (CRC). They analyzed serum metabolites from 101 CRC patients and 102 healthy subjects using gas chromatography time-of-flight mass spectrometry (GC-TOFMS) and ultraperformance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-QTOFMS). The investigators discovered a metabolite signature in CRC patients consisting of metabolites involved in the tricarboxylic acid (TCA) cycle, urea cycle, glutamine, fatty acids, and gut flora metabolism. This study demonstrates the potential of non-invasive, metabolite-based tests for the diagnosis of CRC in patients.
Metabolomics Current Contents

4) Metabolomics Current Contents

Recently published papers in metabolomics:
MetaboNews

5) MetaboNews
9 Jul 2013
IMDEA Food and Metabolon, Inc. Announce Strategic Collaboration to Advance Nutrition-based Personalized Medicine

IMDEA Food, a Translational Research Institute from the Community of Madrid, dedicated to investigating the relationships among nutrition, food and health, and the US-based company Metabolon Inc., the pioneering leader in the field of metabolomics and molecular diagnostics serving the pharmaceutical and food industries, today announced  an ambitious collaboration program. The agreement, signed today in Madrid by Dr. John Ryals, President and CEO of Metabolon, and Dr. Guillermo Reglero, Director of IMDEA Food, establishes the framework for future strategic projects aimed to develop functional foods and diagnostic tools. 
 
Of particular interest is the prevention of prevalent chronic diseases with high societal impact, such as cardiovascular disease, cancer, obesity and neurological diseases, which is highly dependent on understanding food science and nutritional impact. To achieve this goal, individual in-depth studies to characterize the molecular mechanisms underlying the health benefits of foods and food components are needed.
 
“These studies promise to lead toward an efficient decrease of morbimortality due to chronic degenerative diseases and a better quality of life. IMDEA Food and Metabolon will combine their knowledge to advance towards this objective. A combined functional genomics and metabolomics approach involving complementary technologies  and multidisciplinary expertise is paramount to achieve the scientific rigor and level of evidence required to bring nutrition-based personalized medicine to the public with the final objective of living longer and healthier”, commented  Prof. Jose Ordovas of Tufts University, a world-renowned pioneer in nutrigenomics. Prof. Ordovas serves as the Senior Scientist and Director for the Nutrition and Genomics Laboratory and as the Chair of the Functional Genomics Core of the Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University.  Since its inception in 2007 Prof. Ordovas has been Chairman of the Board and Scientific Director of IMDEA Food.
 
The IMDEA Food Institute carries out human nutrigenomic studies, which are reviewed by a Research Ethical Committee, on its platform comprised of common services for genomics, biostatistics, bioinformatics and nutritional counseling. Metabolon is the world leader in metabolomic analysis of complex biological samples and has made major contributions to the discovery of biomarkers and biochemical pathways associated with nutrients and drugs, and which have led to the development of unique diagnostic tools. Scientists from IMDEA Food and Metabolon have met in IMDEA Food’s new headquarters located in Madrid to define the lines of common interest and greatest priority and to launch the first of a series of studies aimed at defining the molecular basis of action of key food ingredients.
 
Dr. Steve Watkins, Chief Technology Officer, Metabolon commented, “Collaborative studies with IMDEA will employ the combined resources and expertise of our organizations to identify appropriate biomarkers of disease risk and prevention and to monitor biological impact of nutritional components in foods. This strategic collaboration is pivotal to advancing our understanding of nutrition’s influence on health and disease.” 

 
1 Jul 2013
Metabolomics—Young Field, Bright Future
Emerging Market Predicted to Double in the Next Five Years to Well Over One Billion Dollars

Metabolites have been used as biomarkers for decades. The presence of sugar in urine for diabetes may be their oldest application, but in the past five or six years, their occasional use has become the discipline of metabolomics. This attention to metabolites is resulting in a growing number of biomarkers that is transforming the industry.

“It’s difficult to dissect ‘biochemistry’ from ‘metabolomics’ in research. Where classical approaches end and ‘metabolomics’ begins is something of a philosophical question,” notes Anthony Walker, Ph.D., partner, Alacrita.

However, “It is probably fair to say the value of metabolomics will be as surrogate markers of active protein pathways, which may help guide more targeted analysis of gene and protein expression to discover new targets and disease markers. In terms of drug discovery, the main area of focus has been monitoring toxicology studies and predicting their outcomes.”

According to Dr. Walker, the next five years will see a continued focus on the central relevance of regulatory pathways across all therapeutic areas and their relevance to the production of metabolites.

“Essentially all of biology is regulated by proteins interacting with substrates to manifest a particular biological event—nucleic acid transcription and translation, protein and amino acid recycling, energy transfer, anabolic processes, catabolic processes, active transport, et cetera,” he continues.

“Metabolomics provides a selected view of the end-products of a set of these processes. That will be an important addition to knowledge but, in the near term, may be a relatively poor substitute for measuring the protein pathways and their activation status directly.

The big change, as he sees it, is the realization that such pathway analysis applies to neurobiology as much as to oncology, metabolic disease, inflammation, etc.

“Systems biology approaches are likely to become much more prominent. It’s clear that everything interacts, and much historic progress has been made on the basis of reductionism,” Dr. Walker says.

That approach has yielded breakthroughs, “but ultimately, a holistic, systems-wide approach will be needed to explain the huge degree of biological complexity,” he explains, while suggesting that making tangible advances in metabolomics may require another 20 years of research.

 
10 Jun 2013
Species for the MetaboLights Reference Layer Survey

Researchers at the the European Bioinformatics Institute (EBI) are preparing a reference layer of metabolism knowledge for the MetaboLights database. MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. The MetaboLights team would like to gauge the interest that the metabolomics community has regarding the organisms that this reference layer should include. For this purpose they have designed a Google survey and would really appreciate your input.

 

Please note: If you know of any metabolomics news that we should feature in future issues of this newsletter, please email Ian Forsythe (metabolomics.innovation@gmail.com).

Metabolomics Events

6) Metabolomics Events
6 Aug 2013

Frontiers in Nutritional Science: The Inaugural Australian Symposium on Nutritional Metabolomics
Venue: Rydges World Square - Sydney, Australia
When: 6 August 2013, 8:30am - 5:00pm

Early Bird Registration ends this Friday, July 12, 2013 - Save $50 (Australian Dollars)

This one day symposium will bring together international and national experts to provide a comprehensive, up-to-date overview of the emerging field of nutritional metabolomics.

About the event

Nutritional Metabolomics is an exciting, emerging frontier field of science.

Metabolomics (measuring metabolites from physiological process) provide information, 'windows into the body', which have the potential to transform how we measure health, how we identify and monitor people most at risk of disease, and the way we monitor food intake.

The event will provide food and health science professionals and researchers, an exciting insight into how this new science can be applied to better understand the ways in which food, diet and the body interact.

To stimulate interest and collaboration in this frontier field of health sciences, we are organising a symposium which aims to explore opportunities for using metabolomics to improve human health by nutritional means.

This one day symposium will bring together international and national experts to provide a comprehensive, up-to-date overview of this fast growing field.
The event will provide food and health science professionals and researchers, an exciting insight into how this new science can be applied to better understand the ways in which food, diet and the body interact.

Topics to be covered include:
  • How can metabolomics be used in nutritional science?
  • What tools and technologies are available for metabolomics in nutritional science?
  • Applications of metabolomics in nutritional science
  • Using breath as a measure of health and nutritional status.
This symposium is organised by CSIRO Animal, Food and Health Sciences, in conjunction with UniSA’s Sansom Research Institute. Speakers will be by invitation only.
For more information, visit http://www.csiro.au/en/Organisation-Structure/Divisions/Animal-Food-and-Health-Sciences/Nutritional-Metabolomics-Symposium.aspx?goback=%2Egde_4185659_member_229009122.
13-17 Aug 2013

Metabolic Signaling & Disease: From Cell to Organism
Venue: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

Abstract Deadline: May 31, 2013

Organizers:
Daniel Kelly, Sanford-Burnham Medical Research Institute
Mitchell Lazar, University of Pennsylvania
Susanne Mandrup, University of Southern Denmark

We are pleased to announce the first Cold Spring Harbor meeting on Metabolic Signaling & Disease: From Cell to Organism which will begin on Tuesday evening, August 13 and end at noon on Saturday, August 17, 2013.

Metabolic regulation is at the intersection of many scientific fields, ranging from basic biochemistry and molecular biology to physiology, to the study of disease pathogenesis. Currently, a major challenge for these diverse fields is to define commonalities and differences in metabolic pathways and their regulation, and determine the role of these processes for physiology and disease states. This meeting will fill an important gap by bringing together outstanding researchers focused on diverse pathways, cell types, or diseases with a common theme of understanding how metabolism is regulated in physiology and disease states.

For more information, visit http://meetings.cshl.edu/meetings/2013/metab13.shtml.
9-11 Sep 2013

First International Environmental ‘Omics Synthesis Conference
Venue: Cardiff University, UK

First annual International Environmental ‘Omics Synthesis conference will be held in Cardiff, UK, on September 9-11th, 2013. This conference is supported by NERC Mathematics and informatics for Environmental ‘Omics data Synthesis program and the UK Science and Technology Facilities Council Futures Programme under the coordination of the recently established Environmental ‘Omic Synthesis Centre (EOS).

The aim of this conference is to bring together researchers and organisations from a range of disciplines representing those involved in the development of new approaches in data handling and generation with those harnessing ‘Omics to advance key areas in Environmental Science. It is our hope is that the resulting interaction and exchange of ideas will lead to novel approaches, new collaborations and the establishment of a wider integrated ‘Omics community.

iEOS2013 – Announcement Poster: http://environmentalomics.org.gridhosted.co.uk/wp-content/uploads/2013/03/iEOS2013-Final-Announcement.pdf
 
For more information, visit http://environmentalomics.org/iEOS2013/.
1-3 Oct 2013

The 10th International Symposium on Milk Genomics and Human Health
Venue: Davis, California, USA

Join us October 1-3, 2013 in Davis, California to celebrate the 10th Anniversary of the International Symposium on Milk Genomics and Human Health. This year's theme is Milk Leading Life Sciences Research in the 21st Century.

The venue for this year's event is the U.C. Davis Conference Center located on the University of California, Davis campus in the United States.

Program
The three day event will bring together international experts in nutrition, genomics, bioinformatics and milk research to discuss and share the latest breakthroughs and their implications.
 
The Annual Symposium is our flagship event that features scientific research related to milk and human health done throughout the world. The  symposium draws from the diversity of its memberships to cover the breath of genomics themes that reflect the interest of the Consortium. The goal of the Consortium is to bring together the research and dairy communities to share, translate, and interpret data that are happening within the fields of the "-omics" science.  
 
For more information, visit http://milkgenomics.org/symposia/the-10th-international-symposium-on-milk-genomics-and-human-health-october-1-3-2013.
7-11 Oct 2013

Metabolomics course: SLC-Tjärnö marinebiological laboratory
Venue: Center for Marine Chemical Ecology at SLC Tjärnö on the Swedish West coast

Do you work, or want to work with metabolomics? This intensive course in mass spectrometry based metabolomics targets the complete procedure, from experimental design and data acquisition to post processing and statistical analysis. A mixture of lectures and hands-on experience guided by international experts will help you develop your metabolomics skills. The course is intended for PhD students and Post Docs. Priority will be given to students in chemical ecology, but we also welcome applications from other disciplines. The course will be held at the Center for Marine Chemical Ecology at SLC Tjärnö on the Swedish West coast. Food and lodging is covered by a generous grant from the Swedish Royal Academy of Science. Students will need to cover travel costs form other sources. The course corresponds to 2.5 HP (ECT).

Application should include a short motivation (<1 page) and a brief CV. Submit by E-mail to erik.selander@bioenv.gu.se

Application deadline 15th of August 2013

Teachers:
Prof. Georg Pohnert, Biorganic Analytics, Friedrich Schiller University, Jena
Prof. Johan Trygg, Department of Chemistry, Umeå University
Dr. Ulf Sommer, NERC Metabolomics Facility, University of Birmingham

Contact and inquiries:
Erik Selander erik.selander@bioenv.gu.se
Göran Nylund goran.nylund@bioenv.gu.se
 
Course Flyer: http://www.metabonews.ca/May2013/events/Metabolomics%20course%20flyer.pdf
24-26 Mar 2014

3rd International Conference and Exhibition on Metabolomics & Systems Biology
Venue: Hilton San Antonio Airport, USA

Theme: Multi-Omic Approaches to Envision the Role of Metabolites in Biological Systems

The annual Metabolomics conference mainly aims in bringing Metabolomics and Systems Biology researchers from around the world under a single roof, where they discuss the research, achievements and advancements in the field.

After the success of Metabolomics-2012 & Metabolomics-2013, OMICS Group is proud to announce the 3rd International Conference and Exhibition on Metabolomics & Systems Biology which is going to be held during March 24-26, 2014 at Hilton San Antonio Airport, USA.

Metabolomics-2014 meeting promises a program full of practical workshops and parallel sessions covering the broad range of biological and technological metabolomics topics, providing rich opportunities for networking and approach towards biomedical and biological scientific research.

Join us at Metabolomics-2014 as we gather together to share ideas, insights and advances  in the field of Metabolomics and Systems Biology.

Conference Highlights
  • Novel Approaches to Cancer Therapeutics
  • Analytical and Bio-Analytical Techniques in Metabolomics
  • Transcriptomics
  • Toxicology and Drug Metabolism
  • Current Trends and Innovations in Metabolomics
  • Computational Biology, Synthetic Biology and Systems Biology
  • Computational Genomics
  • Metabolomics Syndrome
  • Recent Approaches in Proteomics and Genomics
  • Glycomics and Lipidomics

To share your views and research, please click here to register for the Conference.

For more information, visit http://www.metabolomicsconference.com/.
23-26 Jun 2014
Newly announced

Metabolomics 2014: 10th Annual International Conference of the Metabolomics Society
 The Official Joint Conference of the Metabolomics Society and Plant Metabolomics Platform
The Official Annual Meeting of the Metabolomics Society
Venue: Tsuruoka, Japan

Health, medical, pharmaceutical, nutritional, agricultural, microbial, bioenergy, environmental and plant sciences meet biochemical, analytical and computational technologies.

Early registration and abstract submission due March 31, 2014.

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Please come back later for detailed information about Metabolomics 2014 by visiting http://metabolomics2014.org.

Please note: If you know of any metabolomics lectures, meetings, workshops, or training sessions that we should feature in future issues of this newsletter, please email Ian Forsythe (metabolomics.innovation@gmail.com).

Metabolomics Jobs

7) Metabolomics Jobs

This is a resource for advertising positions in metabolomics. If you have a job you would like posted in this newsletter, please email Ian Forsythe (metabolomics.innovation@gmail.com). Job postings will be carried for a maximum of 4 issues (8 weeks) unless the position is filled prior to that date.

Jobs Offered

Job Title Employer Location Posted Closes Source
Assistant/Associate Professor Tenure Track Positions McGill University Montreal, Canada 30-May-2013 31-Aug-2013
 Metabolomics Society
Senior Scientist LipoScience Raleigh, NC, USA 18-Jun-2013 30-Aug-2013
 Metabolomics Society
Research Assistant / Research Associate - Bioinformatics Imperial College London
 London, UK
 11-Jul-2013 22-Jul-2013
 Imperial College London
Postdoc in NMR-based metabolomic profiling of intact prostate tissues  Umeå University Umeå, Sweden 15-Jun-2013 15-Aug-2013
 naturejobs.com
Postdoctoral Research Fellow (m/f) Max Planck Gesellschaft Köln, Germany 24-Jun-2013 6-Aug-2013
 naturejobs.com
Development, implementation and use of NMR and atmospheric pressure ionization mass spectrometry databases for metabolomics MetaboHUB Bordeaux Metabolome Facility, INRA Bordeaux Center, F-33140 Villenave d'Ornon, France
 22-May-2013 2-Aug-2013
 MetaboHUB
Post-Doctoral Fellowship in Metabolomics University of Maryland, School of Pharmacy
 Baltimore, MD, United States 27-Jun-2013 31-Jul-2013
 naturejobs.com
Web server administration and development (IT Manager) - expires July 15, 2013 MetaboHUB Toulouse, France
 7-Jun-2013 15-Jul-2013
 MetaboHUB
Scientific database and web interface building (web developer) MetaboHUB Clermont Ferrand, France
 7-Jun-2013 15-Jul-2013 MetaboHUB


Jobs Wanted

This section is intended for very highly qualified individuals (e.g., lab managers, professors, directors, executives with extensive experience) who are seeking employment in metabolomics. We encourage these individuals to submit their position requests to Ian Forsythe (metabolomics.innovation@gmail.com). Upon review, a limited number of job submissions will be selected for publication in the Jobs Wanted section.
  • Research or Lab Manager Position Sought (Candidate has extensive NMR metabolomics experience and knowledge including NMR instrumentation maintenance): [Candidate's CV]

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