MetaboNews Masthead

MetaboNews
Issue 21 - May 2013

CONTENTS:


Online version of this newsletter:
http://www.metabonews.ca/May2013/MetaboNews_May2013.htm

Welcome to the twenty-first issue of MetaboNews, a monthly newsletter for the worldwide metabolomics community. In this month's issue, we feature a Software Spotlight article on MassCascade-KNIME, software for stepwise LC-MS metabolomics data processing. In May 2012, we introduced a new section called MetaboInterviews that features interviews with metabolomics experts from around the world. This issue includes an interview with Mark Viant, Professor of Metabolomics at the University of Birmingham, Director of the UK’s NERC Environmental Metabolomics Facility, and President of the International Metabolomics Society. This newsletter is produced by The Metabolomics Innovation Centre (TMIC, http://www.metabolomicscentre.ca/), and is intended to keep metabolomics researchers and other professionals informed about new technologies, software, databases, events, job postings, conferences, training opportunities, interviews, publications, awards, and other newsworthy items concerning metabolomics. We hope to provide enough useful content to keep you interested and informed and appreciate your feedback on how we can make this newsletter better (metabolomics.innovation@gmail.com).

Note: Our subscriber list is managed using Mailman, the GNU Mailing List Manager. To subscribe or unsubscribe, please visit https://mail.cs.ualberta.ca/mailman/listinfo/MetaboNews

Current and back issues of this newsletter can be viewed from the newsletter archive (http://www.metabonews.ca/archive.html).

 Software Spotlight

1) Software Spotlight

 MassCascade-KNIME Logo

MassCascade-KNIME: Stepwise data processing for LC-MS metabolomics data

Article contributors: Stephan Beisken1, Dr. Luis F. de Figueiredo1, Dr. Christoph Steinbeck1

Affiliation: 1. Cheminformatics and Metabolism Group, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.

Processing liquid chromatography-mass spectrometry (LC-MS) metabolomics data requires complex data processing and analysis workflows, combining different programs, tuning parameters, pulling in additional information from databases, and performing statistical analysis. Consequently, pipelines have been built concatenating existing tools [such as 1, 2].

Workflow platforms such as KNIME (http://knime.org/) offer the potential for an all-in-one solution. The Konstanz Information Miner (KNIME) is an open-source workflow and statistical analysis platform that supports a wide range of functionality and has an active cheminformatics and bioinformatics community.

MassCascade and its KNIME plug-in (http://sbeisken.github.com/MassCascadeKnime/) is a library and node suite for stepwise LC-MS metabolomics data processing that have been specifically developed with workflow environments in mind (Figure 1). Established workflows can be run in a completely unsupervised fashion, but the results can also be inspected interactively during workflow development at the intermediate node level. Instead of moving data and generated results back and forth between different tools, we attempt to unify the task of data processing while maintaining a level of flexibility similar to scripted pipelines.

Click on the thumbnail below to view a larger size image

Overview of the MassCascade plug-in for KNIME

Figure 1. Overview of the MassCascade plug-in for KNIME. An example workflow is shown with two result windows. The left window illustrates total ion chromatograms of three samples. The third, bottom-most sample, row 33, results from a failed injection. The right window depicts a PCA plot (PC1/PC2) from processed quality control samples.

The MassCascade plug-in contains a set of nodes, also known as workers (Figure 2). Each node carries out a particular function for processing input data. MassCascade is intuitive to use and comes with a set of pre-defined nodes. Every node can be utilized via drag and drop and configured using node dialog windows. Various node types exist for processing, visualisation, and statistical analysis. Workflows can be built or rearranged fast, LC-MS data comprehensively explored, and complete sets of workflows exchanged between collaborators, including all parameters for reproducibility. The integration into a workflow environment also makes it easy to maintain an overview of the complex analysis workflow and explore new methods and approaches for data analysis.

Click on the thumbnail below to view a larger size image

Screenshot of the KNIME workflow platform with MassCascade-KNIME


Figure 2. Screenshot of the KNIME workflow platform with MassCascade-KNIME. The node repository on the left contains all available nodes. Nodes can be moved onto the editor view in the centre via drag and drop, where they can be configured and run. Additional information is provided in the node description at the bottom.

Every step in the analysis is transparent and can be visually inspected or corrected if required. Parameter settings can be explored using smaller datasets before re-running the workflow for larger data sets. KNIME uses a tabular data model that is used to transport data between nodes. In the case of MassCascade that is LC-MS data. Because all nodes follow the same data model, generic KNIME nodes from different projects can be seamlessly integrated in the same workflow.

Consequently, resulting tables can be analysed with generic KNIME nodes or installed extensions. For example, the statistical computing language R can be used within KNIME to analyse result tables (Figure 3). Alternatively other nodes (implemented tools or methods) can be used. In any case, MassCascade-KNIME provides smooth integration of LC-MS data processing capabilities for the rich workflow platform KNIME.

Screenshots of a data table and plot of m/z traces

Figure 3. Screenshots of a data table and plot of m/z traces. The left window shows a typical table containing scan data and profile cells. Scan data cells outline the total ion chromatogram of a sample; profile cells plot a histogram of m/z traces in the time domain. The right window depicts an interactive plot to inspect m/z traces (time vs m/z).

Currently the library contains a set of standard algorithms for LC-MS data processing and is under active development. We believe that a workflow-driven approach is intuitive, visual, interactive, and helps with standardization and reproducibility. To that effect, we promote the use of open-source workflow applications that allow the combination of various tools into one to facilitate LC-MS data processing.

More information on MassCascade and the plug-in can be found on the Wiki pages (https://github.com/SBeisken/MassCascadeKnime/wiki) of the project or obtained from the primary author of this article.

References
  1. Peironcely, J. E. et al. An Automated Pipeline For De Novo Metabolite Identification Using Mass Spectrometry-Based Metabolomics. Anal Chem. 2013 Apr 2;85(7):3576-83. doi: 10.1021/ac303218u. Epub 2013 Mar 21. [PMID: 23368721]
  2. Jankevics, A. et al. Separating the wheat from the chaff: a prioritisation pipeline for the analysis of metabolomics datasets. Metabolomics. 2012 Jun;8(Suppl 1):29-36. Epub 2011 Jul 31. [PMID: 22593722]


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

 MetaboInterview Icon

2) MetaboInterviews
MetaboInterviews, a new section as of May 2012, 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 Mark Viant of the University of Birmingham, UK.


Mark Viant

 Professor of Metabolomics at the University of Birmingham, Director of the UK’s NERC Environmental Metabolomics Facility, and President of the International Metabolomics Society
 Mark Viant
Biography
Mark R. Viant is a Professor of Metabolomics at the University of Birmingham, Director of the UK’s NERC Environmental Metabolomics Facility, and President of the International Metabolomics Society. He received his BSc in Chemistry and PhD in Chemical Physics at the University of Southampton, UK, before conducting postdoctoral research in chemistry and then environmental toxicology at the University of California, Berkeley and then UC Davis, respectively. Upon returning to the UK in 2003, as a NERC Advanced Fellow at the University of Birmingham, he built a research group focusing on the development of metabolomics approaches and their application to the environmental sciences. His current interests include (1) the development of optimised analytical approaches for mass spectrometry based metabolomics and high throughput biology; (2) development of optimal computational workflows including database resources for metabolomics; (3) the application of these technologies primarily to investigate the metabolic pathways underlying stress and toxicity in aquatic organisms, with a particular focus on nanoparticle toxicology and the freshwater invertebrate Daphnia as a model organism; and (4) the translation of metabolomics based ‘discovery’ research into mechanistically-based tools for environmental diagnostics.


Metabolomics Interview (MN, MetaboNews; MV, Mark Viant)

MN: How did you get involved in metabolomics?

MV: Just over a decade ago, as a postdoc in the Department of Environmental Toxicology at the University of California, Davis, I was investigating the metabolic responses of marine shellfish to toxicants, in vivo, using 31P NMR spectroscopy. I was frustrated at only observing a few phosphorylated metabolites – albeit important ones and in real time (cool!) – and then read about Jeremy Nicholson’s 1H NMR metabonomic studies of earthworms. I decided the considerable gain in metabolic information outweighed the loss of moving from in vivo experiments to studying tissue extracts. So I ground up my samples in perchloric acid, changed the 31P for a 1H NMR probe, wrote some Matlab code for processing the spectra (my PhD was in chemical physics, specifically high resolution gas phase spectroscopy, which inadvertently had prepared me for my metabolomics career), and a year later published the first metabolomics study in aquatic biology (http://pubs.acs.org/doi/abs/10.1021/es034281x, M. R. Viant, E. S. Rosenblum and R. S. Tjeerdema, NMR-Based Metabolomics: A Powerful Approach for Characterizing the Effects of Environmental Stressors on Organism Health, Env. Sci. Technol. 37, 4982-4989 (2003)).

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

MV: There are two, the science and the people I work with. The science: I am particularly excited about developing new methods that help us to measure metabolites more accurately, more confidently, more rapidly and with greater coverage of the metabolome, and ideally using automation. Using these approaches we’re then able to probe the molecular mechanisms which underline the interactions between an organism and its environment. My particular interest is how aquatic organisms respond to environment stressors. We’ve recently discovered a novel mechanism of toxicity of zinc oxide nanomaterials which is hugely exciting. The people: upon arriving at Birmingham in 2003 I built my first research group. You cannot beat working with a dozen plus young scientists, in various stages of their training, and watching them evolve into critically thinking, independent and ambitious scientists! Recently I’ve taken the reins of the international Metabolomics Society, which is also proving extremely exciting and rewarding, and in this case find myself surrounded by a fantastic team of Board members, but more about that later.

MN: What key metabolomics initiatives are you pursuing at your research centre or institute? What is happening in your country in terms of metabolomics?

MV: The last 12 months at the University of Birmingham has undoubtedly been the most active and exciting to date. As part of our programme in environmental ‘omics research we have recruited Professor John Colbourne from the US (Professor of Environmental Genomics), greatly expanded our research into the water flea (Daphnia, a NIH model organism), and launched a new Joint Environment and Health Centre with the BGI in China. Our research programme in clinical metabolomics has also expanded greatly, funded by the University under an initiative called Systems Science for Health. This has allowed us to recruit Dr Warwick Dunn to the team, paving a way to exciting research projects in translational biomedical metabolomics. In the last few weeks we have also formed a Technology Alliance Partnership with Thermo Fisher Scientific, to accelerate research in high-resolution accurate mass and triple quadrupole LC-MS based metabolomics and proteomics (University of Birmingham press release). With a focus on both novel hardware and software solutions for LC-MS research, we are now posed for major advances in both our clinical and environmental research programmes.

As for national activities, the Research Councils in the UK have and continue to be highly supportive of metabolomics research. For further details, see the recent article “Metabolomics across the globe” (http://link.springer.com/article/10.1007/s11306-012-0491-8). The research facilities and associated activities in the UK include the Biotechnology and Biological Sciences Research Council (BBSRC) funded National Centre for Plant and Microbial Metabolomics located at Rothamsted Research; the Natural Environment Research Council (NERC) funded Biomolecular Analysis Facility (NBAF) - Metabolomics Node at the University of Birmingham; the UK Medical Research Council (MRC) funded lipidomics facility at the MRC Human Nutrition Research, Cambridge; the Scottish Metabolomics Facility (Scotmet) at Glasgow and Strathclyde Universities; and the MRC-NIHR National Phenome Centre at Hammersmith Hospital, London, and the closely allied Imperial Clinical Phenome Centre at St Mary’s Hospital, London.


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

MV: My group’s vision, working at part of the Environmental Systems Biology theme at the University of Birmingham, is to translate our basic ‘omics research into applied chemical and ecological risk assessment. Over the next decade we aim to transform the tools used to measure the health of our environment. We believe through more information rich measurements we can reduce uncertainty in risk assessment, which we hope will ease the regulatory burden on industry while maintaining a healthy environment. The challenge goes far beyond simply advancing our knowledge of the fundamental molecular mechanisms underpinning environmental stress, and necessarily will involve regulators and policy makers. As such we’ve established collaborations with the UK Environment Agency and relevant Government department (Department for Environment, Food and Rural Affairs), and are now building links to our Law School at the University.

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

MV: It’s ability to discover the unexpected! As Donald Rumsfeld said “There are known knowns; there are things we know we know. We also know there are known unknowns; that is to say, we know there are some things we do not know. But there are also unknown unknowns—the ones we don’t know we don’t know”. Metabolomics is the perfect tool for discovering the unknown unknowns, and moving them to known unknowns and beyond. You cannot of course expect to reveal a full mechanistic understanding of a system from an ‘omics investigation. From the initial ‘omics discovery we transition into classical hypothesis driven research and, given the correct experimental design, can improve our understanding of the system; i.e., moving it from a known unknown towards a known known!

MN: What do you see as the greatest barriers for metabolomics? What improvements, technological or otherwise, need to take place for metabolomics to really take off?

MV: Two primary challenges lie ahead. First, and of no surprise to any of the readers, robust metabolite identification is in my view the single greatest technological challenge that we face. This has plagued our field for a decade. Fortunately the on-going advances in mass spectrometry, data analysis workflows and, critically, the continuing expansion of metabolic databases are all chipping away at this problem. Along with each technological and informatic improvement we are able to peer one level deeper into the metabolomes of the plants, animals and microbes that we study. Maybe in the near future we will be able to say that a considerable fraction of organism X’s metabolome is characterised; now there is a challenge! A detailed knowledge of organism X’s metabolome brings us to the door of the next challenge: so what functional significance do these metabolites (or metabolic pathways) have in organism X? Identification alone will certainly make our experimental investigations more robust, will allow us to compare data from across labs, will facilitate meta-analysis, but it won’t suddenly reveal the phenotypic importance of these metabolites; it's the functional significance within an ecological context that is of great interest to my lab. In fact to truly address the challenges in environmental toxicology and risk assessment we will need to integrate the measurement of ‘omic responses with that of whole organism physiological and behavioural responses, all within a framework of ultra-high throughput biology.

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

MV: I am very positive about the funding climate, as long as you propose the right scientific questions in your grant applications! If our metabolomics community continues to deliver very high impact research findings, highlighting the phenomenal capability of metabolomics to discover the unknown unknowns and then through further studies to translate this knowledge to the benefits of society, we are in a strong position to lobby the funding agencies to keep the money flowing. For example within environmental ‘omics research in the UK the NERC has recently announced a $6M programme “Mathematics & Informatics for Environmental Omic Data Synthesis” (http://www.nerc.ac.uk/research/programmes/omics/). In terms of human health, the NIH Common Fund’s Metabolomics program (http://commonfund.nih.gov/metabolomics/) is a timely and much needed funding scheme.

 MN: What role can metabolomics standards play?

MV: They are absolutely vital. Fortunately there are some new exciting international initiatives that will at last address this important need of the community. Leading the way in Europe is the EBI’s MetaboLights database for metabolomics experiments, which “is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments.” (http://www.ebi.ac.uk/metabolights/). In addition the COSMOS project (Coordination of Standards in Metabolomics, http://www.cosmos-fp7.eu/) will bring together European data providers to set and promote community standards to enable dissemination of metabolomics data through the life sciences. The NIH Common Fund’s Metabolomics program will also fund activities in data standards and databases. For further information and training on this topic, please consider attending the 9th Annual Conference of the Metabolomics Society, 1-4 July 2013, Glasgow, UK (http://www.metabolomics2013.org/), in which there will be a workshop on “Data dissemination, standardization and exchange”, with contributors from both the EBI and NIH.

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

MV: As the President of the international Metabolomics Society I cannot possibly end the interview without making a pitch for the Society! (http://www.metabolomicssociety.org/) As I said above I am surrounded by a team of fantastic, dedicated Board members who are as committed as I am to building our community and advancing the science of metabolomics and metabonomics. The single most important point to make here is that the Metabolomics Society exists to serve our community. So I will end the interview by asking a question of your readers: in what ways do you wish your research community to grow and how can the Metabolomics Society assist in that? Please drop me any thoughts at President@MetabolomicsSociety.org.
Biomarker Beacon

3) Biomarker Beacon

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


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

In the following two recent studies, metabolomic approaches were used to develop tools for the identification of biomarkers associated with asthma and breast cancer, respectively.
  1. Jung J, Kim SH, Lee HS, Choi GS, Jung YS, Ryu DH, Park HS, Hwang GS. Serum metabolomics reveals pathways and biomarkers associated with asthma pathogenesis. Clin Exp Allergy. 2013 Apr;43(4):425-33. doi: 10.1111/cea.12089. [PMID: 23517038]

    In this paper, the research team sought to identify novel biomarkers associated with asthma pathogenesis. The investigators used proton nuclear magnetic resonance-based metabolomics coupled with multivariate statistics to evaluate serum samples from patients with asthma (n=39) and healthy controls (n=26). In patients with asthma, the authors of this study discovered increased levels of glutamine, methionine, and histidine and decreased levels of methanol, acetate, formate, choline, arginine, glucose, and O-phosphocholine. These metabolites are involved in immune response, hypermethylation, and response to hypoxia. The identified metabolites may be useful for the diagnosis of asthma and for monitoring its pathogenesis.

  1. Qiu Y, Zhou B, Su M, Baxter S, Zheng X, Zhao X, Yen Y, Jia W. Mass spectrometry-based quantitative metabolomics revealed a distinct lipid profile in breast cancer patients. Int J Mol Sci. 2013 Apr 12;14(4):8047-61. doi: 10.3390/ijms14048047. [PMID: 23584023]

    While mammography serves as a powerful screening tool for breast cancer, about 20% of breast cancer cases are missed using this approach. A reliable and accurate diagnostic for breast cancer could help detect an increased number of cases in women. In this study, the researchers used a mass spectrometry quantitative metabolomics approach to look at plasma samples from 55 breast cancer patients and 25 healthy controls. The investigators developed an accurate orthogonal partial least squares-discriminant analysis (OPLS-DA) model that consisted of 39 metabolites and discovered three metabolites in particular (lysoPC a C16:0, PC ae C42:5 and PC aa C34:2) that are especially important for differentiating between breast cancer patients and healthy controls. Both sensitivity and specificity of this diagnostic were very high at 98.1% and 96.0%, respectively.
Metabolomics Current Contents

4) Metabolomics Current Contents

Recently published papers in metabolomics:
MetaboNews

5) MetaboNews
23 Apr 2013
Metabolon Expands Biochemical Profiling Capabilities with the New TrueVision™ Metabolomics Offering and Online Client Tools

Metabolon, the pioneering leader in metabolomics-driven biomarker discovery and analysis, today announced expanded capabilities in its extensive biochemical profiling technology. The new TrueVision™ offering combines Metabolon’s powerful biochemical profiling discovery platform with complex lipid profiling. With this expansion, Metabolon can survey biological samples for over 4000 known metabolites contained in its chemical library and provide a more complete picture of lipid metabolism. The acquisition of Lipomics Technologies in 2012, now operating as a division of Metabolon with core competency in lipidomics, has enabled this unprecedented new capability.

“The new TrueVision™ offering is the result of our commitment to meet our clients’ needs to find answers to their critical biological questions, advance their research, and is evidence of our dedication to continuous innovation in the field of metabolomics.”

Michael Milburn, Chief Scientific Officer at Metabolon, commented “The new TrueVision™ offering is the result of our commitment to meet our clients’ needs to find answers to their critical biological questions, advance their research, and is evidence of our dedication to continuous innovation in the field of metabolomics.”

Metabolon’s TrueVision™ platform has extensive application across the life sciences for biomarker discovery and elucidation of the effects of drugs or nutrients on metabolism. In addition, TrueVision™ provides insight into disease biology, in particular metabolic diseases, which are a family of disorders driven in large part by the subtle, long-term dysregulation of lipid metabolism. Metabolism in general and especially lipid metabolism are thought to play an important role in the development of cancer, inflammatory and central nervous system disorders which makes this comprehensive offering ideally suited for research in these therapeutic areas.

The company is also unveiling the newest version of Client Tools, a secure web portal for data delivery, interpretation and visualization of its lipidomics profiles. Client Tools includes Lipomics Surveyor® pathway maps for each analytical panel, allowing customers to view differences in lipid metabolism between treatment groups, organized by metabolic pathways. “This new software tool expands the ability of clients to visualize, present and interpret their focused lipid panel study data”, states Steve Watkins, Chief Technology Officer, Metabolon.
Source: Business Wire
 
10 Apr 2013
An efficient post-hoc integration method improving peak alignment of metabolomics data from GCxGC/TOF-MS

Since peak alignment in metabolomics has a huge effect on the subsequent statistical analysis, it is considered a key preprocessing step and many peak alignment methods have been developed. However, existing peak alignment methods do not produce satisfactory results.

Indeed, the lack of accuracy results from the fact that peak alignment is done separately from another preprocessing step such as identification. Therefore, a post-hoc approach, which integrates both identification and alignment results, is in urgent need for the purpose of increasing the accuracy of peak alignment.

Results: The proposed post-hoc method was validated with three datasets such as a mixture of compound standards, metabolite extract from mouse liver, and metabolite extract from wheat.

Compared to the existing methods, the proposed approach improved peak alignment in terms of various performance measures. Also, post-hoc approach was verified to improve peak alignment by manual inspection.

Conclusions: The proposed approach, which combines the information of metabolite identification and alignment, clearly improves the accuracy of peak alignment in terms of several performance measures.

R package and examples using a dataset: http://mrr.sourceforge.net/download.html

Paper: Jeong J, Zhang X, Shi X, Kim S, Shen C. BMC Bioinformatics. 2013 Apr 10;14(1):123. doi: 10.1186/1471-2105-14-123. An efficient post-hoc integration method improving peak alignment of metabolomics data from GCxGC/TOF-MS. [PMID: 23575005]


 
28 Mar 2013
Thermo Fisher Scientific Forms Technology Alliance Partnership With the University of Birmingham, UK

Collaboration aimed at advancing LC-MS techniques in life science research

Thermo Fisher Scientific Inc., the world leader in serving science, has entered into a Technology Alliance Partner agreement with scientists at the University of Birmingham, UK, establishing a collaboration to accelerate research in high-resolution accurate mass (HRAM) and triple quadrupole liquid chromatography-mass spectrometry (LC-MS) for life science applications.

The alliance will focus on two research areas:
  • Metabolomics, where the Thermo Fisher Scientific team will work with the laboratories of Professor Mark Viant and Dr. Warwick Dunn, to develop and test new hardware and software approaches for metabolite detection and identification for environmental and clinical research.
  • Proteomics, working with Dr Helen Cooper’s lab to exploit high resolution mass spectrometry and gas-phase ion chemistry for top-down and bottom-up analysis of proteins.
The Technology Alliance Partnership establishes a broad collaboration between Thermo Fisher Scientific and the University of Birmingham. It includes: engaging in research, sharing samples and data that could lead to development of better techniques, exchanging ideas for improving instrument and software performance, ongoing conversations about current technology issues, promoting the training of graduate students, and publishing new methodology and scientific advances.

Thermo Fisher’s Technology Alliance Partnership program is an ongoing initiative to drive innovation through the sharing of ideas and expertise between a number of academic research laboratories and the company.

“The University of Birmingham scientists share our drive to make the world healthier, cleaner and safer,” said Iain Mylchreest, vice president, research and development, Thermo Fisher. “We look forward to a very productive collaboration with this innovative, creative group for advancing metabolomic and proteomic research.”

“We are excited to become Thermo Fisher Scientific’s first Technology Alliance Partner within Europe,” said Professor Adam Tickell, the University’s pro vice chancellor for research and knowledge transfer. “We anticipate that innovations from this research will translate directly into improved healthcare and environmental diagnostics. We are particularly excited by Thermo Fisher’s commitment to supporting graduate research.”

The partnership builds upon the University of Birmingham’s Systems Science for Health initiative, which focuses on introducing a variety of life science technologies into clinical research. It follows almost a decade of collaboration between the two organizations.

Source: Thermo Fisher Scientific

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

Metabolomics Events

6) Metabolomics Events
13-14 May 2013

First Belgian-Netherlands Joint symposium on Metabolomics: Translational approaches in metabolomics - Spa, Belgium
Venue: Sol Cress in Spa, Belgium

Metabol(n)omics is a newborn cousin to genomics and proteomics. Specifically, metabolomics involves the rapid, high throughput characterization of the small molecule metabolites found in an organism. Since the metabolome is closely tied to the genotype of an organism, its physiology and its environment, metabolomics offers a unique opportunity to look at genotype-phenotype relationships. Metabol(n)omics is increasingly being used in a variety of health, pharmaceutical and food applications including, among others, pharmacology, pre-clinical drug trials, toxicology, transplant monitoring, newborn screening, clinical chemistry, taxonomy, food and medicinal plants quality control.

“Small molecules involved in biochemical processes provide a great deal of information on the status and functioning of a living system under study both from effects causes by changes in gene expression, and also by differences in life style and diet in humans and other mammals. The process of monitoring –and evaluating such changes is termed ‘metabonomics’. A parallel approach has also been under way, mostly in model organisms and in plant systems, and that has led to the term ‘metabolomics’”[1].

Metabol(n)omics utilizes NMR and MS spectroscopy together with multivariate analysis approaches to characterise perturbations in metabolic pathways occurring during biological processes. This new predictive tool holds great promises for applications in a variety of scientific fields ranging from basic biology through to food sciences.

This two day symposium aims to initiate the discovery of the metabolomics approach for the uninitiated but also to present high level and interest conferences for those involved in basic and industrial researches and interested in understanding altered biochemical processes in various living system. The symposium will mainly focus on Translational approaches in metabolomics.

Two educational sessions are scheduled  for the PhD students.

All the sessions are organized in the Sol Cress in Spa on May 13 & 14, 2013.

The symposium is organized under the aegis of the CIRM, the Belgian FNRS and the “école doctorale thématique en sciences pharmaceutiques” in collaboration with the Netherlands Metabolomics Center (NMC).

For more information, visit http://www.metabolomicscentre.nl/news/first-belgian-netherlands-joint-symposium-metabolomics-translational-approaches-metabolomics-sp?goback=%2Egde_2414599_member_224905745.
22-24 May 2013

International Conference on FoodOmics, a Science for Nutrition, Health and Wellness in the post-genomic era
Venue: Cesena, Italy

Foodomics: a new comprehensive approach to food and nutrition
 
Francesco Capozzi and Alessandra Bordoni
 
In the past 20 years, the scientific community has faced a great development in different fields due to the development of high-throughput, omics technologies. Starting from the four major types of omics measurements (genomics, transcriptomics, proteomics, and metabolomics), a variety of omics subdisciplines (epigenomics, lipidomics, interactomics, metallomics, diseasomics, etc.) has emerged.

Thanks to the omics approach, researchers are now facing the possibility of connecting food components, foods, the diet, the individual, the health, and the diseases, but this broad vision needs not only the application of advanced technologies, but mainly the ability of looking at the problem with a different approach, a “foodomics approach”.

Foodomics is the comprehensive, high-throughput approach for the exploitation of food science in the light of an improvement of human nutrition. Foodomics is a new approach to food and nutrition that studies the food domain as a whole with the nutrition domain to reach the main objective, the optimization of human health and well-being […].

For more information, visit http://www.foodomics.eu/.
28-29 May 2013

NSF hands-on workshop and symposium “Metabolic pathways in microorganisms for biofuels”
Venue: UC Davis Genome Center auditorium, room 1005, Davis, California, USA

Symposium  (Flyer)

May 29, 2013, 10.00am- 4.00pm
UC Davis Genome Center auditorium, room 1005
451 Health Sciences Drive, Davis, CA 95616

A poster session is planned for the breaks. Poster size: 35’’x 57’’


Hands-on workshop in metabolomics
for up to 20 graduate students and postdocs

May 28, 2013, 9am- 6pm
UC Davis Genome Center, room 1314

Mass spectrometry, compound identification, data processing.

Please register with: Jeannette Martins, jmartins@ucdavis.edu

Please register posters with: Jeannette Martins, jmartins@ucdavis.edu

Speakers:
  • Oliver Fiehn, UC Davis
  • James Liao, UCLA
  • John Morgan, Purdue University, IN 
  • Yasuo Yoshikuni, Bio Architecture Lab, CA 
  • Shota Atsumi, UC Davis
  • Roger Ruan, University of Minnesota 
  • Jason Papin, University of Virginia 
  • Jean VanderGheynst, UC Davis
For more information, visit http://www.genomecenter.ucdavis.edu/events/nsf-hands-on-workshop-and-symposium-metabolic-pathways-in-microorganisms-for-biofuels.
1-7 June 2013

GRC on Computational NMR and Associated Seminar on Metabolomic NMR
Venue: Mount Snow Resort, West Dover, Vermont, USA

The organizers of the Gordon Research Conference on Computational Aspects of Biomolecular NMR are pleased to announce that the GRC and a related Gordon Research Seminar (GRS) on Metabolomic NMR for graduate students and postdocs will be held at the Mount Snow Resort in Vermont from June 1-7, 2013.

The meeting is the eighth GRC on Computational NMR and the first to include a dedicated Seminar for graduate students and postdocs. The focus of the GRS is to discuss new contributions in computational Nuclear Magnetic Resonance to the growing field of metabolomics and will feature a keynote talk by David Wishart, University of Alberta, and discussions led by experts in metabolomic NMR as a complement to oral presentations by graduate students and postdocs.

For more information: http://www.grc.org/programs.aspx?year=2013&program=grs_bionmr

For registration: http://www.grc.org/application.aspx?id=15572

We do hope that you will both consider attending and provide this information to your students and postdocs and encourage them join us in Vermont for what we anticipate will be an enjoyable and stimulating meeting.
1-4 Jul 2013

9th Annual International Meeting of the Metabolomics Society
Venue: Glasgow, Scotland

We are delighted to announce that the 9th Annual International Conference of the Metabolomics Society will be held in Glasgow, Scotland 1st – 4th July 2013 at the award-winning Scottish Exhibition & Conference Centre (SECC). This appealing combination of an excellent city location and the best scientific research will guarantee this a memorable conference.

We expect this to be the 'must attend' meeting in 2013 for researchers from around the world, where the best speakers in the world and rising stars of the future will present their work in a mixture of plenary and parallel sessions. The Metabolomics Society came into being with the development of the Metabolomics as a discipline and as a result provides a focus for the most varied aspects of the subject ranging from microbes to man. As a result of this it brings together a diverse mixture of scientists from many disciplines, which produces very stimulating meetings.

One of the main aims of the conference will be to create a unique platform for young scientists. Come and listen and talk to the top experts in the field.  Find out about the latest exciting technologies that can advance your own research, but most of all come and enjoy Scotland's largest and most vibrant city and the beautiful countryside around it.

We look forward to welcoming you to Glasgow in 2013!

Dave Watson
Chair, Local Organising Committee
Metabolomics Glasgow 2013

For more information, visit http://www.metabolomics2013.org/.
2-4 Jul 2013

3rd European Lipidomic Meeting
Venue: Pardubice, Czech Republic

We would like to cordially invite you to participate in the 3rd European Lipidomic Meeting, which will be held in Pardubice, Czech Republic, July 2-4, 2013. The meeting is organized by the Czech Society for Biochemistry and Molecular Biology and the University of Pardubice in cooperation with organizers of previous successful Graz Lipid Mass Spec Meetings in 2010 and 2012. Based on the mutual agreement, we have decided to continue in this series and invite colleagues interested in the lipid research from all over the world. The conference title is changed to the European Lipidomic Meeting, but the original numbering is kept to demonstrate the continuity of Graz meetings. The word "European" shows the intention to rotate the organization among different European locations. We have removed "Mass Spec" from the title to emphasize that scientists from all branches of chemistry, biology and medicine are welcome with a single connecting idea - interest in lipids and lipidomics. The analytical chemistry and mass spectrometry in particular will certainly play a significant role again, but intensive interactions and complementary expertise of analytical chemists, biologists, medical doctors, nutrition specialists and experts from other fields could result in better knowledge of biological roles and metabolism of lipids. The conference program will consist of invited plenary lectures, oral and poster contributions. We can proudly announce the list of prominent plenary speakers confirmed so far:
  • Edward A. Dennis (University of California, San Diego, La Jolla, CA, USA)
  • Stephen J. Blanksby (University of Wollongong, Australia)
  • Andrej Shevchenko (Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany)
  • Xianlin Han (Sanford-Burnham Medical Research Institute, Orlando, FL, USA)
  • Kim Ekroos (Zora Biosciences, Espoo, Finland)
  • Bernhard Spengler (University of Giessen, Germany)
  • Harald C. Köfeler (Medical University of Graz, Austria)
The scientific part of the meeting will be complemented by rich social program emphasizing the local history. Participants will have a chance to visit Pardubice chateaux with exhibitions of Czech glass and taste beer from old Bohemian brewery. The conference venue is easily accessible from Prague, which has regular flight connections with many European and overseas destinations. Trains between Prague and Pardubice run frequently and fast (only 60 minutes). Pardubice city is famous due to the local production of gingerbread, high concentration of chemical industry and important sport events (horse race Velká Pardubická steeplechase, Golden Helmet of Pardubice speedway competition, ice-hockey, etc.).

For more information, visit http://mab.uochb.cas.cz/iochb/ELM2013/.
8-9 Jul 2013

Informatics and Statistics for Metabolomics (2013)
Venue: Downtown Toronto, Ontario, Canada

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

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

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

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

For more information, visit http://bioinformatics.ca/workshops/2013/informatics-and-statistics-metabolomics-2013.
6 Aug 2013

Frontiers in Nutritional Science: The Inaugural Australian Symposium on Nutritional Metabolomics
Venue: Rydges World Square - Sydney, Australia

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

About the event

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

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

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

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

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

Topics to be covered include:
  • How can metabolomics be used in nutritional science?
  • What tools and technologies are available for metabolomics in nutritional science?
  • Applications of metabolomics in nutritional science
  • Using breath as a measure of health and nutritional status.
This symposium is organised by CSIRO Animal, Food and Health Sciences, in conjunction with UniSA’s Sansom Research Institute. Speakers will be by invitation only.

Registrations for the event will open soon.

Find out more about CSIRO's work in Animal, Food and Health Sciences and Preventative Health.

Program Download: The Nutritional Metabolomics Symposium program (PDF)

For more information, visit http://www.csiro.au/en/Organisation-Structure/Divisions/Animal-Food-and-Health-Sciences/Nutritional-Metabolomics-Symposium.aspx?goback=%2Egde_4185659_member_229009122.
13-17 Aug 2013

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

Abstract Deadline: May 31, 2013

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Application deadline 15th of August 2013

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

Contact and inquiries:
Erik Selander erik.selander@bioenv.gu.se
Göran Nylund goran.nylund@bioenv.gu.se
 
Course Flyer: http://www.metabonews.ca/May2013/events/Metabolomics%20course%20flyer.pdf
Summer 2015

11th Annual Metabolomics Society Conference
Venue: North America (specific location to be determined)

The 11th Annual Conference will be held in summer 2015, in North America. Are you interested in hosting this event? If so, please email conference@metabolomicssociety.org for further information, or visit the Metabolomics Society website at http://www.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

7) Metabolomics Jobs

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

Jobs Offered

Job Title Employer Location Posted Closes Source
Postdoctoral position in malaria mass spectrometry-based metabolomics Pennsylvania State University State College, Pennsylvania, USA
 2-May-2013
Penn State University
Postdoc Position Palacky University Olomouc, Czech Republic 30-Apr-2013 15-Jun-2013 naturejobs.com
Permanent Metabolomist Position DEINOVE Montpellier, France
 29-Apr-2013
DEINOVE
LC-MS Metabolomics Specialist Metabolomic Discoveries GmbH Potsdam, Germany 26-Apr-2013 21-Jun-2013 Metabolomic Discoveries
PhD Studentship in Department of Twin Research & Genetic Epidemiology King's College London London, United Kingdom 20-Apr-2013 17-Jun-2013 naturejobs.com
Full-Time Research Coordinator University of Alberta Edmonton, Canada
 17-Apr-2013
University of Alberta
Sr Scientist - Metabolomics Technical Marketing-AB 001492 AB SCIEX Foster City, California, USA
 4-Apr-2013
AB SCIEX
Scientist / Specialist Mitochondrial Function The Nestlé Institute of Health Sciences Lausanne, Switzerland 25-Mar-2013 24-May-2013 naturejobs.com
Omics Data Analyst The Nestlé Institute of Health Sciences Lausanne, Switzerland 7-Mar-2013 7-May-2013 naturejobs.com
Metabolomics / Lipidomics Analyst The Nestlé Institute of Health Sciences Lausanne, Switzerland 7-Mar-2013 7-May-2013 naturejobs.com
Sales Representative / Business Developer (m/f) Metabolomic Discoveries GmbH Potsdam, Germany 27-Feb-2013
metabolomicdiscoveries.com
Internship/Thesis: Development of suitable plugins for the knowledge base Metabolomic Discoveries GmbH Potsdam, Germany 27-Feb-2013
metabolomicdiscoveries.com


Jobs Wanted

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

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