MetaboNews Masthead

MetaboNews
Issue 24 - August 2013

CONTENTS:


Online version of this newsletter:
http://www.metabonews.ca/Aug2013/MetaboNews_Aug2013.htm

Welcome to the twenty-fourth issue of MetaboNews, a monthly newsletter for the worldwide metabolomics community. In this issue, we feature a Research Spotlight article on a GC×GC-TOFMS strategy for combined quantitative and untargeted profiling of polar metabolites. 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 Kazuki Saito of the RIKEN Center for Sustainable Resource Science in Japan. 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) Research Spotlight

 VTT Logo

GC×GC-TOFMS strategy for combined quantitative and untargeted profiling of polar metabolites

Feature article contributed by Tuulia Hyötyläinen and Matej Orešič, VTT Technical Research Centre of Finland, Espoo, FIN-02044 VTT, Finland

Metabolomics aims for comprehensive characterization of metabolites and their pathways in biological systems. Ideally, any analytical strategy for metabolomics would thus allow for broad as well as sensitive coverage of a metabolome across several chemical and functional classes of metabolites. While such approaches are already possible today, they usually come at a cost. The so-called untargeted metabolic profiling methods are usually qualitative or semi-quantitative, thus not enabling determination of absolute concentrations of the metabolites measured. This presents at least two challenges: (1) it is difficult to compare the results across different experiments and platforms, and (2) knowledge of absolute concentrations may be important for the interpretation of the data. On the other hand, targeted approaches which cover only a pre-selected set of metabolites are usually more limited in metabolite coverage and do not allow for the discovery of novel, important metabolites in the specific experimental setting.

Over the past years we have been establishing a metabolomics platform which combines the targeted as well as the untargeted approach, based on two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC-TOFMS) [1]. Compared to traditional GC-MS approaches, the sensitivity of GC×GC-TOFMS is typically 10-40 times higher and the separation efficiency is up to 20-fold better. Moreover, the quality of mass spectra obtained with GC×GC-TOFMS is much better than those obtained with GC-MS, and thus, identification is more reliable. Method development of GC-MS methods (including GC×GC-TOFMS) is straightforward and much easier than e.g., LC-MS. Also, quantitation is more reliable, because matrix effects in GC-MS are generally not a critical issue. An additional advantage of all GC-based methods is the repeatable characteristics of retention, particularly when nonpolar stationary phases are used. This makes it possible to use universal retention indices, which are highly useful in the identification of unknown compounds, in combination with mass spectral detection. Large spectral libraries for GC(×GC)-MS, combined with retention index data is a valuable tool in the identification of unknown compounds. Even if a particular MS spectrum is not present in the spectral database, the fragmentation pattern can be used to obtain information about the compound class of a metabolite [1].

Over 1000 metabolites can be detected by GC×GC-TOFMS in a single sample run, covering a functionally wide range of small molecules such as amino acids, fatty acids, sterols, carboxylic acids, sugars, alcohols, and amines. Of interest to biomedical researchers and microbiologists, the platform can also detect many metabolites produced by gut microbiota [2]. Despite being first introduced to the metabolomics community already several years ago [3], the GC×GC-TOFMS-based metabolic profiling approach has not yet been widely adopted in metabolomics. There have been three major challenges concerning the application of the platform: (1) derivatization of polar metabolites is required, (2) the qualitative nature of the data when a global screening approach is adopted, and (3) difficulties with processing large amounts of data, given their multi-dimensional nature.

In our research, we have aimed to overcome the limitations of GC×GC-TOFMS (Figure 1). As usual in GC-MS-based metabolomics methods, derivatization of metabolites is performed in a sequential, automated manner using an autosampler. In order to enable semi-quantitative and quantitative analysis in parallel, internal standards for selected metabolites to be quantified are added prior to extraction. The selected metabolites, typically about 30 in number, are then quantified using the external calibration curves and by manual checks of peak integration. This step is time consuming and is performed by an expert analytical chemist. Additional internal standards are utilized also for the global profiling of all other metabolites, where the data undergoes automated data processing. Data for these metabolites is normalized using the internal standards, thus enabling semi-quantitative analysis [1]. In order to facilitate global metabolic profiling by GC×GC-TOFMS, we also developed an open source software package Guineu for automated processing of GC×GC-TOFMS data [1]. Guineu takes the processed data (peak list) from vendor software for each sample, then performs additional steps such as alignment of the data, normalization, data filtering, utilization of retention indices in the verification of identification as well as automated group-type identification of the compounds.

Typical GC×GC-TOFMS metabolic profiling workflow

Figure 1. Typical GC×GC-TOFMS metabolic profiling workflow.

Although the platform is repeatable over extended periods of time [1], metabolic profiling by GC×GC-TOFMS is unlikely to be applied in studies requiring analyses of large numbers of samples such as in epidemiological studies. The throughput is still rather low for such studies, requiring typically about 45 minutes for a single sample analysis. Given its extensive coverage of the metabolome, metabolic profiling by GC×GC-TOFMS is particularly suited for tackling problems where the metabolome is still poorly characterized (e.g., in the brain, or at the host-microbial interface) or where the discovery of novel biomarkers is sought. For example, we found GC×GC-TOFMS to be a powerful analytical strategy in our studies of diseases of the central nervous system. In an Alzheimer’s disease (AD) study, an untargeted approach by GC×GC-TOFMS allowed us to identify a plasma metabolite 2,4-dihydroxybutyric acid which is associated with later progression to AD [4]. In a follow-up study, we also found that this metabolite is a strong predictor of AD when measured in cerebrospinal fluid (CSF) (unpublished data), thus suggesting the detected changes in plasma reflect the changes in brain metabolism in early AD. Recently, GC×GC-TOFMS was also applied to characterize patient-matched plasma and CSF samples [5], thus providing a valuable resource on the composition of the CSF metabolome and how it compares to the plasma metabolome.

In conclusion, metabolic profiling by GC×GC-TOFMS is a powerful approach for comprehensive characterization of small polar metabolites, allowing for both quantitative and semi-quantitative analysis in parallel. Its unique strengths make GC×GC-TOFMS a complementary platform to other more established analytical strategies for metabolomics such as LC-MS(/MS) and NMR.

References
[1] S. Castillo, I. Mattila, J. Miettinen, M. Orešič, T. Hyötyläinen, Data analysis tool for comprehensive two-dimensional gas chromatography-time of flight mass spectrometry, Anal. Chem. 83, 3058–3067 (2011). [PMID: 21434611]
[2] A.-M. Aura, I. Mattila, T. Hyötyläinen, P. Gopalacharyulu, C. Bounsaythip, M. Orešič, K.-M. Oksman-Caldentey, Drug metabolome of the Simvastatin formed by human intestinal microbiota in vitro, Mol. BioSyst. 7, 437-446 (2011). [PMID: 21060933]
[3] W. Welthagen, R.A. Shellie, J. Spranger, M. Ristow, R. Zimmermann, O. Fiehn, Comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC-GC-TOF) for high resolution metabolomics: biomarker discovery on spleen tissue extracts of obese NZO compared to lean C57BL/6 mice, Metabolomics 1, 65-73 (2005).
[4] M. Orešič, T. Hyötyläinen, S.-K. Herukka, M. Sysi-Aho, I. Mattila, T. Seppänan-Laakso, V. Julkunen, P. V. Gopalacharyulu, M. Hallikainen, J. Koikkalainen, M. Kivipelto, S. Helisalmi, J. Lötjönen, H. Soininen, Metabolome in progression to Alzheimer’s disease, Transl. Psychiatry 1, e57 (2011). [PMID: 22832349]
[5] M. Hartonen, I. Mattila, A.-L. Ruskeepää, M. Orešič, T. Hyötyläinen, Characterization of cerebrospinal fluid by comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry, J. Chromatogr. A 1293, 142-149 (2013). [PMID: 23642768]


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

 MetaboInterview Icon

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


Kazuki Saito

 Deputy Center Director and Metabolomics Group Director at RIKEN Center for Sustainable Resource Science (Japan), Professor at Graduate School of Pharmaceutical Sciences, Chiba University (Japan), and a Board Director of The International Metabolomics Society
 Kazuki Saito
Biography
Kazuki Saito obtained his Ph.D. from the University of Tokyo in 1982. After staying in Keio University in Japan and Ghent University in Belgium (Prof. Marc Van Montagu's laboratory) as a post-doc, he was appointed in 1995 as a full professor at Graduate School of Pharmaceutical Sciences, Chiba University, until now. He now holds the post of Deputy Director of RIKEN Center for Sustainable Resource Science, where he also serves as Group Director of the Metabolomics Research Group. He is one of the pioneers in the field of plant metabolomics and uses an integrated approach that includes functional genomics and transcriptomics. For his distinguished research, he was awarded The Prize for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology, Japan, in 2010, and The Award for Distinguished Research from the Japanese Society for Plant Cell and Molecular Biology in 2011. He was also selected as one of American Society of Plant Biologists (ASPB) TOP AUTHORS in 2010. His research interest is metabolome-based functional genomics, biochemistry, molecular biology, and biotechnology of primary and secondary metabolism in plants.

Related Web:
http://www.csrs.riken.jp/en/labs/mrg/index.html
http://www.p.chiba-u.ac.jp/lab/idenshi/index-e.html
http://www.researcherid.com/rid/D-2670-2009


Metabolomics Interview (MN, MetaboNews; KS, Kazuki Saito)

MN: How did you get involved in metabolomics?

KS: My research background is the elucidation of mechanism and identification of genes for the biosynthesis of plant metabolites, which include sulfur-containing metabolites, amino acids, flavonoids, polyphenols, alkaloids, terpenoids, and lipids—compounds which pretty much imply ‘metabolome’. Therefore, for me, metabolomics is not necessarily a brand new area but an extension of my research field of biosynthesis of plant (specialized) products. In 2000 there was a big chance to explore more on this exciting field; that was a call for grant applications from the Japan Science Technology Agency (JST), which was devoted to advanced plant science. Since this grant was a relatively big grant lasting 5 years, I decided to apply for this grant with my colleagues focused on plant functional genomics and metabolomics. The application was luckily accepted in 2000, when the genome sequence of Arabidopsis thaliana was completed as the first genome unveiled from higher plants. Thus, we were very lucky to start plant metabolomics research supported by the availability of genome sequence of A. thaliana and of the research resources of functional genomics of this model plant. Based on the success of this research project by JST, from 2005 I was further involved as the Group Director to establish the Metabolomics Group in the RIKEN Plant Science Center, now renamed the Center for Sustainable Resource Science since 2013.

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

KS: The first one is the identification of novel genes, metabolites, and networks by metabolomics with a model plant A. thaliana. The key technology is an integrated analysis of metabolomics and transcriptomics. The technology is further applied to crops and medicinal plants to identify the key genes in their specialized metabolism. (For a recent review, refer to http://www.sciencedirect.com/science/article/pii/S1369526613000496.) Through this study, I believe we could show the feasibility of metabolomics for plant functional genomics. The second exciting aspect is the development of metabolomics and related multi-omics technology such as databases and analytical tools, collectively accessible at our website ‘PRIMe’ (http://prime.psc.riken.jp/), which have been extensively used in the research community. Last but not least, we are applying metabolomics to biotechnology and breeding of major crops such as rice, tomato, and soybean—this is directly associated with an innovative social challenge for sustainability of our lives.

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

KS: Since April 2013, RIKEN established a new center, the Center for Sustainable Resource Science (CSRS, http://www.csrs.riken.jp/en/), that combines the activities of plant science, chemical biology, and catalysis chemistry. One of the major goals of this new center is to develop sustainable resources, thus replacing the use of fossil resources. Obviously the metabolomics study on crops, bioenergy plants, medicinal plants, and photosynthetic microorganisms is an area with a high priority for the strategic research conducted at our Center. In addition, the application to sophisticated synthetic biology and metabolic engineering is also expected as a direct outcome of the fundamental research based on metabolomics.

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

KS: In Japan, since a natural disaster of a big earthquake and the following Tsunami and nuclear power plant accident in 2011, we have been trying to restore our lives, industries, and economy to normal or even strive to attain a more advanced situation by reconsidering the sustainability of resources. Two of the major national challenges, ‘Life Innovation’ and ‘Green Innovation’, promote the innovative development of social infrastructure and industries regarding medicine, social security, energy, natural resource, food, and agriculture based on the initiative of cutting-edge scientific advancements. Metabolomic research is expected to be one of the key areas for these ‘Innovative’ priorities, and thus several major national funding programs are now available in Japan.

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

KS: I expect our findings on genes and metabolites can be used for breeding and biotech application of crops and medicinal/industrial plants. The databases and bioinformatic tools that we have developed can be widely used by the community.

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

KS: As often said, the metabolome represents the ultimate phenotype of cells by the perturbation of gene expression and the modulation of protein functions caused by the environment or mutations. Thus, for phenotyping of the cells, whether of human, microbial, or plant origin, metabolomics is particularly powerful. The other point is that once unknown metabolomic signals are identified, many may turn out to be identical to those found in other organisms—reducing the amount of ambiguity in the identification of unknown metabolites. This is a striking difference from the case in genes, where genes in various organisms may be 'highly similar' but never 'identical'. For example, two similar, but not identical, genes in humans and rice play the exact same functional role. However, once a new metabolite is characterized in humans, this metabolite will be identical in rice.

I would also like to emphasize that metabolomics is particularly important in the plant field; because plants collectively produce a huge variety of chemical compounds, far more than animals and even microorganisms. In addition, most of the human-beneficial properties of plants, as foods, medicinal resources, or industrial raw materials, are ascribed to plant metabolites.

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

KS: Chemical annotation of the unknown metabolomic signals is still a major bottleneck in metabolomics. However, these will be improved gradually by several international initiatives; for example, here are two in particular http://www.nsf.gov/news/news_summ.jsp?cntn_id=122045 and http://www.jst.go.jp/pr/announce/20111107/index_e.html. The second one is the establishment of a data depository of metabolomics expression. I would really like to see the metabolomic version of the Arabidopsis transcriptome, AtGenExpress. We have initially developed an ‘AtMetExpress’ (http://prime.psc.riken.jp/lcms/AtMetExpress/), which has, however, not yet been completed. This is also being developed by several international initiatives.

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

KS: For chemical annotation, more direct empirical structure elucidation as exemplified in this paper (http://www.nature.com/nature/journal/v495/n7442/full/nature11990.html) should be developed together with an improvement of computational methods. Metabolite imaging at single-cell resolution or of organelles could be further developed for more precise biological insights.

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

KS: It should be promising—we all have to put efforts to convince funding agencies and stakeholders to fund metabolomics. Metabolomics is the key technology for our social challenge of all biology-related fields such as medicine, pharmaceuticals, food, agriculture, and the environment in the future.

 MN: What role can metabolomics standards play?

KS: As I said, chemical annotation and data depositories are the major bottlenecks, and thus metabolomic standards play an important role in the further development of metabolomics.


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

KS: I would highly encourage younger colleagues to contribute wholeheartedly to metabolomics and develop their careers in this field. Since metabolomics is a newly-emerging, multi-disciplinary field, having less than 15 years of history and no authoritative scholars. Therefore, young individuals with strong ambitions could relatively easily become the leaders of the next generation in this field, which demonstrates the great promise and bright future of metabolomics.

 
Biomarker Beacon

3) Biomarker Beacon

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


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

In the following two recent studies, metabolomic approaches were used to develop tools for the identification of biomarkers associated with hepatocellular carcinoma and cystic fibrosis, respectively.
  1. Baniasadi H, Nagana Gowda GA, Gu H, Zeng A, Zhuang S, Skill N, Maluccio M, Raftery D. Targeted Metabolic Profiling of Hepatocellular Carcinoma and Hepatitis C using LC-MS/MS. Electrophoresis. 2013 Jul 16. doi: 10.1002/elps.201300029. [Epub ahead of print] [PMID: 23856972]

    Hepatitis C virus (HCV) infects the liver and causes global health problems. HCV infections can also put patients at risk for developing hepatocellular carcinoma (HCC). There is a need for a sensitive test that can detect HCC at an early stage, offering patients better treatment options. In this paper, the research team sought to identify metabolites associated with cirrhotic HCV patients with a high risk to develop HCC. Using liquid chromatography resolved tandem mass spectrometry (LC-MS/MS), the investigators quantitatively profiled 73 blood metabolites from 30 HCC patients and 22 cirrhotic HCV patients. They observed significant differences (p < 0.05) in 16 of the 73 targeted metabolites when comparing HCC and HCV. They selected 4 of the 16 metabolites (methionine, 5-hydroxymethyl-2'-deoxyuridine, N2,N2-dimethylguanosine and uric acid) to develop a classification model. This study describes a promising method for differentiating between HCV patients at high risk to develop HCC and those who have already advanced to HCC.


  2. Joseloff E, Sha W, Bell SC, Wetmore DR, Lawton KA, Milburn MV, Ryals JA, Guo L, Muhlebach MS. Serum metabolomics indicate altered cellular energy metabolism in children with cystic fibrosis. Pediatr Pulmonol. 2013 Jul 12. doi: 10.1002/ppul.22859. [Epub ahead of print] [PMID: 23847148]

    Cystic fibrosis (CF) affects not only the respiratory system but multiple organs and cells as well. In this study, the researchers sought to utilize a metabolomics-based approach to differentiate between children with CF and non-CF children with other lung diseases. They analyzed serum metabolites from 31 CF patients and 31 non-CF age and gender matched subjects using gas and liquid chromatography. The investigators detected 459 metabolites and discovered that a subset of 92 metabolites enabled them to discriminate between CF and non-CF individuals. Several pathways were strikingly different when comparing CF to non-CF, including low ketone bodies, low medium chain carnitines,     decreased 2-hydroxybutyrate from amino acid metabolism, and elevated di-carboxylic acids. In this study, the investigators successfully used serum metabolomics to distinguish between patients with CF and non-CF patients.
Metabolomics Current Contents

4) Metabolomics Current Contents

Recently published papers in metabolomics:
MetaboNews

5) MetaboNews
18 Jul 2013
Biochemical mapping helps explain who will respond to antidepressants

Duke Medicine researchers have identified biochemical changes in people taking antidepressants – but only in those whose depression improves. These changes occur in a neurotransmitter pathway that is connected to the pineal gland, the part of the endocrine system that controls the sleep cycle, suggesting an added link between sleep, depression and treatment outcomes.

The study, published on July 17, 2013, in the journal PLOS ONE, uses an emerging science called pharmacometabolomics to measure and map hundreds of chemicals in the blood in order to define the mechanisms underlying disease and to develop new treatment strategies based on a patient's metabolic profile.

"Metabolomics is teaching us about the differences in metabolic profiles of patients who respond to medication, and those who do not," said Rima Kaddurah-Daouk, PhD, associate professor of psychiatry and behavioral sciences at Duke Medicine and leader of the Pharmacometabolomics Research Network.

"This could help us to better target the right therapies for patients suffering from depression who can benefit from treatment with certain antidepressants, and identify, early on, patients who are resistant to treatment and should be placed on different therapies."

Major depressive disorder – a form of depression characterized by a severely depressed mood that persists two weeks or more – is one of the most prevalent mental disorders in the United States, affecting 6.7% of the adult population in a given year.

Selective serotonin reuptake inhibitors (SSRIs) are the most commonly prescribed antidepressants for major depressive disorder, but only some patients benefit from SSRI treatment. Others may respond to placebo, while some may not find relief from either. This variability in response creates dilemmas for treating physicians where the only choice they have is to test one drug at a time and wait for several weeks to determine if a patient is going to respond to the specific SSRI.

Recent studies by the Duke team have used metabolomics tools to map biochemical pathways implicated in depression and have begun to distinguish which patients respond to treatment with an SSRI or placebo based on their metabolic profiles. These studies have pointed to several metabolites on the tryptophan metabolic pathway as potential contributing factors to whether patients respond to antidepressants.

Tryptophan is metabolized in different ways. One pathway leads to serotonin and subsequently to melatonin and an array of melatonin-like chemicals called methoxyindoles produced in the pineal gland. In the current study, the researchers analyzed levels of metabolites within branches of the tryptophan pathway and correlated changes with treatment outcomes.

Seventy-five patients with major depressive disorder were randomized to take sertraline (Zoloft) or placebo in the double-blind trial. After one week and four weeks of taking the SSRI or placebo, the researchers measured improvement in symptoms of depression to determine response to treatment, and blood samples were taken and analyzed using a metabolomics platform build to measure neurotransmitters.

The researchers observed that 60 percent of patients taking the SSRI responded to the treatment, and 50 percent of those taking placebo also responded. Several metabolic changes in the tryptophan pathway leading to melatonin and methoxyindoles were seen in patients taking the SSRI who responded to the treatment; these changes were not found in those who did not respond to the antidepressant.

The results suggest that serotonin metabolism in the pineal gland may play a role in the underlying cause of depression and its treatment outcomes, based on the biochemical changes that were seen to be associated with improvements in depression.

"This study revealed that the pineal gland is involved in mechanisms of recovery from a depressed state," said Kaddurah-Daouk. "We have started to map serotonin which is believed to be implicated in depression, but now realize that it may not be serotonin itself that is important in depression recovery. It could be metabolites of serotonin that are produced in the pineal gland that are implicated in sleep cycles.

"Shifting utilization of tryptophan metabolism from kynurenine to production of melatonin and other methoxyindoles seems important for treatment response but some patients do not have this regulation mechanism. We can now start to think about ways to correct this."

The identification of a metabolic signature for patients who have a milder form of depression and who can improve with use of placebo is critically important for streamlining clinical trials with antidepressants. The Duke team is the first to start to define in depth early biochemical effects of treatment with SSRI and placebo, and a molecular basis for why antidepressants take several weeks to start showing benefit.

In future studies, researchers may collect blood samples from patients during both the day and night to define how the circadian cycle, changes in sleep patterns, neurotransmitters and hormonal systems are modified in those who respond and do not respond to SSRIs and placebo. This can lead to more effective treatment strategies.
Source: EurekAlert!
 
1 Jul 2013
Partnership For New Cross-Platform Metabolomics Data Analysis Solution Between AB SCIEX, Genedata & LECO

AB SCIEX, Genedata, and LECO announce a technology partnership that will deliver a collaborative software system, which will enable metabolomics researchers to comprehensively process and analyze experimental data across different GC/MS and LC/MS platforms.

LECO Corporation, a global leader in accurate mass technologies and GC/MS instrumentation, is offering combined solutions with both AB SCIEX, a global leader in LC/MS technology, and Genedata, a global leader in advanced software solutions for drug discovery and life science research. The companies are collaborating to provide a seamless solution to extract valuable biological information from high fidelity LC and GC data. The solution will give metabolomics researchers the ultimate tool for truly comprehensive metabolomics investigations. The partnership announcement was made at the 9th Annual Conference of the Metabolomics Society (July 1-4).

“The ability to bring data from different vendors and technologies onto a single platform, which can process and merge data for maximum biological inference, is where the industry needs to be to effectively evaluate the entire metabolome,” said Dr. Vladimir V. Tolstikov, Scientist, Tailored Therapeutics of Eli Lilly and Company. 

The close collaboration of the three companies has resulted in the latest version of Genedata Expressionist® MSX software, developed for metabolomics experiments performed with LECO and AB SCIEX MS systems. Genedata Expressionist MSX, which is compatible with other data formats and technologies as well, is a comprehensive, end-to-end solution for the analysis of mass spectrometry data generated in metabolomics experiments. The software can be downloaded directly via the Internet for immediate installation. 

Source: AZoM.com
 
10 Jun 2013
Thermo Fisher Scientific Transforms Triple Quadrupole LC-MS with New Levels of Sensitivity, Robustness and Usability
New Thermo Scientific TSQ Quantiva LC-MS breaks attogram sensitivity barrier; New TSQ Endura LC-MS delivers high sensitivity, extreme uptime

Thermo Fisher Scientific Inc., the world leader in serving science, today introduced a new-generation triple quadrupole liquid chromatography-mass spectrometry (LC-MS) platform designed to transform quantitation experiments with extreme sensitivity, productivity, precision and usability.

The platform, which includes the new Thermo Scientific Quantiva triple-stage quadrupole mass spectrometer and the new Thermo Scientific Endura triple-stage quadrupole mass spectrometer, made its debut at the ASMS Conference on Mass Spectrometry and Allied Topics, being held in Minneapolis from June 9-13 at the Minneapolis Convention Center in booth 154.

“Evolving applications continue to push the limits of instrument performance,” said Iain Mylchreest, vice president of research and development, chromatography and mass spectrometry, Thermo Fisher Scientific. “We have created a completely new instrument platform, built from the ground up, to deliver extreme sensitivity and uptime. Equally important is a great user experience, easy method creation and accessible data analysis and review. We believe this is the highest-performing, most-usable triple quad on the market today.”

The TSQ Quantiva triple quadrupole mass spectrometer employs Active Ion Management (AIM) to optimize ion creation and transmission from the source to the detector, resulting in extreme sensitivity. This enhanced level of sensitivity greatly improves results in applications such as peptide quantitation, metabolomics and biopharmaceutical QA/QC compared to previous Thermo Fisher triple quads. In company laboratories, AIM-enhanced systems have measured 70 attograms of verapamil in plasma on column with excellent precision, an unprecedented level of performance.

The TSQ Quantiva MS system is also extremely productive, with the ability to perform 500 SRM experiments per second, and positive/negative polarity switching in 20ms with no signal loss. Productivity is enhanced by a new Ion Beam Guide and Neutral Blocker that helps keep  components free of contamination and eases maintenance when it is required. The TSQ Quantiva MS has been shown using synthetic serum stress tests to operate approximately three times longer between maintenance intervals than the company’s previous best systems, without loss of signal.

The TSQ Endura triple quadrupole mass spectrometer shares much of the advanced technology of the TSQ Quantiva MS, but was designed to deliver higher uptime than any competitive triple quadrupole instrument. It was built for workhorse applications requiring trace level quantitation, such as food testing, environmental analysis and pharmaceutical QA/QC.

 

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

Metabolomics Events

6) Metabolomics Events
6 Aug 2013

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

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

About the event

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

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

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

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

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

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

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

Abstract Deadline: May 31, 2013

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Application deadline 15th of August 2013

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

Contact and inquiries:
Erik Selander erik.selander@bioenv.gu.se
Göran Nylund goran.nylund@bioenv.gu.se
 
Course Flyer: http://www.metabonews.ca/May2013/events/Metabolomics%20course%20flyer.pdf
7-11 Oct 2013

Hands-on LC-MS for Metabolic Profiling Course
Venue: Imperial International Phenome Training Centre, Imperial College, South Kensington Campus, Exhibition Road, London, UK

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

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

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

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

Day 5
Application lectures, tips, tricks and troubleshooting.

Download the full programme here: LCMS_Metabolic_Profiling

For more information, visit http://www1.imperial.ac.uk/iiptc/courseinfo/lcms/.
10-14 Mar 2014

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

Date: Monday, March 10, 2014 - Friday, March 14, 2014

Organizers:
Reza Salek, EMBL-EBI & Cambridge University, UK
Laura Emery, EMBL-EBI, UK
Christoph Steinbeck, EMBL-EBI, UK

Registration Deadline:
Friday, January 10, 2014

Participation:
Open application with selection

Details of the course (programme, trainers and the cost) are yet to be confirmed and are subject to funding arrangements. If you would like to see details of similar courses from previous years please take a look at: http://www.ebi.ac.uk/training/past-courses-held-embl-ebi

If you would like to register your interest in this course and be the first to hear of any updates please send us an email using the following link: keep me posted

For more information, visit http://www.ebi.ac.uk/training/course/metabolomics-2014.
24-26 Mar 2014

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

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

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

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

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

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

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

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

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

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

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

Early registration and abstract submission due March 31, 2014.

Follow us on Twitter:
 Visit us on Facebook.

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

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

Metabolomics Jobs

7) Metabolomics Jobs

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

Jobs Offered

Job Title Employer Location Posted Closes Source
Assistant/Associate Professor Tenure Track Positions McGill University Montreal, Canada 30-May-2013 31-Aug-2013
 Metabolomics Society
Senior Scientist LipoScience Raleigh, NC, USA
 18-Jun-2013 30-Aug-2013
 Metabolomics Society
Research Fellow Beth Israel Deaconess Medical Center (BIDMC) / Harvard Medical School Boston, MA, USA 16-Jul-2013 15-Aug-2013
 naturejobs.com
Postdoc in NMR-based metabolomic profiling of intact prostate tissues  Umeå University Umeå, Sweden 15-Jun-2013 15-Aug-2013
 naturejobs.com
Postdoctoral Research Fellow (m/f) Max Planck Gesellschaft Köln, Germany 24-Jun-2013 06-Aug-2013
 naturejobs.com
Engineer non-permanent position in metabolomics. BDX-IR-1-WP1a Plateforme Métabolome Bordeaux Villenave d'Ornon, France 17-Jul-2013 02-Aug-2013 naturejobs.com
Development, implementation and use of NMR and atmospheric pressure ionization mass spectrometry databases for metabolomics MetaboHUB Bordeaux Metabolome Facility, INRA Bordeaux Center, F-33140 Villenave d'Ornon, France
 22-May-2013 02-Aug-2013
 MetaboHUB
Post-Doctoral Fellowship in Metabolomics University of Maryland, School of Pharmacy
 Baltimore, MD, USA 27-Jun-2013 31-Jul-2013
 naturejobs.com
Research Assistant / Research Associate - Bioinformatics Imperial College London London, UK 11-Jul-2013 22-Jul-2013 Imperial College London
Postdoctoral or Research Associate Position Concordia University Montreal, Canada 07-Jun-2013
Metabolomics Society


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]

Free Subscription
To subscribe/unsubscribe, simply visit https://mail.cs.ualberta.ca/mailman/listinfo/MetaboNews. Please forward this newsletter to any interested colleagues or collaborators. Send your comments and feedback about this newsletter to metabolomics.innovation@gmail.com.

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