A newsletter published in partnership between TMIC and the Metabolomics Society
Issue 29 - January 2014


Online version of this newsletter:

Welcome to the twenty-ninth issue of MetaboNews, a monthly newsletter published in partnership between The Metabolomics Innovation Centre (TMIC, and the international Metabolomics Society (, 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. MetaboNews now represents the one-stop-shop for the very latest and most critical news about the science of metabolomics. In this issue, we feature a Partnership Spotlight article on the importance of industry partnerships in metabolomics research and a metabolomics interview with Giuseppe Astarita of Waters Corporation.

This issue of MetaboNews is supported by:

Biocrates --
                                Standardized Metabolic Phenotyping  
Chenomx --
                                Metabolite Discovery & Measurement
Biocrates Life Sciences AG

Chenomx Inc.

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Metabolomics Society News

Conference: Analytical Tools for Cutting-edge Metabolomics
A reminder that the first in a new series of shorter, science topic-focused Metabolomics Society organised, or jointly organised, meetings kicks off in 2014. This first one-day meeting, jointly organised with the UK’s Royal Society of Chemistry, will be focused on analytical metabolomics.
Location: Chemistry Centre, Burlington House, London, UK
Date: 30th April 2014

We have a fantastic line up of speakers including:
•    Professor Jeremy Nicholson (Imperial College, London)
•    Professor Roy Goodacre (University of Manchester)
•    Dr Julian Griffin (MRC Human Nutrition Research, Cambridge)
•    Dr Steffen Neumann (Leibniz Institute of Plant Biochemistry, IPB Halle, Germany)
•    Professor Paul Thomas (Loughborough University)
•    Professor Jean-Luc Wolfender (University of Geneva, Switzerland)
Early-bird registration closes on 14th March 2014
Abstract submission deadline is also 14th March 2014
Please visit the website above to learn more, including about the Metabolomics Society Travel Awards that are available.

Membership renewal for 2014

If you have not already done so, it is now time to renew your membership for 2014 at Membership in the Society is based on the calendar year, so all current members will have to renew their membership to stay in good standing. We hope that you have enjoyed being part of and benefited from the considerable expansion of the Metabolomics Society during the past 12 months, and will remain a loyal member of our growing community. As the society continues to expand, we expect to be able to offer further membership benefits including discounted member registration at the 10th Annual Metabolomics Society Conference in Tsuruoka, Japan and for new Regional/Topical meetings (please see the announcement of the joint meeting hosted by the RSC and the international Metabolomics Society below). Student members with over 3 months standing are also able to apply for our Student Prize and Travel Awards. Remember to renew now to take advantage of our early bird discounted registration fees.

Member benefits (for all Members)
1. No membership fee increases for 2014.
2. Networking and information exchange with an international membership of professionals devoted to furthering metabolomics related science: via conferences and workshops, the Society’s many Interest Groups, and social media including the Society’s Facebook page and Twitter feed.
3. Discounted registration fees for Metabolomics Society conferences.
4. Subscription for electronic access (and optional print copies*) to the Metabolomics journal, the official publication of the Society.
5. Receive information and electronic notices of metabolomics conferences, workshops and seminars.
6. Posting of job advertisements on the Society's website and via Twitter.
7. Monthly electronic update on the Society's activities.
8. Eligibility to nominate individuals for an Honorary Fellowship of the Society** and to vote in Society elections.
9. Eligibility to stand for Office within the Society**.
* Additional fee applies, see registration website; Members will also have electronic access to all issues and therefore print copies of back issues will not be available to Members who register late in the calendar year.
** Not applicable for Student Members.
Further benefits for Student Members
Students who are active members more than 3 months prior to a Metabolomics Society conference are also eligible to:
10. Apply for Metabolomics Society student travel awards.
11. Apply for Metabolomics Society student prizes.

For more information about membership, visit

Early-Career Members Network (EMN)

The EMN is dedicated to, and run by early-career scientists who are members of the Metabolomics Society and are from either academia, government or industry. The network aims to provide a forum for metabolomics researchers at the start of their professional career. Please follow us on Twitter (@MetabolomicsSoc) and Facebook (Metabolomics Society) to stay up-to-date on all news and upcoming events.

The EMN is planning to establish a series of online webinars exclusive to members of the Metabolomics Society that will allow early-career scientists to connect with senior scientists globally. These sessions will range from very basic requirements across our discipline to informal training of data processing techniques and equipment as well as more dedicated sessions with top scientists in metabolomics. Why not turn to our society for the very latest metabolomics technologies and the most basic needs that an early-career scientist might have?

We are also planning two workshop sessions at the 10th Annual International Conference of the Metabolomics Society in Tsuruoka (Japan) where you can expect tailored talks specifically for the early-career scientist and a chance to meet others like you in a stimulating and creative environment.

Please contact us with ideas that you might have on any of the aforementioned events via We are looking forward to hearing from you!

Status of Data Standards
This section is contributed regularly by Christoph Steinbeck (Chair of the Society’s Data Standards Task Group) and Reza Salek ( from EMBL-EBI, Cambridge UK.
The coordination outcome will be published on the COSMOS ( website.

2014 Honorary Fellows of the Metabolomics Society
An Honorary Fellowship is a significant lifetime award granted by the Society to exceptional members of our community. Commissioned in 2012, and with up to two awards each year, the Board of Directors welcomes nominations for these Fellowships, with a closing date of February 1st, 2014. See for further details.


Metabolomics journal, Vol. 9, Issue 6, December 2013
See the latest issue of our journal at:
In addition to the many excellent research papers, each issue contains a section of typically four pages that is contributed by the Society. For the December 2013 issue there are two short pieces:
•    News: The year in review: Highlights of the Metabolomics Society in 2013
•    News: Metabolomics Society Board Election 2013: introduction of new board members

Stay abreast of the latest metabolomics news via the Twitter feed on the front page of the website. Also you can follow us on Twitter: Metabolomics Society @MetabolomicsSoc and Metabolomics journal @Metabolomics. And you can visit us on Facebook.


Partnership Spotlight

The importance of industry partnerships in metabolomics research: from vendors to technology users

Warwick Dunn 1, Ute Roessner 2, and Mark Viant 1
1. School of Biosciences, University of Birmingham, UK
2. School of Botany, University of Melbourne and Metabolomics Australia, Australia

The metabolomics community is rapidly growing; we are observing increasing numbers of scientific publications (for example, in 2013 the journal Metabolomics expanded from 4 to 6 issues each year) and increasing numbers of attendees at metabolomics conferences (for example, the 9th Annual Meeting of the Metabolomics Society in 2013 was the highest attended annual meeting so far with greater than 700 attendees).

Synergistic relationships within industry and also between industry and academia are important to drive forward the growth of metabolomics. A report published in 2013 on the worldwide metabolomics market for clinical disease biomarker research and application anticipates double-digit growth up to 2017 [1]. The report defines the supportive factors as being:

It is clearly observed in this survey that a synergistic relationship is required between technology providers (vendors) and users of these technologies in industry (for example, pharma, agrichemical, service providers) and academia. Examples of how these relationships can benefit both parties are shown in Figure 1 and are discussed below.

Synergistic relationships are required between
        technology providers and users of these technologies in

Figure 1. Synergistic relationships are required between technology providers and users of these technologies in industry and which can provide beneficial support for both groups. The same relationships are observed between technology providers and users of these technologies in academia.

Strong collaborative arrangements between vendors and technology users are one of the changes helping to drive this reported growth. These two groups can help drive innovation in technology development and perform high-quality biological research. As an example, let’s investigate the mutual benefits of collaborative agreements between academic researchers and vendors. There are a number of these collaborative agreements operating globally. Two of potentially many examples include Thermo Fisher Scientific’s Technology Alliance Partnerships with academic institutions, including with the University of Birmingham [2], and similar relationships between Agilent Technologies and academia, for example with Metabolomics Australia [3]. These publicised and official collaborative agreements are typically, but not always, developed following years of collaboration leading to success for both parties and where trust and respect have been gained.

For the vendors these collaborations provide the following advantages:
For academic groups these collaborations provide
These are just a limited numbers of examples to highlight the importance to both parties of these collaborative partnerships. Many of the above points are also applicable between vendors and technology users in industry. As metabolomics continues to grow, it is expected that the number of these synergistic interactions will also increase.

To enhance the synergies that are readily apparent above, the international Metabolomics Society has recently formed an Industry Engagement Task Group that has the following goals. First and foremost it seeks to enhance the relationships between the Metabolomics Society, the scientific community that it serves, and several different types of companies including software and hardware vendors, service providers, and users of metabolomics technologies within industry. As part of this, the second goal is to improve the benefits provided by the Metabolomics Society to support the growth of metabolomics within industry, both as a tool for scientific discovery and as a commercial product. The third goal is to improve the benefits provided by industry to aid the growth of the international metabolomics community. A more specific but equally important goal is to search for opportunities for synergistic collaborations between industry and academia, for example in the provision of metabolomics training, focused building of metabolomics research capacity, in technology development, and in scientific dissemination as highlighted above. The Industry Engagement Task Group is currently being expanded from the five members of the Metabolomics Society board (chaired by Professor Mark Viant, University of Birmingham, UK,, and is developing a framework to deliver the goals outlined above. This group welcomes views from the community.


Conflicts of interest
Authors hold collaborative agreements with Thermo Fisher Scientific (WD, MV), Agilent Technologies (UR), and Bruker (UR).

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



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 Giuseppe Astarita.

Giuseppe Astarita

Principal Scientist at Waters Corporation, Milford, Massachusetts, USA, and Adjunct Professor at Georgetown University, Washington, DC, USA

 Giuseppe Astarita


Giuseppe Astarita, a principal scientist at Waters Corporation (Milford, Massachusetts USA) and adjunct professor at Georgetown University (Washington, DC USA), specializes in the areas of lipidomics and metabolomics. His research interests include lipid mass spectrometry and metabolomics, as applied to translational medicine and biomarker discovery. Dr. Astarita is applying the latest technologies in the study of health and disease as well as food and nutrition. In his current position at Waters, he brings his background to bear in contributing to the development of the company's metabolomics business.

Metabolomics Interview (MN, MetaboNews; GA, Giuseppe Astarita)

MN: How did you get involved in metabolomics?

GA: I like to say that I got involved in metabolomics starting with lipidomics and I got involved in lipidomics one lipid at a time. Back in the day, I studied biochemistry. Yet I always had a strong interest in neurochemistry and nutrition. So in 2003, I joined Dr. Daniele Piomelli's lab at the University of California, Irvine to study lipids as they relate to cognition and appetite. We used to monitor the levels of a class of lipids called endocannabinoids because they bind to the same receptor of tetrahydrocannabinol, the active ingredient of Cannabis. We investigated the physiopathological regulation of endocannabinoids in response to behavioral, pharmacological, or genetic manipulations. The year 2003 was also the year that the term "lipidomics" began to appear in peer reviewed manuscripts. At the time, we had only a single-quadrupole instrument in the lab, but it was enough to start profiling tens of molecules similar in structure to the class of the endocannabinoids. In 2005, thanks to a partnership with Agilent, we started using tandem MS. Thus we could expand the analysis of endocannabinoids to their precursors and metabolites, performing a sort of “endocannabinoid lipidomics” (PMID: 19171504). Then, the path from lipidomics to metabolomics was short and also necessary to fully understand biochemistry. Lipid metabolism indeed is heavily interconnected with the metabolism of more polar metabolites like the ones involved in energy metabolism.

I suppose I was at the right place at the right time, lucky to have had great tutors and collaborators along the way, and Dr. Piomelli was certainly one of them. Now, working at Waters, I stand on the shoulders of metabolomics gurus like Drs. John Shockcor and Robert Plumb, and I work with a talented team of scientists in multiple omics disciplines led by Dr. James Langridge. I'm fortunate also to have found a long list of academic collaborators with whom I explore the limits of our understanding of biology using Waters’ latest technological tools.

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

GA: I enjoy working at the border between technology and biology. In seeking answers to real biological questions, Waters encourages me to play with the latest "toys". I find myself at the forefront of a technology that is growing exponentially, an exciting technology that offers limitless potential for discovery. I'm continually discovering new ways to apply metabolomics to various fields, from basic to translational research in pharmaceuticals, nutrition, food chemistry, clinical, microbial, and energy research. Thus I'm almost constantly interacting with internal and external collaborators as well as key leaders in metabolomics from both academia and industry.

My work allows me investigate the still-unknown world of what we eat and what our bodies are made of. Indeed, I've always been perplexed by the fact that we don’t entirely know that seemingly basic information (PMID: 24009004). Metabolomics offers us the opportunity to better understand the molecular definition of health and disease, or what wellness means in molecular terms. The famous astronomer Carl Sagan once said “we are made of star-stuff.” Paraphrasing his statement I would say “we're made of metabolite-stuff." Indeed metabolites not only act as messengers or energy sources but they are actually the building blocks of all biological matter. On this point, I agree with the ancient Greek philosophers, who said that we are the air we breathe, the food that we eat. To that, we might add that “we are our metabolome”. That is, we're made of metabolites, and we interact with the environment through a continuous exchange of metabolites.

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

GA: Working in the field of MS-based metabolomics, we came to realize that there's a limit to what accurate mass can achieve. Consider, for example, isobaric and isomeric species. Neither is resolvable solely by mass spectrometry. So we're working to enable the use of innovative technologies, integrating them in more traditional protocols for MS-based metabolomics applications. New orthogonal analytical tools can indeed allow a more confident identification of the metabolites.

For example, we currently use ion mobility to support traditional UPLC-MS metabolomics protocols. From ion mobility we can derive collision-cross sections, a measure of the shape of molecules. Collision-cross sections offer an additional coordinate for identifying metabolites. Along with accurate mass and retention time, this coordinate, can be annotated in databases. In this context, we worked on new informatics solutions that process ion-mobility MS data, filtering them on the basis of collision-cross-section values and improving the fragmentation results. In our group, we are also working toward expanding the applications of ion mobility in metabolomics using desorption-ionization MS and ambient-ionization MS. A post-ionization separation tool like ion mobility becomes particularly useful when no chromatographic separation occurs before MS detection, as in the case of MALDI, DESI, DART, or LAESI.

Ion mobility to support traditional
        UPLC-MS metabolomics protocols

We are also using monodimensional or multidimensional UPLC and new chromatographic tools to improve metabolomics separations before MS detection (monodimensional lipidomics separation; monodimensional polar metabolites separation; bidimensional lipidomics; multidimensional lipidomics). For example, we are working with ultra performance convergence chromatography (UPC2), which uses liquid CO2 as mobile phase, and represents an evolution of supercritical fluid chromatography, in terms of speed and reproducibility of analysis. UPC2 is enabling new ways of separating lipids (lipidomics; fatty acids; triacylglycerols) and other chiral metabolites. Another interesting chromatographic tool we are working on is a novel microfluidic device for lipidomics applications, which offers the advantages of increased sensitivity, decreased solvent consumption, and lower injection volume over traditional UPLC. Reducing solvent consumption is highly desirable when analyzing hundreds of samples. Both UPC2 and microfluidics technologies operate at an environmentally friendly, cost-saving, scale with respect to solvent consumption and waste disposal. Having such advantages, while maintaining UPLC-like performance in terms of chromatographic resolution, robustness and reproducibility of analysis, could be a real game-changer for chromatography.

A novel microfluidic device for lipidomics

Finally, in collaboration with Non Linear Dynamics, a leader in omics software, we have been working on new informatics solutions that can handle “big data” in a user-friendly way, delivering the results of complex metabolomics analyses with only a few mouse clicks. The software's latest version solves the identification problems that we typically see in metabolomics. Thus you interrogate publicly available databases and better identify individual metabolites by scoring them according to their accurate mass, isotopic pattern, retention time, collision cross section, and either theoretical or experimental fragments.

New informatics solutions that can handle “big data” in
        a user-friendly way

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

GA: In the US—and worldwide—I'd say, we are definitely noticing a growing number of metabolomics initiatives, thanks to both public and private funding: 1) new grants to academia and industry for metabolomics research, 2) a huge rise in the number of conferences in lipidomics and metabolomics, and 3) broader interest from the scientific community toward applying a systems biological approach to answer scientific questions. Until a few years ago, most of the scientific community ignored metabolomics. But now, more and more scientists understand metabolomics' value. Finally, both academia and industry are increasingly working to develop new analytical approaches, techniques, and software to make tasks associated with metabolomics easier.

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

GA: Part of what we do is enable new technology to bring innovation in metabolomics. Innovative metabolomics solutions are already helping to elucidate novel biochemical pathways and to discover new metabolites that have, so far, remained undiscovered. Some of these metabolites could be biological markers for a disease. Others could shed light on a disease mechanism. Still others could be markers of food quality, as I explained in a recent editorial in Analytical Scientist magazine. The possibility for developing standard procedures for analyzing such metabolites could lead to the development of metabolomics kits, facilitating routine analysis for quality control and clinical research. The integration of metabolomics data with complementary information from proteomics and genomics could lead to a systems biological strategy that would help us better describe the complexity of biological organisms. 

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

GA: The benefits of untargeted and targeted metabolomics differ. Untargeted metabolomics offers the capability to explore, in an unbiased fashion, the composition of a sample. This exploration can lead to, for example, unexpected discoveries of new metabolites. Comparative untargeted analysis offers investigators the opportunity to identify new biomarkers or novel mechanistic pathways involved in health and disease or nutrition. All of these possibilities are exciting for scientists.

Targeted approaches validate and quantitate unbiased discoveries. Multi-targeted profiling studies allow monitoring of hundreds of selected metabolites so that we could profile entire biochemical pathways, including biological precursors and their metabolites. Also, targeted approaches can increase analytical sensitivity, which is often required to analyze very low abundance metabolites, for example, oxygenated lipids.

Finally, let’s not forget the expanding field of MS imaging, like MALDI imaging, which provides spatial information about the metabolite composition in tissues, a sort of molecular microscope. The use of other ambient ionization tools, especially when coupled with ion mobility-MS, could allow single-day, rapid screenings of metabolites for predictive, preventive, and personalized medicine as well as quick quality and forensic checks.

              screening of metabolites

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

GA: As of now, some of the greatest barriers are 1) trying to make sense out of all the data and 2) metabolite identification. For data interpretation, we are only now beginning to develop novel bioinformatics solutions that account for processing and sharing enormous amounts of data. Software solutions should allow us to integrate metabolomics data with multi-disciplinary information, including genomics and proteomics data, for pathway analysis and also variables such as clinical records or other environmental parameters. When sharing data with other collaborators, the inter-labs reproducibility would require more focus on the standardization of procedures for sample preparation and analysis. The implementation of automatic solutions could help in this regard.

For metabolite identification, we could benefit from the integration of orthogonal measurements to be more confident in the assignment of the chemical structure. Orthogonal measurements should include exact mass, fragmentation information, collision-cross sections, retention times, and integration of other analytical techniques such as UV and NMR.

Although implementing new solutions to face these barriers will be ongoing, much remains that's easily achievable, as evidenced by the increasing numbers of publications in high-profile journals that adopt metabolomics approaches.

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

GA: Metabolomics workflows must be reproducible and cost-effective; software for data processing and visualization of results needs to be user-friendly and easy to use without reading a manual or knowing how to code. Metabolomics may have started out as a field exclusively for analytical chemists or bioinformatics, but it is increasingly becoming a field for biologists and clinicians. In their hands, metabolomics is just another tool—a very basic one—because it helps answer fundamental questions like these:  What is in my sample? Can I differentiate two groups of samples like healthy versus diseased subjects using a panel of metabolites? What is in my food or drinks?

One day, perhaps, individuals will be able to routinely screen panels of metabolites to determine the quality of the food they eat—or even their own health status.

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

GA: In the past, exploratory studies were always considered a “fishing expedition” and therefore risky investments. But now the inability of traditional research approaches to provide the results we expect is breathing new life into innovative solutions like metabolomics. Metabolomics is the modern “out of the box” tool. Time will tell, of course. As of now, though, we're seeing a boom of potential clinical biomarkers that have been discovered using metabolomics approaches, and this fact is generating a new market to invest in.

The pharmaceuticals and food industries may also provide fresh resources to fuel metabolomics. Pharma is using metabolomics to reinvent itself in areas of research where old hypotheses need refreshing with unbiased views regarding the biology underlying diseases. A recent article on the New Yorker notes the pitfalls associated with developing a drug without understanding the cause of the disease that it is trying to treat. Increasingly, our lack of understanding of fundamental biology is leading big pharma to halt research programs especially in conceptually complex fields like neuroscience. This evidence suggests that a hypothesis-based, reductionist approach may not always be the best way to begin a drug's development. As an alternative, the holistic approach of metabolomics could generate new hypotheses, shedding light on new pharmacological targets. As for the food industry, it, too, is betting on metabolomics to discover biomarkers that detect the safety, quality, and traceability of food products.

MN: What role can metabolomics standards play?

GA: Standard operating procedures are keys to developing reliable and reproducible measurements of metabolites. Reproducibility is particularly important when we speak of targeted analysis, either for validation of initial discoveries or routine analysis for clinical research and quality control. Yet standardization of procedures could prove useful also for untargeted metabolomics approaches, where hundreds of samples must be analyzed in different batches or where a standardized procedure for the identification of metabolites can facilitate the reproducibility of some measurements, such as retention times.

Common, quality-control samples should also be used to establish a system's suitability before performing both targeted and untargeted metabolomics analysis. Finally, reference standards available for the entire community could allow creation of in-house databases that would facilitate identification and quantification. The availability of such reference standards would also allow the possibility for many scientists around the world to contribute to a publicly available database by adding orthogonal physicochemical measurements, including collision cross sections and fragments, or even retention times.

MN: Do you have any other comments that you wish to share about metabolomics?

GA: I am always fascinated to see how both young and older scientists are captivated by the possibilities of metabolomics. Old hypotheses are hard to change, but metabolomics could offer a good excuse to do so.

Let’s train new students in metabolomics. Let’s add new metabolomics courses to medicine, chemistry, and life science departments. Let’s involve students from other disciplines such as bioinformatics and biostatistics to help develop new software tools. Let's encourage biophysicists and engineers to develop new hardware solutions. Let's persuade nutritionists, clinicians, and biologists to use metabolomics as a tool for their research. And by all means, let’s keep doing metabolomics!

Biomarker Beacon

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 Parkinson's disease and septic shock, respectively.
  1. Roede JR, Uppal K, Park Y, Lee K, Tran V, Walker D, Strobel FH, Rhodes SL, Ritz B, Jones DP. Serum metabolomics of slow vs. rapid motor progression Parkinson's disease: a pilot study. PLoS One. 2013 Oct 22;8(10):e77629. doi: 10.1371/journal.pone.0077629. [PMID: 24167579]

    There is a lot of variation from patient to patient in how quickly Parkinson's disease (PD) progresses; some patients progress slowly, while other progress rapidly. These researchers sought to identify metabolite markers that would allow them to differentiate between rapidly and slowly progressing PD patients. Using high resolution mass spectrometry-based metabolic profiling, they compared serum from these two patient groups. With the aid of statistical analyses, e.g., false discovery rate analysis and partial least squares discriminant analysis, they identified a number of statistically significant metabolic features. One metabolite in particular, N8-acetyl spermidine, was highly elevated in rapid progressors, when compared to controls and slow progressors. As this work demonstrates, N8-acetyl spermidine may prove to be a useful biomarker for the identification of rapidly progressing PD.

  2. Mickiewicz B, Duggan GE, Winston BW, Doig C, Kubes P, Vogel HJ; for the Alberta Sepsis Network. Metabolic Profiling of Serum Samples by 1H Nuclear Magnetic Resonance Spectroscopy as a Potential Diagnostic Approach for Septic Shock. Crit Care Med. 2013 Dec 23. [Epub ahead of print] [PMID: 24368342]

    There is a need for reliable biomarkers for diagnosis and mortality prediction of septic shock in intensive care unit (ICU) patients. In this study, the research team sought to utilize a nuclear magnetic resonance-based metabolomics approach to differentiate between septic shock patients and ICU control subjects. Although the ICU control subjects had systemic inflammatory response syndrome, they were not suspected of having an infection. Using proton NMR spectroscopy and multivariate statistical analysis (e.g., orthogonal partial least squares discriminant analysis), they analyzed serum metabolites from the above two patient groups and were able to distinguish between the two groups.
    To predict patient mortality, they used NMR spectroscopy to compare septic shock survivors with nonsurvivors and develop accurate prediction models. Thus, the two major outcomes of this study were: 1. Identification of a set of biomarkers for distinguishing between septic shock patients and control patients, and 2. Development of accurate prediction models to predict patient survival outcomes.
Metabolomics Current

Metabolomics Current Contents

Recently published papers in metabolomics:


2 Dec 2013

Time to put your feet up: A new automated metabolite analysis tool

Ideally, biologists studying differences in metabolite expression between two groups of samples, such as healthy and diseased tissue, would like a system that could simply take in samples at one end and then pop out interesting biological information at the other. This information would include which metabolites are differently expressed in the two samples and which metabolic pathways have been thrown out of kilter by the disease process.

Although biologists can already obtain this information, they generally have to work for it. First, they need to analyze the metabolite samples with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Then they need to convert the resultant data into a useable form by removing background noise, detecting individual peaks and aligning those peaks between different samples.

Once the data is in a useable form, the biologists then need to analyze it with appropriate statistical techniques in order to discover which metabolites are differently expressed between the healthy and diseased samples. Finally, they need to determine the identity of the differently expressed metabolites, usually by scrutinizing a spectral database, and then work out what metabolic pathways those metabolites might take part in.

Understandably, this all takes time and effort, and also requires expertise in bioinformatics and statistical analysis, which many biologists lack. Hence the attraction of a completely automated system that accepts samples at one end and produces information at the other. And just recently, such systems have begun to appear.

Earlier this year saw the release of a web-based software tool called XCMS Online, which was specifically designed to open up metabolomics to biologists with little knowledge of bioinformatics (see Metabolomics for all). In one simple automated process, XCMS Online detects peaks, aligns retention times between samples, determines metabolites that are present at different concentrations in different samples, assigns possible identities to those metabolites, and performs multivariate statistical analyses.

Now, XCMS Online has been joined by another web-based software tool called MetaboLyzer, which was also specifically designed to open up metabolomics to more biologists. Whereas XCMS Online covers the whole data analysis process, however, MetaboLyzer focuses on the stage after the initial noise reduction, peak detection and alignment steps. Albert Fornace and his colleagues at Georgetown University Medical Center in Washington, DC, US, who developed MetaboLyzer, chose to focus on this later stage because a lot of tools already exist for conducting the initial data processing. In addition, they thought there was more scope for improving the later analytical stage.

Traditionally, biologists conducting metabolite studies have tended to apply standard multivariate statistical techniques such as principle component analysis to the cleaned-up metabolite data. But these techniques were not specifically developed for metabolite data, which have their own unique idiosyncrasies that can create problems for these standard techniques.

One of the most important of these idiosyncrasies is that metabolite datasets often contain missing data, in which an ion with a certain mass-to-charge ratio simply doesn’t show up in the data for a specific sample when it does in other identical samples. Standard analytical techniques can struggle to deal with this missing data and so biologists have to resort to estimating likely values, which can mess up the resulting analysis.

With MetaboLyzer, Fornace and his colleagues adopted a different approach. The first thing MetaboLyzer does with metabolite data is to highlight those ions that are missing in a certain proportion of the samples, say over 10%, which are termed partial presence. Those ions that are present in more than 90% of the samples are termed complete presence.

Next, it determines which ions are present at different abundances in the two different sample groups, but employs a simpler statistical technique for partial presence data than for complete presence data. It then assigns metabolites to the ions found at different abundances in both the partial presence and complete presence data by scrutinizing four small-molecule databases

After this, it only conducts further analysis, including uncovering relationships between the different ions and producing heat maps and volcano plots, on the complete presence data. In this way, MetaboLyzer can focus its analytical efforts on the detailed data, while still having access to less detailed data that can back up any findings from the detailed data.

All of which helps with the automated uncovering of interesting biological information.

  • Publication: Mak TD, Laiakis EC, Goudarzi M, Fornace AJ Jr. MetaboLyzer: A Novel Statistical Workflow for Analyzing Postprocessed LC-MS Metabolomics Data. Anal Chem. 2013 Nov 22. [Epub ahead of print] [PMID: 24266674]

1 Dec 2013

Enhancing Colon Cancer Screening through Polyp Detection

Metabolomic Technologies (MTI) has developed a technology that detects colonic polyps, the precursor to colorectal cancer (CRC), using a noninvasive urine test. Unlike fecal-based tests, PolypDx™ detects polyps before they become cancerous, according to the company. The assay, now in beta testing, has the potential to improve patient compliance. By enabling early intervention, it also may reduce the high healthcare costs associated with treating CRC, by reducing the numbers of surgeries and hospitalizations.

“In Canada, colonoscopies are not the first line of defense. Instead, our healthcare system uses fecal-based tests,” Reg Joseph, CEO, explains. For those tests, patients collect their samples at home and send them to a lab. With that approach, compliance rates across Canada are as low as 14%. “Because the fecal tests detect CRC only 50% of the time, often people without polyps and cancer undergo colonoscopies. Eighty percent of patients referred for colonoscopies that are based upon fecal tests do not have CRC. Because of the invasive nature of this procedure and lack of patient compliance, many are not screened in time.”

PolypDx addresses those issues, MTI reports. It is a single spot test that analyzes metabolites in the urine to determine whether patients have CRC and, more importantly, whether they have colonic polyps. The test has a sensitivity of 71% and a specificity of 61% in terms of polyp detection. In contrast, standard-of-care fecal-based tests are designed to detect CRC—not colonic polyps. When used to detect polyps, fecal-based tests have sensitivities of 1–15%. Therefore, PolypDx represents a significant advance in polyp detection.

“We’re continuing to improve sensitivity and specificity for PolypDx by screening against a larger metabolomic library,” Joseph says. The current version is based on an NMR platform. An improved version offering higher throughput and enhanced ease of use is being developed on a mass spectroscopy platform. It is expected to become available in 2015. Mass spec instruments are used routinely in large diagnostics labs, so this new test kit can be integrated easily into current workflows.

“We’re working with Alberta Health Services and DynaLIFEDx to look at scaling up this test for large population screening,” Joseph says. Alberta Health Services is collaborating with MTI to release the assay kit as early as possible. MTI plans to commercialize the first version of the test in late 2014.

Ultimately, MTI envisions PolypDx as a routine screening tool that will be used before patients undergo a colonoscopy. “We’d like to be able to screen thousands of patients per day using one instrument,” Joseph says.

“More than 95% of colon cancer patients develop cancer through adenomatous colonic polyps. If we can identify these patients before the onset of cancer, the chance of survival is more than 90%.” The PolypDx assay kit is expected to be priced at about $50. The annual U.S. burden for CRC treatment is $14 billion.

MTI’s platform also may be harnessed for other diseases. MTI is developing ColoDx™ for CRC. Additionally, “We can see the preliminary signatures for prostate and breast cancers.” Urine-based assays for those diseases are in the early development phase.

The technology spun out of the University of Alberta in Canada, which is known globally for metabolomics research. Company founders, gastroenterologist Richard Fedorak, M.D., and colorectal surgeon Haili Wang, M.D., collaborated with the university’s metabolomics group, which was collecting bio-samples to identify potential diagnostics for a variety of diseases. A retrospective study led to a prospective study and, eventually, PolypDx.

“MTI is actively seeking partnerships and strategic commercial partners,” Joseph says.

MTI is collaborating with BGI-Shenzhen to develop the assays for the Chinese market. The assay is undergoing validation and clinical trials in China. According to Yong Zhang, Ph.D., head, proteomic division, BGI-Shenzhen, “Our company is the best positioned to co-develop MTI’s diagnostic tests for the Chinese market, assist with the regulatory process, and market the technology.”

“In the West, the regulatory landscape for multivariate tests like metabolomics is a bit gray. China, however, has a progressive regulatory framework that is focused around driving down the costs of disease for a large, new middle class that is demanding high-quality healthcare.” Therefore, “Preventive strategies—including diagnostics—are on the fast track.” Additionally, the University of Alberta has had research collaboration with BGI-Shenzhen for the past five years. Leveraging that relationship enables MTI to showcase a translational project and make a real difference, quickly, in individuals’ health.

Joseph says MTI’s finances are sound. MTI is funded by angel and super angel investors and by grants from Alberta Innovates—Health Solutions, the National Research Council of Canada’s Industrial Research Assistance Program, and Alberta Enterprise and Advanced Education. “Our burn rate isn’t excessively high, so regional financing will take us through the next few years.”

22 Nov 2013

The NIH Metabolomics Program’s Standards Synthesis Centers

The National Institute of Health’s Common Fund Metabolomics program aims to increase capacity in metabolomics by supporting the development of next generation technologies. The goal is to enhance the sensitivity and speed with which specific elements of the cellular metabolome can be identified and quantified. As a component of this program, two metabolite standards synthesis centers (Research Triangle Institute and Stanford Research Institute) have been awarded contracts to chemically synthesize metabolite standards and make them available to the scientific community. Nominations are being sought from the metabolomics research community for metabolite standards that are not readily available from other sources. Nominations can be made at: and metabolites will be prioritized for synthesis after review by the program’s executive committee.

Source: Pothur Srinivas, personal communication, November 22, 2013

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

Metabolomics Events

Metabolomics Events

3-5 Feb 2014

PANIC: Practical Applications of NMR in Industry Conference
Venue: Hilton Charlotte University Place, Charlotte, North Carolina, USA

Mission Statement

Practical Applications of NMR in Industry Conference (PANIC) was initiated to provide an interactive forum for discussion of the latest developments in the use of NMR for practical applications to real problems faced by scientists in industry and research institutions. The emphasis is the practicality of the solution and “getting the job done”. The forum will provide a venue for presentation of practical applications, and workshops for discussion of real-world experiences relevant to current product development needs with an opportunity to share case studies to drive further development of NMR technology. Solution-state, solid-state, time-domain, and zero-field applications are all equally welcome at PANIC. The forum also will provide a venue for industrial, regulatory, government, and academic scientists to meet, network, and participate in exchanges of knowledge for mutual education in and advancement of the use of NMR techniques.

About This Conference

The PANIC meeting is intended to address topics that occur daily in industrial, government, and academic research laboratories whose primary task entails the application of NMR to a diverse set of analytical problems. Topics will include quantitation, molecular structure characterization, trace component and mixture analysis, and product support for a variety of materials that include small molecules, polymers, heterogeneous mixtures, natural products, biosimilars, polysaccharides, and proteins. The conference will provide in-depth discussions of the “nuts and bolts” of basic NMR experiments that accent the underlying best-practices developed to address these everyday problems. It also will explore the regulatory aspects of the applications of these experiments.

Greater insights will be provided into the less frequently explored techniques used in NMR such as quantitation, chemometrics, automation, relaxometry, and at/on line instrumentation. Attendees will have the opportunity to learn about and discuss applications of NMR to polymers, petroleum, food, agriculture, and nutritional supplements that are rarely discussed at other NMR meetings. Ample opportunity will be given to Network with people who are experts in inventing NMR experiments to solve real world problems in a timely and efficient manner that is demanded by working in the venue of product delivery.

For more information, visit

3-7 Feb 2014

The Imperial International Phenome Training Centre is offering "Hands-on LC-MS for Metabolic Profiling"
Venue: The Imperial International Phenome Training Centre, Imperial College, London, UK

This week long course aims to cover how to perform a metabolic profiling experiment, from start to finish. It will cover study design, sample preparation, the use of mass spectrometry for global profiling and targeted methodologies and data analysis.

Day 1
Introductory lectures in mass spectrometry and chromatography, study design and sample preparation.

Days 2 & 3
Analysis of biofluids through global profiling and targeted analyses; one day spent on each of the newest QToF instrumentation and the newest TQ instrumentation. Instrument set up, method development and acquisition will be covered. As we have set a maximum of 4 attendees per instrument this allows for hands-on participation by all.

Day 4
Lectures in data analysis, followed by workshops where attendees will process the data acquired from the previous day, allowing for development of interpretation skills.

Day 5
Application lectures, tips, tricks and troubleshooting.

Download the full programme here: LCMS Metabolic Profiling Feb 2014

For more information, visit

Early March 2014

mzTab for Metabolomics Workshop
Venue: Tübingen, Germany

In early March 2014 we're planning to hold the first “mzTab for metabolomics” workshop in Tübingen, Germany. This would be a joint MSI and PSI workshop to improve the representation of Metabolomics and Small-Molecule Identification and Quantification in mzTab. The workshop is another step towards coordination of standards between the proteomics and metabolomics communities and we would like to invite the interested individuals to join in our effort.

  • mzTab can be used for reporting both metabolite identification and metabolomics quantification. After extensive research and discussions within the consortium and members of the MSI and PSI community, we concluded that mzTab is the medium of choice for capturing and reporting such metabolomics results.
  • To test and evaluate the standard, the mzTab development is accompanied by early implementations, e.g., in development versions of the OpenMS (, or separate export functions for XCMS and CAMERA ( software tools.
  • In addition, the MetaboLights metabolomics database ( accepts the quantification and identification of metabolites in a subset of mzTab,soon to be updated to the full compatible version, once the final discussions on the mzTab format for small molecules are completed.
For more information, visit

17-21 Mar 2014

EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists
Venue: The European Bioinformatics Institute, Hinxton, UK (See map: Google Maps)

Date: Monday, March 17, 2014 - Friday, March 21, 2014


Reza Salek, EMBL-EBI & Cambridge University, UK
Laura Emery, EMBL-EBI, UK

Registration Opens:
Thursday, August 1, 2013
Registration Deadline:
Friday, January 17, 2014 (12:00 midday GMT)
Acceptance Notification Date: Friday, January 31, 2014
Participation: Open application with selection

This course will provide an overview of key issues that affect metabolomics studies, bioinformatics tools, and procedures for the analysis of metabolomics data. It will be delivered using a mixture of lectures, computer-based practical sessions and interactive discussions. The course will provide a platform for discussion of the key questions and challenges in the field of metabolomics.

This course is aimed at PhD students and researchers with a minimum of one year’ s experience in the field of metabolomics who are seeking to improve their skills in metabolomics data analysis. Participants must have experience using R (including a basic understanding of the syntax and ability to manipulate objects) and the UNIX/LINUX operating system.

For more information, visit

7-11 Apr 2014

Leiden University: Workshop Metabolomics 2014
Basics and Applications to Plant Sciences
Venue: Leiden, The Netherlands

April 7 - 11, 2014, workshop
April 14 - 18, 2014, hands-on (optional)
April 21 - 25, 2014, wrapping up of workshop and hands on (optional)

Description and aim of the workshop
Metabolomics has become an important tool in life sciences, including studies of plant interaction with its environment and studies on the activity of medicinal plants. The workshop is organized by the Institute of Biology, Leiden University. The workshop is particularly aimed at researchers experienced with the isolation and identification of natural products but do not have experience yet with metabolomics.


  • Primary and Secondary Metabolism in Plants
  • Analytical Techniques: Chromatography, MS, NMR
  • Basics of Multivariate Data Analysis
  • Applications in Plant Sciences

    800 Euro for the workshop.
    Including handout, lunches (April 7-11), drinks and one workshop dinner
    (hotel accommodation is not included)

    200 Euro for the hands-on.
    Including supervision and use of the laboratory equipment
    (hotel accommodation is not included)

    25 Euro for the wrapping up.
    Including supervision
    (hotel accommodation is not included)

Maximum number of participants
(First come first served)
    For the workshop, April 7-11: 25 participants
    For the hands-on, April 14-18: 10 participants
    For wrapping up, April 21-25: 10 participants

Organized by Young Hae Choi, Jos Frantzen, and Rob Verpoorte
. For more information, email

Registration deadline
: 31 March 2014

The workshop flyer is available here. For more details, please visit

30 Apr 2014

Analytical Tools for Cutting-edge Metabolomics - a joint meeting of the Analytical Division of the RSC and the international Metabolomics Society
Venue: Chemistry Centre, Burlington House, London, UK (Google Map Location)

Date: 30 April 2014, 09:30-16:45

Analytical chemistry has been one of the driving forces behind the development of metabolomics research over the past decade. The conference will bring together exceptional scientists for a program consisting of plenary and invited talks, posters, as well as an oral session devoted to early career researchers. It will be an excellent opportunity for analytical chemists to learn more about metabolomics and its application, and for metabolomics scientists to improve their knowledge of cutting-edge bioanalytical tools.

Deadline for submission of abstracts: 14 March 2014

Speaker Information:
Prof. Jeremy Nicholson, Imperial College, London UK - Plenary speaker
Dr Julian Griffin, MRC Human Nutrition Research, Cambridge, UK
Prof. Roy Goodacre, University of Manchester, UK
Prof. Jean-Luc Wolfender, University of Geneva, Switzerland
Dr Steffen Neumann, Leibniz Institute of Plant Biochemistry, IPB Halle, Germany
Prof Paul Thomas, Loughborough University
For more details, please visit the event website.

16-17 Jun 2014

Informatics and Statistics for Metabolomics (2014)
Venue: Vancouver, BC, Canada

Course Objectives
A poster announcing this workshop can be found here.

The workshop will cover many topics ranging from understanding metabolomics technologies, data collection and analysis, using pathway databases, performing pathway analysis, conducting univariate and multivariate statistics, working with metabolomic databases and exploring chemical databases. Participants will be given various data sets and short assignments to assist with the learning process.

Target Audience
This course is intended for graduate students, post-doctoral fellows, clinical fellows and investigators who are interested in learning about both bioinformatic and cheminformatic tools to analyze and interpret metabolomics data.

Prerequisite: Your own laptop computer. Minimum requirements: 1024x768 screen resolution, 1.5GHz CPU, 1GB RAM, recent versions of Windows, Mac OS X or Linux (Most computers purchased in the past 3-4 years likely meet these requirements). If you do not access to a laptop, you may loan one from the CBW. Please contact for more information.

Pre-Readings: You are expected to have completed the following tutorials in R beforehand. The tutorial should be very accessible even if you have never used R before. Please complete the following: R Tutorial
For more information, visit

23-26 Jun 2014

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.

We are delighted to host the 10th Anniversary of the International Conference of the Metabolomics Society (Metabolomics2014) at Keio University in Tsuruoka City, where the very first meeting of the society was held in 2005. Since then, Tsuruoka has grown to “a city of metabolomics”; various additional research buildings have been built, and two spin-out companies established. Tsuruoka is a pretty city located 500 km north of Tokyo (about 1 hour flight), and surrounded by beautiful Japanese nature, historic spots, and exotic culture. You will also enjoy the best authentic Japanese food and sake (rice wine), as well as hot springs. So, come celebrate the 10th anniversary of the society, and enjoy high-quality scientific presentations by top-notch researchers around the world.

Early registration and abstract submission due March 31, 2014.

For detailed information about Metabolomics 2014, visit

10-12 Sep 2014

Metabomeeting 2014
Venue: The Royal Institution, London, UK

SELECTBIO are delighted to announce that we are partnering with the Metabolic Profiling Forum (MPF) to host Metabomeeting 2014. The MPF will focus on the conference program while SELECTBIO will take care of logistics, promotion and exhibition/sponsorship activities.We are expecting up to 300 attendees offering a unique opportunity to network with key researchers who are making innovative discoveries within this field.

Call for Papers
If you would like to be considered for an oral presentation at this meeting, Submit an abstract for review now!
Oral Presentation Submission Deadline: 31 January 2014

Call for Posters
You can also present your research on a poster while attending the meeting. Submit an abstract for consideration now!
Poster Submission Deadline: 27 August 2014

Agenda Topics
Applied Metabolomics
Drug Discovery and Pharma
Human Disease
Human Health and Nutrition
Microbial, Invertebrate and Environmental Applications
Data Analysis and Integration with Systems Biology
Metabolite Identification

For more details, please visit the conference website.

28 Jun to 2 Jul 2015

Metabolomics 2015: 11th Annual International Conference of the Metabolomics Society
The Official Annual Meeting of the Metabolomics Society
Venue: San Francisco, USA

Details to follow.

Stay abreast of the latest Metabolomics Society news via the Twitter feed on the front page of the website ( Also you can follow us on Twitter: Metabolomics Society @MetabolomicsSoc and Metabolomics journal @Metabolomics. And you can visit us on Facebook.

Please come back later for detailed information about Metabolomics 2015 by visiting

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 Jobs

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 ( 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
Experimental Officer in Bioinformatics University of Birmingham Birmingham, UK
29-Dec-2013 27-Jan-2014
The University of Birmingham
BBSRC and Thermo Scientific-funded PhD studentship (clinical metabolomics and metabolite annotation) University of Birmingham Birmingham, UK 29-Dec-2013 31-Jan-2014
BBSRC and Thermo Scientific-funded PhD studentship (environmental metabolomics and safety assessment of engineered nanomaterials) University of Birmingham Birmingham, UK 29-Dec-2013 17-Jan-2014
Research Scientist (NMR Spectroscopist to support Business Development group) Bruker BioSpin Billerica, USA
Bruker BioSpin
Assistant Research Scientist (NMR Spectroscopist to support R&D efforts for Business Development group) Bruker BioSpin Billerica, USA 2-Dec-2013
Bruker BioSpin

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 ( Upon review, a limited number of job submissions will be selected for publication in the Jobs Wanted section.
  • Jobs Wanted in Germany: [Candidate's CV]
  • 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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