Published in partnership between
TMIC and the Metabolomics Society

Issue 36 - August 2014


Online version of this newsletter:

Welcome to the thirty-sixth 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 represents the one-stop-shop for the very latest and most critical news about the science of metabolomics. In this issue, we feature an Database Spotlight article on the Golm Metabolome Database, and a metabolomics interview with Therese Koal, Head of Research and Development at BIOCRATES Life Sciences AG.

This issue of MetaboNews is supported by:

Metanomics Health
Chenomx --
                                Metabolite Discovery & Measurement
Metanomics Health GmbH

Chenomx Inc.

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Metabolomics Society News


11th Annual International Conference of the Metabolomics Society
Location: San Francisco, US
Date: June 29 - July 2, 2015

Challenges and advances in the annotation and de novo identification of small molecules
Co-organised by the Metabolomics Society’s Metabolite Identification Task Group
Location: Gif-sur-Yvette, France
Date: October 23 - 24, 2014
This is the first in a series of workshops to promote the emergence of a community interested in developing and standardizing methods and reporting guidelines for the characterization of natural products and the annotation and identification of other small molecules including metabolites. Metabolite annotation and identification is central to the study of metabolism in many different organisms and is of prime importance in the discovery of bioactive products. A progressive merger between the disciplines applied in natural products research and metabolomics studies is expected and will profit from a common effort in developing and sharing methods, expertise and reporting guidelines.

New Members-only benefit: Are you organizing a metabolomics event?
The Metabolomics Society can provide small grants to support events that promote metabolomics. The funding may be used to provide student prizes, travel awards or catering for small events such as symposia, workshops, seminars and short-courses. The Society may also sponsor larger conferences where there is strategic opportunity to promote metabolomics science within other scientific disciplines. For more information, or to apply for funding, see:

Report on the 10th Annual International Conference of the Metabolomics Society, Tsuruoka, Japan, 23-26 June 2014
The Metabolomics Society returned to Tsuruoka, Japan for the 10th anniversary of its annual conference. With an attendance of over 500 scientists from 39 countries, delegates enjoyed presentations across 32 scientific sessions. As usual the meeting began with a series of workshops, this year on data standards, software, as well as a new forum introducing the Early-career Members Network. A packed conference program was bracketed with two excellent plenary talks from Prof Kazuki Saito (RIKEN, Japan) and Prof Pieter Dorrestein (UCSD). The closing ceremony of the conference recognised the outstanding work of many scientists, both early career and established, with awards from the Society, the Noble Foundation and Agilent Technologies (see and for details). In addition to the excellent science, delegates had many opportunities to enjoy the culture and environment of Japan including wonderful food, tours to local points of historical interest, and an exciting display of Japanese drumming at the conference banquet. The Society would again like to thank the sponsors ( without whom the event would not have been possible. We look forward to seeing you all in San Francisco for Metabolomics 2015, details listed above!


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 academia, government, or industry. The network aims to provide a forum for metabolomics researchers at the start of their professional career.

Announcement of Opportunity: Applications are sought from three additional early-career scientists to expand the EMN and achieve a more balanced geographical distribution
Deadline: 31st August 2014
As introduced during the Metabolomics Society Annual Conference in Tsuruoka, Japan, in June 2014, we are inviting three early career researchers to join the nine early-career committee members in the Society's new Early-career Members Network (EMN). The mission of the EMN is to recognize the value and importance of our early-career members, to ensure that their views are heard and acted upon, ultimately improving their experience in metabolomics science and our community. We are looking for creative thinkers to address challenges, such as, how do we aid early-career scientists to enter and engage with our scientific community? What mechanisms can we construct to allow student contributions (talks and posters) to be openly discussed in a safe environment, where senior scientists can teach and advise, and where no question is too basic? What activities and benefits can we develop to encourage students and postdocs to want to join (and remain members of) the Metabolomics Society even in years when they do not attend the annual conference? What training courses are required? How else can the Society serve its early-career members?
Existing Members of the EMN Committee
Sastia Putri (Osaka University, Japan), David Liesenfeld (German Cancer Research Center Heidelberg, Germany), Thomas Payne (Imperial College London, UK), Ralf Weber (University of Birmingham, UK), Nicholas Rattray (University of Manchester, UK), Evangelia Daskalaki (University of Strathclyde, UK), Gabriel Valbuena (Imperial College London, UK), Justin van der Hooft (Glasgow Polyomics, UK), and Vincent Asiago (DuPont Pioneer, USA)
We welcome applications from students conducting higher degrees (Masters, PhDs) in a metabolomics discipline, or from those within 5 years of their PhD who are actively engaged in metabolomics science. As an international society we encourage applications from all continents. Successful applicants must be members of the Metabolomics Society (or should immediately become members upon joining the committee).

Time Commitment
There is much exciting work to be done and much to achieve! Therefore we anticipate a contribution of up to two hours per week (on average). If the Early-career Members Network organises sessions at conferences or other events, time commitments will increase accordingly. Note also that the existing members of the EMN committee span many time zones, so some conference calls may occur early or late in the day. No dedicated travel will be required for the EMN committee discussions. The appointment to the EMN committee is for one year initially, and may be extended up to three years. It is your responsibility to discuss this commitment with your supervisor(s) prior to applying.
Application Procedure
Please send the following, in one document (.docx or .pdf), to the EMN committee (
1. One-page resume with relevant experience in developing and leading networking activities (e.g., student rep for other societies) plus your research experience in metabolomics (e.g., presentations, publications, etc.)
2. Up to 300 words on why you fit the role and up to an additional 300 words (one page in total) on what ideas you are passionate about developing as part of the Early-career Members Network.
Applications will then be reviewed by members of the Metabolomics Society’s Strategy Task Group and the existing EMN committee members and successful candidates informed in September 2014.

Membership News for 2014

Membership of the Society has steadily grown throughout 2014 and we now have over 750 members; a ca. 25% increase on the number of members two years ago when the current board started their terms of office. As part of our ongoing campaign to improve the service we offer you as members, we have switched to a new registration system this year. For security reasons, we have not been able to migrate your old passwords and so members who joined before May 9th 2014 will need to reset your passwords, log in and update your membership information. Full details on how to do this can be found at Anybody who has received membership of the Society as a result of attending Metabolomics 2014 conference can also set their passwords in this way.


Data Standards Task Group
A workshop was organized by COSMOS and the Data Standards Task Group of the Metabolomics Society during the annual Metabolomics Society conference in June held at Tsuruoka, Japan. Reza Salek (EMBL-EBI, UK) presented the current status and on-going developments worldwide on data standards, particularly the role of COSMOS ( Steffen Neumann (Leibniz IPB, Halle Germany) gave an overview of data exchange formats in MS and how to get the users and instrument vendors involved. Philippe Rocca-Serra (Oxford e-Research Centre, UK) presented ISA-Tools for capturing metabolomics metadata, semantics and usage of RDF in metabolomics. In the second session, Scott Edmunds and Rob Davidson (GigaScience, Hong Kong) presented the Gigajournal point of view on publishing metabolomics data and workflows with the GigaScience, GigaDB and GigaGalaxy platforms. Susanna-Assunta Sansone (Nature Scientific Data) introduced NScD’s role in placing importance on data and the role that the NScD is playing on putting value in your datasets. The last two presentations were by Reza Salek and Padma Maruvada (NIH/NIDDK, USA) giving an overview of metabolomics repositories, MetaboLights and NIH Metabolomics WorkBench. We had plenty of interested discussion points on usage and promotion of standard, metabolomics data deposition and dissemination.

In June 2014, also supported by a BBSRC UK-China partnering award (BB/J020265/1), the Biomed Central Gigascience Team at BGI Hong Kong, and the ISA Team at the University of Oxford e-Research Centre organized a hackathon in Hong Kong, with participation of young scientists and ‘-omics’ data producers from local university and the UK metabolomics standards community (EMBL-EBI, COSMOS and Birmingham Metabolomics Centre). The goal was to establish common standards and curation practices for omics data as well implement new ISA software ( functionalities to facilitate deposition to MetaboLights repository ( and support feature requests from journal using ISA formats, such as GigaScience ( and Scientific Data ( The fruitful interaction between the participants over the duration of the meeting resulted in the delivery of an ISA-Tab viewing component for web browsers ( for the code and, and the conversion of MetaboLights ISA-Tab content to RDF. Finally, efforts to deliver an API supporting the programmatic creation of an ISA-Tab document are well under way. Owing to the success on this first ISA-thon event, the same teams will be organizing a follow-up meeting. We will keep you posted and, if interested joining, do get in touch with us (


Australian & New Zealand Metabolomics Network (ANZMN) – An Update from Down Under
The ANZMN was formed in 2012 by staff from Melbourne, Auckland, Monash, La Trobe and RMIT Universities, the Bio21 Institute and the Centre for AgriBioscience. We aim to support metabolomics in the Asia-Pacific region.

There is a lot of experience and skills in metabolomics ‘down under’. The ANZMN is looking forward to (and will be well represented at) Omics week at Bio21 as well as the 15th International Conference on Systems Biology ( and the International Association for Plant Biotechnology Congress (, which are both being held in Melbourne this year and follows hot on the heels of the recent  'Systems Biology - From Genomes to Life' meeting; a mix of international speakers and three weeks of practical workshops which took place at the Centre for AgriBioscience at La Trobe University earlier in the year.

The ANZMN also held a dinner at the recent international Metabolomics Society conference in Tsuruoka, Japan, where 15 members (and some international special guests) tried out the excellent Japanese Shonai cuisine. Given the extensive distances between many of the metabolomics labs across Australia and New Zealand this was a great chance for everybody to get together and discuss the latest developments in the field. More events are planned in the near future, for example a joint ANZMN/Metabolomics Australia Metabolomics workshop will be running in October 2014, which will focus on both practical work and data analysis. Watch this space for details.

Korea Metabolomics Society (KoMetS)

Workshop “Bearing metabolomics: from sample preparation to data analysis”
KoMetS plans to organize a workshop at Hana square, Korea University for future leaders in metabolomics research. The workshop will cover basics of metabolomics including study design, sample preparation, analytical instrumentation, data process, and statistics (Oct 6th 2014). The workshop is design for whoever is new to and interested in the field, graduate students, technicians, postdocs, and faculty who are new to the field. The course will be will be managed by the Organizing Committee, Dr Man Ho Choi (KIST) and Prof. Yun-Gon Kim (Soongsil University).

Workshop at Hana square, Korea University

Réseau Français de Métabolomique et Fluxomique (RFMF)

The 8th Scientific Meeting of Réseau Français de Métabolomique et Fluxomique ( was held in Lyon 19, 20 & 21 May 2014. This meeting, dedicated to applications in and developments for metabolomics, lipidomics and fluxomics, gathered about 250 participants. The abstract book is now available at

The RFMF organizes a Summer School on ‘Metabolomics by Mass Spectrometry’ from experimental design to data integration in metabolic networks. It will take place at La Colle sur Loup (France) from 6 to 10 October 2014. There are only a limited number of attendees that can be accepted. Good proficiency of the French language is a requirement for participation (email contact: The RFMF can provide a limited number of travel grants to PhD students or junior non-permanent scientists (under 35 years old).

A French-Singapore networking event, Merlion Metabolomics Workshop Singapore 2014, will take place at University Town, National University of Singapore from 19 to 21 November 2014. The Metabolomics Society and the RFMF can provide a limited number of travel grants for French students or for non-French students working in a French laboratory, wishing to attend (email contact for eligibility:


Metabolomics journal, Vol. 10, Issue 4, August 2014
See the latest issue of our journal at:

In addition to the many excellent research papers, this issue contains the following contributions on the Metabolomics Society pages:

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.

Software Spotlight

Database Spotlight

Golm Metabolome
                  Database Banner

The Golm Metabolome Database (GMD)

Jan Hummel, Kenny Billiau, Alexander Erban, Dirk Walther, Joachim Kopka
Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany

The Golm Metabolome Database (; Kopka et al., 2005, Schauer et al., 2005, Hummel et al., 2007) has been developed and is hosted by the Max Planck Institute for Molecular Plant Physiology (Golm, Germany), a pioneer in applying metabolomic studies to plant research. The GMD harbors information on reference compounds and compounds detected in biological samples, respective mass spectra and retention index information for compound annotation in complex mixtures (Schauer et al., 2005), and metabolite level measurements derived primarily from plant material and probed with gas chromatography/mass spectrometry (GC/MS) technology. It currently comprises information on 1,167 reference substances, 1,676 metabolites, 2,588 electron impact ionization mass spectra associated with known compounds and 3,145 spectra for which the compound is not yet identified.

The GMD—a resource for compound annotation by matching to GC/MS reference spectra and retention indices
The GMD can be queried for particular metabolites, reference compounds and respective chemical derivatives searching with text, sum formula, molecular weight, functional chemical groups, KEGG identifiers, and other properties. All compounds contained in the GMD are displayed with a broad array of chemical and physical property information and links to external data resources (Figure 1). Most notably, the GMD permits mass spectra-based queries (Figure 2) thereby facilitating the annotation process of user-obtained GC/MS spectra.

Example of a
        metabolite report card

Figure 1. Example of a metabolite report card (excerpt) providing detailed chemical information on particular compounds contained in the GMD.

Input form for querying the GMD with a mass spectrum

Figure 2. Input form for querying the GMD with a mass spectrum. The query can be performed with or without RI constraints. Two standard RI-systems are supported (Strehmel et al., 2008).

Applying several scoring methods for spectra comparison, matching compounds with similar mass spectra will be ranked and returned in tabular format (Figure 3). Graphical support facilitates the manual evaluation of the automated identification result and the selection of the best matching compound.

Example of a result page obtained from a mass
        spectrum query

Figure 3. Example of a result page obtained from a mass spectrum query. Compounds with similar spectra compared to the user-submitted query are tabulated along with various sortable match-scores and a graphical display of the selected mass spectral hit.

Automated characterization of mass spectra—annotating “unknown” metabolites
Based on the comprehensive compound and associated spectra information content of the GMD, a automated, machine-learning-based annotation of “unknown” spectra has been implemented (Hummel et al., 2010, Hummel et al., 2013). Employing decision trees trained in a rigorous cross-validation setting, mass spectra can be annotated for the presence or absence of a number of 21 different functional groups (Figure 4) that frequently occur in known metabolites, e.g., amino-, alcohol-, or carboxylic acid-moieties. Thereby, even spectra for which no matching reference compound or respective metabolite spectrum can be found in the database, a basic classification of the “unknown” compound can be generated allowing, for example, to identify the likely candidate compounds for subsequent identification steps.

        spectra are annotated for the presence or absence of 21
        different characteristic functional groups

Figure 4. Mass spectra are annotated for the presence or absence of 21 different characteristic functional groups providing assistance in the annotation of compound spectra of unknown identity. Prediction scores and classification rules are provided (Hummel et al., 2010).

From compound-centric to cross-experiment data views
Recently, the development focus of the GMD has shifted from providing compound and spectra-centric towards integrated views of compound sets associated with a particular experimental series, and beyond this experiment-centric view, offering means for the comparative analysis of metabolite profiles across different experiments. Currently, 14 experiments have already been incorporated into the GMD. Various graphics-supported analytical displays facilitate the analysis of compound profiles across different experiments and within single experimental datasets (Figure 5). Compound profiles can also be queried with hypothetical compound level constellations, such as, queries that require metabolite A to be present, metabolite B absent, and metabolite C at twice the level of compound A. In the long term this functionality aims at permitting “experiment” queries which answer questions, such as, under which other conditions do metabolites exhibit similar levels as in a user’s experiment. With the rapidly growing number of experimental datasets, this facility is expected to quickly gain appeal.

The GMD permits
            analyses of metabolite level information across all samples

Figure 5.
The GMD permits analyses of metabolite level information across all samples associated with a particular experiment. Similar metabolite profiles are identified via correlation methods and displayed graphically as network graphs (upper panel) and employing hierarchical clustering methods producing heat map views of the metabolite level data (lower panel).

Inferface to external software systems via web services
The GMD offers a wide array of software interface functionalities allowing the integration of GMD-functionality, e.g., automated classification of mass spectra, into third-party software solutions.

Terms of Use
Access to the online contents and services of the GMD is granted to all users without any limitations pursuant to the regulations stipulated in the GMD website. Commercial licenses for off-line use are available upon request.

  1. Hummel, J., Selbig, J., Walther, D. and Kopka, J. (2007) The Golm Metabolome Database: a database for GC-MS based metabolite profiling. In Nielsen, J. and Jewett, M.C. (eds), Metabolomics. Springer-Verlag, Berlin, Heidelberg, New York, 75-96.
  2. Hummel, J., Strehmel, N., Bölling, C., Schmidt, S., Walther, D., Kopka, J. (2013) Mass spectral search and analysis using the Golm Metabolome Database. In Weckwerth, W., and Kahl, G. (eds) The Handbook of Plant Metabolomics. Wiley-VCH Verlag, Weinheim, 321-343.
  3. Hummel, J., Strehmel, N., Selbig, J., Walther, D., Kopka, J. (2010) Decision tree supported substructure prediction of metabolites from GC-MS profiles. Metabolomics, 6, 322-333.
  4. Kopka, J., Schauer, N., Krueger, S., Birkemeyer, C., Usadel, B., Bergmuller, E., Dormann, P., Weckwerth, W., Gibon, Y., Stitt, M., Willmitzer, L., Fernie, A.R. and Steinhauser, D. (2005) GMD@CSB.DB: The Golm Metabolome Database, Bioinformatics, 21, 1635-1638.
  5. Schauer, N., Steinhauser, D., Strelkov, S., Schomburg, D., Allison, G., Moritz, T., Lundgren, K., Roessner-Tunali, U., Forbes, M.G., Willmitzer, L., Fernie, A.R., Kopka, J. (2005) GC-MS libraries for the rapid identification of metabolites in complex biological samples, FEBS Letters, 579, 1332-1337.
  6. Strehmel, N., Hummel, J., Erban, A., Strassburg, K., Kopka, J. (2008) Retention index thresholds for compound matching in GC-MS metabolite profiling, Journal of Chromatography B, 871, 182-190.


The development of the GMD was supported by grants from the Deutsche Forschungsgemeinschaft (DFG) and the EU (FP-7) as part of the COSMOS initiative

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 Therese Koal.

Therese Koal

Head of Research and Development at BIOCRATES Life Sciences AG, Innsbruck, Austria

 Therese Koal


Therese Koal is responsible for mass spectrometry (MS)-based kit design, product and reagent development including evaluation of future metabolomic kit products and target markets. Product-related business development, IP, and medical device know-how (CE, IVD mark) also belong to Dr. Koal's scope of activities. Before she joined BIOCRATES in 2006, she worked at the Medical School of Hannover (Prof. Volkhard Kaever, Institute of Pharmacology, Germany), where she developed one of the first MS/MS-based clinical routine platform for Therapeutic Drug Monitoring (TDM) of immunosuppressive and antiretroviral drugs in Germany. Dr. Koal earned her doctorate (2000-2002) in analytical chemistry from the University of Leipzig, Germany, in the research group of Prof. Werner Engewald, where she also completed a post-graduate study in toxicology (2000-2003).

Metabolomics Interview (MN, MetaboNews; TK, Therese Koal)

MN: How did you get involved in metabolomics?

TK: I have been following the breakthroughs of tandem mass spectrometry-based newborn-screening (NBS) since 2000. At this time, when establishing the MS-based technology for TDM for clinical routine, I was dealing with the same challenges—standardization of mass spectrometry techniques. Later at BIOCRATES we started the development of our BIOCRATES targeted and quantitative metabolomics platform, which currently covers more than 630 endogenous metabolites. Today this metabolic phenotyping platform is the basis for our kit development and contract service businesses. This allows the quality controlled and reproducible quantitative analysis of endogenous metabolites.

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

TK: That BIOCRATES is in the leading position to overcome the lack of standardization in quantitative metabolomics analysis. This includes the harmonization of data formats, long-term robustness and data comparability—all hot topics which are currently discussed in the metabolomics community. We are successfully on our way to bringing standardization and harmonization to user laboratories with ready-to-use kits, enabling inter-laboratory and inter-instrument comparability across all major MS instrument suppliers. This is the prerequisite to making this –omics technology successful for routine research applications and finally as a standard for clinical laboratory medicine and pharma-drug development.

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

TK: I am part of a company that is a global leader in targeted and standardized metabolomic analysis. Biocrates is supporting the worldwide efforts towards standardization of metabolomic measurements and data analysis. There are two key initiatives that I am pursuing as part of my role at Biocrates. The first is Biocrates' participation in the international ring trials, together with key opinion leaders in the field, to accelerate the process of standardization and turn metabolomics into applicable tools for medical diagnostics, research and drug development. The second example is my involvement in a project to advance the standardization of mass spectrometry based steroid analysis. In collaboration with the MS Harmonisation Working Group, under the auspices of the Asian and Pacific Federation of Clinical Biochemistry (APFCB), we are working together on the establishment of a common calibrator for MS analysis of serum testosterone, where results were first presented at the IFCC Worldlab 2014 meeting a few weeks ago.

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

TK: The application areas of metabolomics are very diverse in Austria, in terms of the size of the investigation subject—anything from mitochondria to dairy cows. For example, we are part of the Austrian Center of Industrial Biotechnology (ACIB), where we contribute to the improvement of production cell lines for pharmaceutical companies. In Austria, we see that metabolome analysis is no longer confined to a small community of researchers on metabolomics methodologies, but almost completely to applied research, such as research projects triggered by clinical researchers looking for functional information on a specific research question, where other methods alone cannot provide the information they need.

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

First, epidemiology is already an important area and will continue to be. Robustness and throughput are essential issues here, the latter likely to become even more important as cohort sizes increase dramatically. Our kit solutions enable researchers to conduct high-throughput analysis ensuring short time-to-results. Second, I am convinced that applications in model systems (animal models and cell culture) are becoming increasingly important. Because our kits use standardized workflows, the generated data are easily reproducible and transferable. Moreover, the small amount of sample volume required (e.g., 10 µL of blood) allows longitudinal studies in animal models. Third, clinical research; we recognize that the importance of mass spectrometry is rising, e.g., for steroid hormones where journals don’t even accept data generated with immunoassays any more. An even larger advantage than quality, though, is the multiplexing capacity. Classical clinical diagnostics markers have been failing to provide significant advantage or progress towards personalized medicine.

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

TK: Clearly, the power to study the metabolic phenotype. Metabolomics gives us the chance to understand pathophysiological processes from a systems biology point of view. Genomics, transcriptomics, and proteomics merely indicate the potential cause for a phenotypic response, but cannot predict what will happen at the next level. Metabolomics is different in that it provides a functional readout of the physiological state of an organism, as determined by the sum of its genetic blueprint, regulation, protein abundance, and environmental influences. Furthermore, I see metabolomics as next generation technology, as a new standard to replace and/or support established methods, e.g., in drug development, early disease prognosis, sub-classification, diagnosis and finally as major steps forward in precision medicine and companion diagnostics. Many powerful publications from different application areas demonstrate the potential of metabolic phenotyping by our targeted metabolomics approach ( A team of researchers in Georgetown, Washington, DC, and Rochester, New York, has identified the world’s first blood-based biomarker panel capable of predicting Alzheimer’s disease: discovered that a set of 10 lipids and acyl carnitines from peripheral blood predicts the development of mild cognitive impairment or Alzheimer’s disease with over 90% accuracy and 2–3 years in advance. The first-of-its-kind study, recently published in Nature Medicine, used the AbsoluteIDQ® p180 test kit by BIOCRATES.

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

TK: The greatest barriers for metabolomics data is the interpretation of this “new” type of data and the integration into established methods in research. We at BIOCRATES try to help researcher and physicians look at the data from a different point of view. Metabolic phenotyping provides deep insights into enzymatic function and regulation, which is important basic research as well as for clinical approaches and pharmaceutical research. The great challenge is to connect metabolic data, concentrations of metabolites, with enzymatic functions, an area where BIOCRATES puts a lot of effort.

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

Data is now said to be the bottleneck in metabolomics, and we see data management as one of the reasons researchers are hesitant to adopt this technology. BIOCRATES developed its own MetIDQ® software that is included with the kits. This offers an operator independent and standardized raw data analysis of FIA-MS/MS, making it easy to transfer (U)HPLC-MS/MS results across AB Sciex, Waters and Thermo triple quadrupole MS instruments. This is a significant step towards reliable longitudinal and retrospective inter-laboratory and inter-instrument comparisons.

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

TK: The question is if metabolomics can help solve important scientific and disease-related questions, and if this can be effectively communicated to funding bodies. We have already observed that increasing metabolomics does not harm the chances of a project getting funded, and in the recent European Horizon 2020 calls, innovative approaches for phenotyping have already been requested; metabolomics is, in my opinion, one of the most promising phenotyping approaches.

MN: What role can metabolomics standards play?

TK: As I have discussed before, standards and standardization are absolutely essential. One of our clients said, “How will metabolomics ever generate significant impact if we cannot even agree on a standard between the research organizations of this city?” Reliability and comparability of metabolomics data is essential to enable the implementation in any routine application, and we at BIOCRATES are the pioneers and key players in the standardization of metabolic phenotyping by our ready-to-use kit products, reagents and our current activities in international ring trials.

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

TK: Metabolomics is not a new science. It started in the 1960s with gas chromatography-based analysis of urine and tissue extracts. Today, metabolomics technologies including standards, harmonization, kits and instrumentation facilitate highly sensitive, robust, and multiplex analysis, allowing new insights into many different application areas (systems biology research, disease-related biomarker discovery, epidemiology, nutrition, drug development, bioprocess optimization) across different biological matrices (mammalians, plants, cell culture). I see a strong future trend towards combining and integrating various –omics (e.g., proteomics and metabolomics) technologies.

Biomarker Beacon

Biomarker Beacon

This section of MetaboNews is supported by:

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 recent study, a metabolomics-based approach was used to identify biomarkers associated with gestational diabetes mellitus.
de Seymour JV, Conlon CA, Sulek K, Villas Bôas SG, McCowan LM, Kenny LC, Baker PN. Early pregnancy metabolite profiling discovers a potential biomarker for the subsequent development of gestational diabetes mellitus. Acta Diabetol. 2014 Jul 27. [Epub ahead of print] [PMID: 25064235]

In this paper, the investigators used a metabolomics approach to identify potential biomarkers for gestational diabetes mellitus (GDM). Using gas chromatography coupled to mass spectrometry (GC-MS) and statistical analysis, they analysed maternal serum at 20 weeks' gestation and identified forty-eight metabolites in serum that were differentially expressed in patients who later developed GDM compared with subjects with healthy pregnancies. From this study, one metabolite in particular, itaconic acid, was significantly more abundant in patients with GDM. With further studies, this metabolite may prove to be a promising early pregnancy diagnostic for GDM.
Metabolomics Current

Metabolomics Current Contents

This section of MetaboNews is supported by:

Recently published papers in metabolomics:



29 Jul 2014

Chenomx Releases NMR Suite 8.0

Chenomx Inc. released its latest version of NMR Suite, an integrated suite of tools that allows users to identify and quantify compounds in NMR spectra. This new version includes the following:
  • Brand New Look and Feel
  • New Reference Compound Additions
  • Improved Autofitting
  • Batch Fit and Batch Edit
  • Graph Grid Lines

For more details on this new release, visit

Metabolomics Events

Metabolomics Events

27-29 Aug 2014

Omics Week @ Bio21: Understanding Genomics, Proteomics and Metabolomics
Venue: Bio21 Institute, 30 Flemington Road, University of Melbourne, Parkville, Victoria, Australia

Registration is now open. You can register to attend, one, two or all three days. These are free events and all are welcome.

Register by 8 August 2014 via link -

Omics is a field that is growing in importance.  Its diverse applications underpin a holistic approach to Systems Biology that overall aims to accelerate our understanding of health and disease. To explore the developments and opportunities in these exciting fields, researchers at the Bio21 Institute, Department of Biochemistry and Molecular Biology and Metabolomics Australia have come together to organise a diverse program that aligns with the Bio21 Institute's commitment to advancing Systems Biology.

The three days will cover:

Wednesday 27 August – Genomics – will highlight cutting edge genomics research that relates to a range of diseases and model organisms. More info on Genomics Day click here

Thursday 28 August – Proteomics/Mass Spec - will combine our popular ‘Mass spec 101 series’ with real examples of how proteomics and mass spec have been used to tackle various problems in biology. More info on Proteomics Day click here

Friday 29 August – Metabolomics – will showcase a series of research experts who will outline how metabolomics has broadened their perspective ranging from the agri- to the biomedical sector and the new tool of imaging mass spectrometry. More info on Metabolomics Day click here

For more information, please visit

8-10 Sep 2014

Mayo Clinic Metabolomics Symposium
Venue: Mayo Clinic, Rochester, Minnesota, USA

Mayo Clinic is a leader in the emerging field of metabolomics — the systematic study of the unique chemical fingerprints that specific cellular processes leave behind. This symposium will present translational science investigators, KL2 and other K-award scholars, and research fellows new to the metabolomics field an opportunity to explore the latest information on metabolomics and network with colleagues and world-recognized experts in the field. The symposium will explore:
  • Methods for incorporating metabolomics into research
  • New information and data from Mayo Clinic's Metabolomics Resource Core through lectures by Mayo Clinic and visiting faculty
  • Education on emerging metabolomics methodologies and their application in basic and translational research
  • Data on the use of metabolomic tools and biomarkers in clinical research
Discussion topics

Specific topics for discussion will include:
  • Tissue ceramides
  • Amino acid and metabolites
  • Citric acid flux
  • Muscle mitochondrial functional measurements
  • Systems biology
  • Nuclear magnetic resonance spectroscopy
  • Quantitative analysis
  • Mass spectrometry-based large-scale metabolomics profiles
  • Mayo Clinic's Metabolomics Mass Spectrometry Core and Metabolomics Nuclear Magnetic Resonance Spectroscopy Core facilities (optional tour)
Event flyer: Clinic Metabolomics Symposium.pdf

For more details, please visit

8-12 Sep 2014

The Imperial International Phenome Training Centre is offering "Hands-on LC-MS for Metabolic Profiling"
Venue: The Imperial International Phenome Training Centre, Sir Alexander Fleming Building, Imperial College, South Kensington Campus, Exhibition Road, London, UK

This week long course using state-of-the-art instrumentation in a world-class facility is run by renowned specialists located in the Section of Computational and Systems Medicine at Imperial College London.

Small groups of trainees can enjoy a friendly, intimate learning experience and interact with highly experienced training centre instructors and guest lecturers.

The course covers how to perform a metabolic profiling experiment, including:
  • Study design, sample preparation, the use of mass spectrometry for global profiling and targeted methodologies and data analysis.
  • Instrument set up, method development and acquisition through global profiling and targeted analyses of biofluids, using the newest QToF and TQ instrumentation.
  • Data analysis workshops allowing attendees to process data acquired, in order to develop interpretation skills.
  • Application lectures, problem solving, tips, tricks and troubleshooting.
This combination of lectures, demonstrations, hands-on laboratory sessions and practical data analysis will equip attendees with skills to implement immediately in their own facilities:

Download the full programme here: LCMS Metabolic Profiling Sept 2014

Online booking is available at:

For more details, visit or contact Dr Elizabeth Want on 0207 594 30230207 594 3023 (

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 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
    • Plants
  • Data Analysis and Integration with Systems Biology
  • Metabolite Identification
Five Travel Awards and One Best Talk Award
We are happy to announce that courtesy of the Metabolomics Society we will be providing 5 travel awards and a best talk award for students attending Metabomeeting who are members of the Metabolomics Society. There are five travel wards of £350 and one prize for the best student talk of £250. To be eligible for these awards all you need be is a student member of the Metabolomics Society. Abstracts and the talk will be judged at the meeting and awards made on the award ceremony on Friday 12th September.

For more details, please visit the conference website.

14-18 Sep 2014

International Chemometrics Research Meeting ICRM 2014
Venue: The Golden Tulip Valmonte Hotel, Berg en Dal near Nijmegen, The Netherlands

The ICRM conference is held once every three/four years and is organized by the Dutch Chemometrics Society (DCS), a working group of the Royal Netherlands Chemical Society. The aim of this conference is to bring together people from a wide range of industry, research and academic backgrounds to share and discuss recent developments in the field of chemometrics. Chemometrics is the discipline concerned with the extraction of information from analytical chemical data. It has numerous successful applications in an extremely wide range of industries, for example in chemical and pharmaceutical research and production. The conference focuses on presentations by prominent speakers from around the globe, who will be invited to share their knowledge both during lectures on a wide range of topics from the field of chemometrics, as well as during the extensive, succeeding discussions. Confirmed keynote lecturers of the conference currently are Alan Gelfand, John H. Kalivas, Olav M. Kvalheim, Iven van Mechelen, Mia Hubert, Dennis R. Helsel and Neil B. Gallagher.

At this ICRM 2014 conference also time has been reserved for contributed lectures. We invite you to submit abstracts for oral contributions, as well as for the two poster sessions. Abstracts can be submitted through the conference website at Submission deadline is May 1st 2014. Note that only submissions from registered attendees are taken into the review process.

Email contact:

For more details, please visit

15-20 Sep 2014

1st International Summer School “Data Acquisition and Analysis in Metabolomics” in Sardinia
Venue: Pula, Sardinia, Italy

Course Objectives
The Summer School will offer students theoretical sessions with lectures by experts, and hands-on in the laboratory aimed to deepen the theoretical and practical knowledge for using the main tools (NMR, MS) techniques and computer analysis in the metabolomic and statistical fields. Particular attention will be given on how to manage a laboratory using a Laboratory Information Management System (LIMS) as well as data standardization and publication.

  • Mass Spectrometer and Metabolomics
  • NMR and Metabolomics
  • Chemometric analysis
  • Visualization and analysis of multi-omics data
  • LIMS applied to metabolomics
  • Public repositories of public data
  • Clinical metabolomics
Target Audience
This course is intended for graduate students, post-doctoral fellows, clinical fellows and investigators who are interested in learning about both technical and cheminformatic tools to analyze and interpret metabolomics data.

Organizing Committee
The school fee is 300 Euros and includes accommodation, coffee breaks, lunches, and the dinners.

Event flyer: Sardinian Summer School.pdf
For detailed information about the Summer School in Sardinia visit:

18-20 Sep 2014

MET-GR III workshop: Metabolic and Protein Network analysis in Systems Biology
Venue: University of Patras, Greece

We are pleased to invite you to participate in the "MET-GR III workshop: Metabolic and Protein Network analysis in Systems Biology", which will take place on September 18-20, 2014 in Patras, Greece.MET-GR III is co-organized by the Institute of Chemical Engineering Sciences of the Foundation for Research and Technology – Hellas (FORTH/ICE-HT) and the University of Patras Research Network “Research and Applications in Medical Molecular Genetics - MGN”. MET-GR III constitutes the 1st summer school of the FP7 European Project in Synthetic Biology – STREPSYNTH, sponsored also from the FORTH Systems Biology Network.

MET-GR III is the third in a metabolomics workshop series in Greece started in Thessaloniki by G. Theodorids & Ian Wilson (2008) and continued in Athens by E. Mikros & G. Theodoridis (2012). The series aims at providing an interdisciplinary forum for researchers already active or interested in the high-throughput analysis of metabolic network activity in the context of systems biology and medicine, to present their research, get trained in recent analytical and computational advances and applications, and creatively interact for the establishment of scientific networks and collaborations. This year the workshop will also expand towards the analysis of protein interaction & regulatory networks discussing current challenges and opportunities from the combined analysis of both molecular levels of cellular function for the comprehensive elucidation of biological systems.

MET-GR III includes presentations from several renowned scientists. Participation from graduate students and junior post-docs is strongly encouraged. Poster presentations will constitute a major element of MET-GR III and those by junior scientists will be considered for best presentation awards. A small number of submitted abstracts will be selected for oral presentation.

Organizing Committee
Maria I. Klapa, FORTH/ICE-HT
Nicholas K. Moschonas, School of Medicine, U. Patras
Georgios Theodoridis, Dept. of Chemistry, Aristotle U. of Thessaloniki
Kristel Bernaerts, Dept. of Chemical Engineering, KU Leuven
Dimitris Kafetzopoulos, FORTH/IMBB

For more details, please visit

29-30 Oct 2014

Clinical Applications of Mass Spectrometry
Venue: Barcelona, Spain

With the ability to measure multiple analytes with high sensitivity, often faster and more cheaply than other methods, mass spectrometry is becoming an attractive method of analysis for the clinic. Featuring an array of leading researchers and clinicians, SELECTBIO’s Clinical Applications of Mass Spectrometry conference aims to provide you with an insight into the latest developments in this area.

As the analytical power of mass spec is realised, the range of applications using this technology continues to expand. Focus at this meeting will be given to both traditional & emerging uses of MS in the clinic. Hot topics to be covered include developments of MS in applications ranging from vitamin D detection to newborn blood spot analysis. Attending this event will provide you with excellent opportunities for networking with like minded peers, helping you to build new relationships and optimise your workflow.

Running alongside the conference will be an exhibition covering the latest technological advances and associated services from leading solution providers within this field. Registered delegates will also have access to the co-located Food Analysis Congress, ensuring a cost effective trip.

Keynote Speakers:
  • Donald Hunt, Professor, University of Virginia
  • Haroun Shah, Head, Molecular Identification Services, Department for Bioanalysis and Horizon Technologies, Public Health England

For more details, please visit

29-30 Oct 2014

Food Analysis Congress
Safety, Quality, Novel Technologies
Venue: Barcelona, Spain

SELECTBIO’s inaugural Food Analysis Congress aims to present the latest developments in food analysis technologies, in response to the increasing demand for rapid and efficient food safety and quality testing.

Focus will be given to advances in both the analysis of natural food allergens and toxins, as well as contaminants introduced through processing and packaging. Points for discussion will also include the ongoing issue of food traceability and efforts to reduce food fraud. Attending this event will provide you with excellent opportunities for networking with like minded peers, helping you to find solutions and build collaborations.

Running alongside the conference will be an exhibition covering the latest technological advances and associated services from leading solution providers within this field. Registered delegates will also have access to the co-located Clinical Applications of Mass Spectrometry track, ensuring a cost effective trip.

For more details, please visit

19-21 Nov 2014

Merlion Metabolomics Workshop Singapore 2014
Developing Metabolomics Platform Technologies through Singapore-French Research Alliance
Venue: University Town, National University of Singapore

This Merlion Metabolomics Workshop will leverage on the strong infrastructure towards applying metabolomics technology in environment, food science and technology, and human health at National University of Singapore (NUS) (acting through NUS Environmental Research Institute (NERI)) and the well-established expertise in the area of nutrition, toxicology at the National Research Institute of Agronomy (acting through MetaboHUB), to encourage technical exchanges and catalyze the development of research collaboration in the field of metabolomics between Singapore and France. This workshop also provides opportunities for the knowledge and technologies developed in Europe to be applied in the Asian context.

This 3-day workshop features three important areas of metabolomics research, namely, Environment, Food Science and Technology, and Human Health. Eight tracks, including two sessions for young researchers to share their research findings, will facilitate knowledge sharing and discussions over 2.5 days during the workshop. A half day technical site visit to research and/or manufacturing facilities will be arranged for a selected group of participants. Prominent scientists in metabolomics from Asia-Pacific region will also be invited to the workshop.

For further details, please visit the workshop website.

3-4 Dec 2014

Australian Lipids Meeting
Venue: University of Wollongong (Innovation Campus), Wollongong, NSW, Australia

We are pleased to announce the 2nd Australian Lipid Meeting, which will be held at the University of Wollongong's Innovation Campus from 3-4 December, 2014.

While the first meeting focused on lipidomics we have expanded the scope for the second meeting to cover all aspects of lipid research. Planned topics include:
  • Imaging
  • Botany
  • Nutrition
  • Health and Disease
  • Technical Developments and Methodology
We look forward to seeing you in "The Gong".

Key Dates
Abstract submissions
  • Open: 1 May, 2014
  • Close: 31 July, 2014
  • Acceptance notification: September 2014
  • Open: 1 August, 2014
  • Early bird: Closes 28 October, 2014
For further details, please visit

11-13 Dec 2014

2nd ICAN (Institute of Cardiometabolism and Nutrition) Conference Series 2014
Venue: St James and Albany Hotel, Paris, France
Diabetes, obesity, and heart diseases

Further Information:
Download the Flyer.

For further details, 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

You are invited to join us for Metabolomics 2015, the official annual meeting of the Metabolomics Society.

This stunning world-class venue will host the most exciting metabolomics conference of 2015. Your host institution, the University of California, Davis, will gladly welcome scientists from all around the world to feel at home and relax while hearing of the latest innovations and breakthroughs in metabolomics.

Details to follow. Please check back soon!

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.

For further details, visit

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
Analytical Scientist (Research & Development)
BIOCRATES Life Sciences AG
Innsbruck, Austria

BIOCRATES Life Sciences AG
Business Development Manager USA
BIOCRATES Life Sciences AG Innsbruck, Austria 1-Aug-2014
BIOCRATES Life Sciences AG
Research Head of NMR Metabolomics Lab
Beaumont Health System and the Beaumont Research Institute Royal Oak, MI, United States 31-Jul-2014

Metabolomics Society Jobs
Applications Support Scientist (f/m) Metabolomics-Lipidomics
Thermo Fisher Scientific Europe 16-Jul-2014

Metabolomics Society Jobs
Postdoctoral Fellow in Metabolomics
The Metabolomics Innovation Centre, University of Alberta
Edmonton, Canada

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.
  • There are currently no "Jobs Wanted" submissions.

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