MetaboNews Masthead
Published in partnership between
TMIC and the Metabolomics Society
Issue 37 - September 2014

CONTENTS:


Online version of this newsletter:
http://www.metabonews.ca/Sep2014/MetaboNews_Sep2014.htm

Welcome to the thirty-seventh issue of MetaboNews, a monthly newsletter published in partnership between The Metabolomics Innovation Centre (TMIC, http://www.metabolomicscentre.ca/) and the international Metabolomics Society (http://www.metabolomicssociety.org/), 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 two customized metabolomics databases for the analysis of TOCSY-type NMR of complex mixtures, and a metabolomics interview with Dominique Rolin and Etienne Thévenot.
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


CONFERENCE and TRAINING CORNER

Training Needs in Metabolomics: Questionnaire jointly organized by the international Metabolomics Society and ELIXIR-UK

Complete the questionnaire below and enter a prize draw for one of THREE $100 Amazon gift vouchers

The international Metabolomics Society was established to stimulate collaboration and association amongst scientists in academia, government and industry, and therefore to help to develop the science of metabolomics. ELIXIR-UK is the United Kingdom node within the European ELIXIR infrastructure and is focused on training that will be delivered in specialised centres, in courses, and through e-learning, in partnership with other European ELIXIR Nodes and agencies. A key mechanism for supporting the growth of metabolomics is through the provision and support of training and this questionnaire will be applied to:
 We request any individual who is engaged in or who wishes to be engaged in metabolomics science, from any scientific backgrounds, any career stage, and importantly from any country or type of employment (academia, industry, government or any other groups) to complete the questionnaire. By “metabolomics science” we include the underpinning science and technology (experimental design, analytical measurements, computational analyses and informatics) and any field of application from microbes to plants and animals, including humans. Personal details will not be shared with any other organisation or society

We intend to distribute the findings from this questionnaire widely to the metabolomics community, for example through the Metabolomics journal and on-line MetaboNews, and we intend for it to guide the development of training programs globally. In particular, the information will be used to guide the development of new training programs by the international Metabolomics Society and ELIXIR UK Node.

Please complete the questionnaire below to enhance our knowledge on training requirements and delivery:
https://www.surveymonkey.com/s/metabolomicstraining

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: http://metabolomicssociety.org/index.php/events/event-funding

11th Annual International Conference of the Metabolomics Society
Location: San Francisco, USA
Date: June 29 - July 2, 2015
Website: http://metabolomics2015.org/

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
Website: http://www.icsn.cnrs-gif.fr/spip.php?rubrique191&lang=en


BOARD OF DIRECTORS OF THE METABOLOMICS SOCIETY

Metabolomics Society Election Results
The Metabolomics Society is proud to announce the election of 8 Directors to lead the Society through the next two years. The winners were voted in by the Society membership from a competitive ballot of 20 high quality nominees. The results included the re-election of 4 board members, Ute Roessner (University of Melbourne), Dan Bearden (NIST), Tim Ebbels (Imperial) and Robert Mistrik (HighChem). These four directors have contributed enormously to the Society over the last two years, including holding executive positions (Ute and Dan) and chairing Society committees (Tim and Robert). The Society is well-placed to continue to benefit from these hard-working volunteers for the next two years.

Four new directors were elected to the board providing new expertise and experience, Susan Sumner (RTI), Reza Salek (EBI, Cambridge), Steffen Neumann (IPB-Halle) and Masanori Arita (NIG, Japan). The new directors will join the Board in October and we look forward to your contributions to continue to advance metabolomics as a science and a community.

Congratulations to the new Directors!

Elections for President, Treasurer and Secretary
On 2nd September 2014 the election process will begin for the three new Officers to lead the development of the Metabolomics Society. Members, please watch out for an email notification about how to vote.


MEMBERS CORNER

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. If you have questions, comments or suggestions, please, feel free to contact us by email: info.emn@metabolomicssociety.org.

The EMN is looking forward to welcoming three new committee members!
We would like to thank all applicants for showing their interest in joining the EMN committee. We are no longer accepting applications. All applications received before 1st September will be reviewed by members of the Metabolomics Society’s Strategy Task Group and the existing EMN committee members during the next few weeks. Successful candidates will be informed at the end of September 2014.

Merlion Metabolomics Workshop Singapore 2014
NUS Environmental Research Institute (NERI) together with MetaboHub, National Research Institute of Agronomy (INRA) and Institut Français de Singapour (IFS) are jointly organizing the Merlion Metabolomics Workshop Singapore 2014 - Developing Metabolomics Platform Technologies through Singapore-French Research Alliance. The workshop will be held from 19 - 21 November 2014 at University Town, National University of Singapore. This workshop provides opportunities for the knowledge and technologies developed in Europe to be applied in the Asian context. The 3-day workshop features three important areas of metabolomics research: Environment, Food Science and Technology, and Human Health. Eight tracks, including two dedicated sessions for young researchers to share their research findings, will facilitate knowledge exchange and discussions throughout the workshop. Our very own EMN Chair, Dr. Sastia Putri of Osaka University will chair one of the young researcher sessions and Prof. Roy Goodacre, Editor-in-Chief of Metabolomics and a Director of the Metabolomics Society, will give a keynote lecture during this workshop. We hope to see you there!


INTERNATIONAL AFFILIATES CORNER

Australian & New Zealand Metabolomics Network (ANZMN)
Visit http://www.metabolomics.com.au/anzmn/index.html

The Metabolomics Australia (MA) team at the University of Western Australia, led by Dr. Mike Clarke and with Ms. Dorothee Hahne have received confirmation that the group has comfortably met the criteria for both precision & accuracy (Fig. 1) for certification in the Vitamin D Standardisation Program being run by the Centers for Disease Control/NIH in the USA. The group will now be listed on the CDC website as a reference facility and with other applications already in the pipeline the group is looking at further certifications in the future. The result has been achieved through dedication and commitment on delivery to a high standard, achieving sensitivities of 2 nmol/L in 50 uL of human serum.

Data points are means of 2 replicates
Figure 1. Data points are means of 2 replicates as submitted by MA.

For more information contact Dr. Mike Clarke at http://www.metabolomics.uwa.edu.au/index.php
For information about Metabolomics Australia please see www.metabolomics.net.au

Korea Metabolomics Society (KoMetS)
Visit http://komets.or.kr/english05.html

2014 International Symposium on MS-based Metabolomics
On June 30th, right after the 10th Annual conference of the Metabolomics Society, a special symposium was held in EWHA Woman’s University, Seoul, Korea, organized by Korea Agilent Technology. Two invited speakers, Professors Oliver Fiehn (UC Davis, USA) and Do Yup Lee (Kookmin University, Korea), presented “Basics and pitfalls of MS-based metabolomics” and “MS imaging analysis”, respectively. More than 150 attendees joined the symposium and had a good opportunity to hear a comprehensive overview from experimental design to data interpretation in the metabolomics field. Korea Metabolomics Society plans to continue the public excitement by holding a workshop on Oct 6th 2014 with more detailed and specialized topics.


PUBLICATIONS CORNER

Metabolomics journal, Vol. 10, Issue 4, August 2014
See the latest articles at:
http://link.springer.com/journal/11306/10/4/page/1

As well as some interesting research articles, we have 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

Customized Metabolomics Databases for the Analysis of TOCSY-Type NMR of Complex Mixtures

Feature article contributed by Kerem Bingol and Rafael Brüschweiler
Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States

 Compound identification of complex mixtures by 2D TOCSY-based NMR spectroscopy using common 1D NMR spectral databases is a challenge because magnetization transfers in TOCSY experiments are limited to spins within the same spin system. This situation frequently leads to unexplained peaks in the 1D NMR spectrum of a metabolite if they belong to different spin systems. To address this, we recently developed NMR metabolomics spectral databases, which were specifically designed to deal with this type of situation.

Our customized metabolomics NMR databases, termed 1H(13C)-TOCCATA [1] and 13C-TOCCATA [2], contain complete 1H and 13C chemical shift information of individual spin systems and isomeric states of over 450 common metabolites. Since this information is directly reflected in cross-sections of 2D 1H-1H TOCSY, 2D 13C-1H HSQC-TOCSY, and 2D 13C-13C TOCSY spectra, these databases allow the accurate and straightforward identification of metabolites of complex metabolic mixtures from these types of experiments.

The 1H(13C)-TOCCATA database is best suited for 2D 1H-1H TOCSY and 2D 13C-1H HSQC-TOCSY spectra of complex mixtures at 13C natural abundance [1], whereas the 13C-TOCCATA is best applied to 2D 13C-13C constant-time (CT) TOCSY spectra of uniformly 13C labeled samples [2]. Both databases can be accessed through public web portals: 1H(13C)-TOCCATA at http://spin.ccic.ohio-state.edu/index.php/toccata2/index and 13C-TOCCATA at http://spin.ccic.ohio-state.edu/index.php/toccata/index.

We illustrate the performance of 1H(13C)-TOCCATA for the 2D 1H-1H TOCSY spectrum of a cell lysate from E. coli (Figure 1), which yields a substantial improvement over other databases as well as 1D 1H NMR-based approaches in the number of compounds that can be correctly identified with high confidence. This database can be equally well applied other biological samples, such as urine, blood, and tissue extracts.

Click on thumbnail below to view a larger version of the image

Schematic representation of the querying approach against the 1H(13C)-TOCCATA database

Figure 1. Schematic representation of the querying approach using the new 1H(13C)-TOCCATA database. In the 2D 1H-1H TOCSY spectrum of an E. coli cell lysate (orange), the 1H TOCSY trace (green cross-section) is extracted and its peaks are queried against the new database. The 1H TOCSY trace is assigned with high accuracy to the only viable hit, which is the nicotinamide ring portion of NADP+.

The green 1H TOCSY trace of the orange spectrum in Figure 1 was directly searched against 1H(13C)-TOCCATA. The search returned a single hit, which is the correct one corresponding to the nicotinamide ring of NADP+. NADP+ is a large metabolite with several substructures, such as adenine, ribose rings, and nicotinamide. Since in a conventional 1D 1H NMR database, the peaks of all parts of the molecule are represented as a single group, searching the peaks of only the nicotinamide ring against the 1D 1H NMR database will create mismatches, which precludes accurate identification. By contrast, with the help of the new 1H(13C)-TOCCATA database, one can easily identify individual spin systems (substructures) and isomeric states of metabolites with optimal accuracy.

Citing TOCCATA

[1] 1H(13C)-TOCCATA is a free and publicly accessible web portal. The link to the database is: http://spin.ccic.ohio-state.edu/index.php/toccata2/index

Publication:
Kerem Bingol, Lei Bruschweiler-Li, Da-Wei Li and Rafael Brüschweiler. Customized Metabolomics Database for the Analysis of NMR 1H-1H TOCSY and 13C-1H HSQC-TOCSY Spectra of Complex Mixtures. Analytical Chemistry, 86, 5494-5501 (2014). http://pubs.acs.org/doi/abs/10.1021/ac500979g

[2] 13C-TOCCATA is a free and publicly accessible web portal. The link to the database is: http://spin.ccic.ohio-state.edu/index.php/toccata/index

Publication:
Kerem Bingol, Fengli Zhang, Lei Bruschweiler-Li, and Rafael Brüschweiler. TOCCATA: A Customized Carbon Total Correlation Spectroscopy NMR Metabolomics Database. Analytical Chemistry, 84, 9395–9401 (2012). http://pubs.acs.org/doi/abs/10.1021/ac302197e


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

 MetaboInterview Icon

MetaboInterviews
MetaboInterviews features interviews with prominent researchers in the field of metabolomics. The aim of these interviews is to shed light on metabolomics researchers around the world and give them an opportunity to share their metabolomics story. In this issue, we feature an interview with Dominique Rolin and Etienne Thévenot.

Dominique Rolin
Head of MetaboHUB, France
 Dominique Rolin
Biography
After a PhD in Plant Physiology from the University of Rennes (France), D. Rolin spent 4 years at the Eastern Regional Research Center in Philadelphia (USA) using in vivo NMR spectroscopy to study nitrogen fixation by Bradyrhizobium bacteria in soybean plant. Since 1994, D. Rolin has been a full professor at Bordeaux University, coordinator of the Master course in Plant Physiology and Biotechnology. He is an expert in the fields of NMR spectroscopy, biology, plant and fruit metabolism, metabolomics and fluxomics. Director of the Fruit Biology Unit at the National Institute for Agronomic Research (INRA) for 8 years, D. Rolin is also widely involved in the emerging field of functional genomics especially in metabolomics. He heads the Bordeaux Functional Genomics Centre, a federation of seven technological platforms (112 permanent staff in 2014) dedicated to the study of living organisms at the tissular, cellular, and molecular levels in the Bordeaux region (Aquitaine Region). In 2002, he set up and led the Metabolome Facility of Bordeaux (BMP), and is considered a pioneer in the field of plant metabolomics in France. D. Rolin is also deeply involved in the promotion of Metabolomics & Fluxomics as co-founder, treasurer (2007-2010), and President (2010-2015) of the French Metabolomics and Fluxomics Network (RFMF, a Scientific Society created in 2005 that aims at the promotion of Metabolomics and Fluxomics in France). D. Rolin was co-organizer of eight national metabolomics congresses and two scientific workshops for metabolomics. Today, D. Rolin is in charge of the MetaboHUB project, the French infrastructure devoted to metabolomics and fluxomics.
Etienne Thévenot
Coordinator of the bioinformatics work packages of MetaboHUB and the Biomargin European project
 Etienne Thévenot
Biography
After an education in mathematics and physics at the MINES ParisTech graduate school, Etienne Thévenot obtained his PhD in neurobiology from the Pierre and Marie Curie University (CNRS laboratory of molecular genetics of neurotransmission and gene therapy of neurological diseases, headed by Jacques Mallet). In 2005, he joined the French Alternative Energies and Atomic Energy Commission (CEA) at the Saclay Centre to work as a biostatistician and bioinformatician at the LIST institute (applied mathematics and software technologies). His research, in partnership with biological and clinical partners focuses on signal processing and statistical analysis of data from omics technologies (transcriptomics, proteomics, and metabolomics). He is coordinator of the bioinformatics work packages of MetaboHUB and the Biomargin European project (biomarker discovery for renal transplant monitoring).

Metabolomics Interview (MN, MetaboNews; DR, Dominique Rolin; ET, Etienne Thévenot)

MN: How did you get involved in metabolomics?

DR: I got the opportunity to attend the First International Congress on Plant Metabolomics organized by Raoul Bino, Linus van de Plas, Emmy van Balen and Robert Hall in Wageningen in April 2002. During the four days at this event, I realized the power of this new discipline, the immensity of the task lying ahead, and I came back to Bordeaux with a full set of ideas and a strong spirit. I started a new scientific life with metabolomics as a guide to solve plant biology questions.

ET: I have always been interested in bridging experimental acquisition and mathematical analysis. As a biologist, I was fascinated by living organisms, but I was also sometimes frustrated because, at the end of several weeks or months of experiments, I did not have enough time left (nor methodological and software tools) to fully exploit the wealth of data. Within the multidisciplinary environment of CEA, we have been taking advantage of our expertise in spectrum signal processing, data analysis and machine learning to build a strong partnership with Christophe Junot's experimental Drug Metabolism Research laboratory (LEMM).

Bioinformatics at MetaboHUB

Bioinformatics at MetaboHUB: from raw data to statistical analysis, annotation, and pathway analysis


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

DR: MetaboHUB is the French metabolomics and fluxomics infrastructure launched in 2013. It combines four MS and NMR metabolomics platforms, corresponding to 50 FTEs. With an initial budget of 42.5 M€ up to 2020, it provides a unique opportunity to merge both analytical (in the fields of agriculture, nutrition, environment, health and biotechnologies) and bioinformatics (data processing, data analysis, and pathway analysis) expertise and infrastructures. I do not consider metabolomics as an objective in its own right but rather as a tool in conjunction with other “omics” to solve plant biology questions. My feelings are the same as a bandmaster: playing with many disciplines (chemistry, biology, statistics, bioinformatics) and dealing with different human competences are two exciting facets of my work in metabolomics. The complexity of the approach is also a fascinating feature.

MetaboHUB analytical and bioinformatics core and advanced services

MetaboHUB analytical and bioinformatics core and advanced services

ET: Experimentation is a difficult task because of ethical considerations, collection duration (e.g., cell culture), control of the parameters and material costs. It is therefore of paramount importance that all bioinformatics resources (e.g., databases) and statistical methods (e.g., algorithms and workflows) be readily available to optimize experimental design and analyses (e.g., to avoid confounding factors). The interplay between experimental questions and bioinformatics' insights is very exciting and challenging.

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

ET: In partnership with the French Bioinformatics Institute (IFB, ABiMS platform), MetaboHUB develops a metabolomics data processing, analysis and identification workflow by using the Galaxy environment (available at workflow4metabolomics.org and coordinated by Christophe Caron and Franck Giacomoni). Galaxy is an open web-based platform enabling users to build their workflow (by selecting among the computational modules proposed), interactively view the results (tables, figures and web pages), store and share their analyses (parameters, input and output files). Galaxy is also very useful for developers, since they can compare alternative algorithms using the same conditions and the same datasets, by wrapping them into workflow modules. A full LC-MS workflow for untargeted analysis is already available (including tools for OPLS modeling) with sample datasets, tutorials and demos. We are now working on additional NMR processing modules. The workflow will also be connected to the MetExplore platform (project leader: Fabien Jourdan) to enable further analysis of genome scale metabolic networks.

Click on the thumbnail below to view a larger version of the image.

The workflow4metabolomics Galaxy portal for data pre-processing, statistics and annotation

The workflow4metabolomics Galaxy portal for data pre-processing, statistics and annotation

In parallel, the MetaboHUB consortium is building an NMR and MS spectral database to enrich feature annotation and facilitate de novo structure elucidation. We take advantage of our previous experience in NMR knowledge bases (MeRy-B, developed by Daniel Jacob) and in MS spectrum structural interpretation (Werner et al., 2008). The database will have its own web interface for interactive query and annotation of a peak list of interest, and will also be connected to workflow4metabolomics to enable automated annotation of peak tables.

MN: What is happening in your country in terms of metabolomics?
DR: Since 2005, the French community has become quite large and well organized. The French Metabolomics and Fluxomics Network (RFMF) is active, strong and very useful to the French community. The RFMF contributes to the development of Fluxomics and Metabolomics and more broadly to the overall analysis of metabolism in France through various actions:
 The 8th annual conference (May 2014) gathered about 300 participants in Lyon. We invited 4 guest speakers (Miroslava Cuperlovic-Culf from Moncton, Canada; Emmanuel Gaquerel from Heidelberg, Germany; Thomas Illig from Hanover, Germany; and Mark Viant from Birmingham, UK). A full session was devoted to the Junior members of RFMF. In addition, the program included 2 satellite workshops and 2 round tables focusing on “High resolution mass spectrometry and metabolomics – Looking for best solutions to three major hurdles” and “Preparation of blood samples for metabolomics analyses”. Next fall, the RFMF and MetaboHUB will organize a 5 day advanced course on MS metabolomics that will take place on the French Riviera. The objective is to train scientists with an MS background on specific metabolomics methodologies and software tools (from ionization and fragmentation principles, sample preparation, quality control, annotation, to statistical and network analysis). The 2015 RFMF annual meeting will take place in Lille and will be organized in collaboration with researchers in Belgium.

ET: In 2010, the French government decided to create national biology and health infrastructures in personalized medicine (genomics, proteomics, structural biology, bioinformatics), imaging, and translational research (biobanks and clinical trials). We expect that these infrastructures will collaborate with each other within multidisciplinary programs of critical mass and standardized protocols to provide innovative and robust diagnostics and treatments, and contribute to the European research space.

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

DR: Metabolomics holds great promise in the post-genomics era as it offers the most direct and integrated measure of physiological activity or biochemical status. MetaboHUB was created to contribute, along with other international initiatives, to the standardization, simplification and automation of the way one measures an organism's biological response to any stressor (i.e., disease, environment, drugs, toxins, etc.). But metabolomics remains just one tool among a large set of complementary post-genomic approaches. It is of paramount importance that these technological developments be driven by biological and clinical questions. One of the main challenges is, in turn, to aggregate the omics results and translate them into meaningful applications.

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

DR: Life consists of a long history of competition that has occurred over a period of 3 billion years. Different forms of life (millions) have been classified for several centuries. The chemistry of life is very complex and it will take some time before we fully grasp the metabolomics evolutionary aspects of the tree of life. This research will be critical to understand the interactions between the genome and the environment: for example, in large sectors of plant metabolism during diurnal cycles, researchers have shown that levels of transcripts (and some metabolic intermediates) exhibit rapid changes. The majority of metabolite variations are much slower, suggesting that an important part of metabolism may be independent of short term or recurring (e.g., diurnal) environmental fluctuations (Gibbon et al, 2006).

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

DR: The greatest challenges in metabolomics include chemical diversity, the wide range of metabolites' abundance, the instability of some molecules, the difficulty of extracting all metabolites in one shot, the capacity to get absolute quantification of metabolites, and the absence of one unique analytical technology for all molecules.

ET: The ever-growing technological developments (two-dimensional liquid chromatography and ion mobility, increase of the spectrometer resolution, data-independent MS/MS acquisition) lead to a massive amount of complex multidimensional raw data. New algorithms and computational resources will be required to efficiently process and visualize such data. In addition, interoperability between data repository is critical (e.g., standard formats, ontologies, etc.). One of the greatest challenges for metabolomics is to deliver fully annotated features that can be mapped to genes and proteins within networks: the objective is to reconcile the reductionist and system approaches and provide a multi-scale understanding of life processes, from pathway overview to molecular zooming.

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

DR: Technological platforms have emerged during the last ten years to pool the analytical (instruments, robots) and bioinformatics resources, combine interdisciplinary expertise, and define standards. This rationalization for more quality management has changed our way of working (in particular, the need to produce standardized metadata on each experimental study). The issue for the next ten years is to build on each continent a strong network of national platforms which will be specialized in specific application fields (plant, health, white biotechnology, environment, etc.). Annotation initiatives are in progress for organisms in specific physiological or physio-pathological conditions. In parallel, the dynamic picture of the metabolome network is emerging (e.g., with fluxomics studies). The challenge is to validate the translation of metabolomics research into diagnostics and address societal issues (agriculture, energy, health, materials, environment, etc.).

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

DR: Several European States have decided to build national metabolomics infrastructures (like the UK, the Netherlands, and now France). In addition, the European Commission favors integration of platforms: in the H2020 work program, several calls focus on European research infrastructures (including e-Infrastructures). Such programs are also open beyond Europe (e.g., to North America). In parallel, the market will also drive the development of metabolomics, as we see for instance in food security (for example, the Profilomic start-up offers solutions for LC-MS based targeted and global detection of emerging pollutants in food and environment).

 MN: What role can metabolomics standards play?

ET: Analytical and bioinformatics standards are mandatory for obtaining robust results, capitalizing on previous experience, and building interoperable knowledge bases. In 2012, Jean-Charles Martin started the Metabo-Ring Initiative: the objective was to compare the results from untargeted analysis of two identical datasets by ten independent platforms across 4 countries (10 MS: Q-TOF and Orbitrap, and 5 NMR; results have been submitted for publication). In addition, reference MS/MS acquisition protocols have been developed to improve the reproducibility of CID spectra between several instrumental platforms in order to facilitate de novo spectra interpretation (Ichou et al, 2014). Regarding bioinformatics, the MetaboHUB Bordeaux platform is involved in the COSMOS European project dedicated to the COordination Of Standards In MetabOlomicS. One of its tasks consists of developing the NMR Markup Language (nmrML). It is very important that all manufacturers include in their software efficient batch export of the raw data to standard formats (i.e., mzML for MS, and, soon, nmrML for NMR).

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

DR: As a professor, I am concerned about the education and training of the young scientists, which is currently a bottleneck in the development of metabolomics. There is a critical need to improve the computational skills of undergraduate students (experimental design, signal processing, data analysis, computer science) as well as their expertise in chemistry and biophysics for MS and NMR. If we do not take the time to teach and educate young scientists, we will not succeed. In France, the RFMF has set up a Junior session to foster the development of the next-generation of metabolomics scientists. So far 30 young scientists (Masters, PhDs and Post-docs from many different fields) have joined RFMF Junior.
Biomarker Beacon

Biomarker Beacon

 This section of MetaboNews is supported by:
LECO

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 colorectal cancer.
Zhu J, Djukovic D, Deng L, Gu H, Himmati F, Chiorean EG, Raftery D. Colorectal Cancer Detection Using Targeted Serum Metabolic Profiling. J Proteome Res. 2014 Aug 15. [Epub ahead of print] [PMID: 25126899]

Colorectal cancer (CRC) is one of the most lethal cancers in the world and robust biomarkers for CRC are sorely lacking. In this paper, the investigators used a metabolomics approach to identify potential biomarkers for CRC. Using targeted liquid chromatography-tandem mass spectrometry and partial least-squares-discriminant analysis (PLS-DA), they monitored 158 metabolites and 25 metabolic pathways in serum samples from three patient groups (66 CRC patients, 76 polyp patients, and 92 healthy controls). They succeeded in differentiating between CRC patients and patients with polyps or healthy patients with high sensitivities (0.96 for CRC patients vs. healthy controls and 0.89 for CRC patients vs. patients with polyps) and good specificities (0.8 and 0.88). This research presents a promising approach to metabolic profiling of patients with CRC.
Metabolomics Current Contents

Metabolomics Current Contents
This section of MetaboNews is supported by:
Bruker Corporation

Recently published papers in metabolomics:

MetaboNews

MetaboNews
28 Aug 2014
The Analytical Scientist Power List 2014
Who Are The Top 40 Under 40?

Last year, we ranked the Top 100 most influential analytical scientists in our inaugural Power List.

This year, we shift the focus to the up-and-coming ladies and gentlemen who are already making waves in our dynamic field. We want to profile 40 analytical scientists under the age of 40 to shine a light on those who are likely to be the scientists, engineers, software developers and business people shaping a bright and innovation-rich future.

Once again, we invite you to nominate the men and women who you believe have what it takes to be the trailblazers of tomorrow. Your suggestions will be considered by our panel of judges who the Top 40 Under 40.

To nominate, either fill out the short questionnaire here: tas.txp.to/PowerList2014 or email rich.whitworth@texerepublishing.com with name, affiliation, reason for nomination, and your connection to the nominee.

For more details, visit the Analytical Scientist. Note: The deadline for nominations is Sunday, 7 September 2014.
14 Aug 2014
IROA Technologies Releases Mass Spectrometry Metabolite Library of Standards (MSMLS)

IROA Technologies released MSMLS, a library of high quality small biochemical standards used to provide retention times and spectra for key metabolic compounds, help optimize mass spectrometry analytical protocols, and qualify and quantify mass spectrometry sensitivity and limit of detection. 
  • Broad metabolite spectrum, key primary metabolites and intermediates
  • Conveniently arrayed in 96-well format, alphanumeric assigned position
  • Supplied as 5 µg dried weight
  • Descriptors: molecular formula, molecular weight, parent CID, CAS, etc.
  • Suitable for manual and automated work flows
For more details, email info@iroatech.com or visit www.iroatech.com.

Metabolomics Events

Metabolomics Events
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: http://www.metabonews.ca/Jul2014/events/Mayo Clinic Metabolomics Symposium.pdf

For more details, please visit http://www.mayo.edu/research/core-resources/metabolomics-resource-core/symposiums
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: http://www1.imperial.ac.uk/iiptc/courseinfo/lcms/

Download the full programme here: LCMS Metabolic Profiling Sept 2014

Online booking is available at:
http://www5.imperial.ac.uk/medicine/coursebookings/metabolicprofiling_0914.html

For more details, visit http://www1.imperial.ac.uk/iiptc/courseinfo/lcms/ or contact Dr Elizabeth Want on 0207 594 30230207 594 3023 (iptc@imperial.ac.uk).
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 www.icrm2014.org. Submission deadline is May 1st 2014. Note that only submissions from registered attendees are taken into the review process.

Email contact: icrm2014@xs4all.nl
Registration: www.icrm2014.org/registration/registration.html.
For more details, please visit http://www.icrm2014.org/
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.

Topic
  • 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
 Registration
The school fee is 300 Euros and includes accommodation, coffee breaks, lunches, and the dinners.

Event flyer: http://www.metabonews.ca/Jul2014/events/Metabolomics Sardinian Summer School.pdf
 
For detailed information about the Summer School in Sardinia visit: http://sites.unica.it/metabolomicaclinica/events/summer-school-2014/
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 http://metgr3.iceht.forth.gr/.
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 http://selectbiosciences.com/conferences/index.aspx?conf=CAMS2014
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 http://selectbiosciences.com/conferences/index.aspx?conf=FAC2014
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.
3-5 Dec 2014

2nd Australian Lipid 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 3-5 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
Registration
  • Open: 1 August, 2014
  • Early bird: Closes 28 October, 2014
For further details, please see the event flyer or visit http://ihmri.uow.edu.au/research-program/australianlipidsmeeting/index.html
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: http://ican-series.com/
Registration: https://www.etouches.com/ereg/newreg.php?eventid=97217&
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 (http://www.metabolomicssociety.org). 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 http://metabolomics2015.org.

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

Metabolomics Jobs

Metabolomics Jobs

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

Jobs Offered

Job Title Employer Location Posted Closes Source
Research Programmer
 University of Alberta Edmonton, Canada 2-Sep-2014
University of Alberta
Research Fellow in Plant Analytical Biochemistry, Faculty of Agriculture and Environment - Camden Campus
 University of Sydney, Australia Sydney, Australia 28-Aug-2014
 26-Sep-2014
 Metabolomics Society Jobs
PhD Studentship
 International Pregnancy Research Alliance (IPRA)
 Chongqing, China 27-Aug-2014
 31-Dec-2014
 Metabolomics Society Jobs
Mass Spectrometry Technician International Pregnancy Research Alliance (IPRA) Chongqing, China 27-Aug-2014 31-Dec-2014 Metabolomics Society Jobs
Research Associate in Metabolomics / Bioanalytical Chemistry, Oxford Road University of Manchester Manchester, UK
 26-Aug-2014
 8-Sep-2014
 Metabolomics Society Jobs
Research Fellow in Toxico-Metabolomics-47388 University of Birmingham Birmingham, UK 15-Aug-2014
 14-Sep-2014 Metabolomics Society Jobs
Analytical Scientist (Research & Development)
 BIOCRATES Life Sciences AG
 Innsbruck, Austria
 1-Aug-2014
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


Jobs Wanted

This section is intended for very highly qualified individuals (e.g., lab managers, professors, directors, executives with extensive experience) who are seeking employment in metabolomics. We encourage these individuals to submit their position requests to Ian Forsythe (metabolomics.innovation@gmail.com). Upon review, a limited number of job submissions will be selected for publication in the Jobs Wanted section.
  • There are currently no "Jobs Wanted" submissions.

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