MetaboNews Masthead

MetaboNews
Issue 13 - September 2012

CONTENTS:


Online version of this newsletter:
http://www.metabonews.ca/Sep2012/MetaboNews_Sep2012.htm

Welcome to the thirteenth issue of MetaboNews, a monthly newsletter for the worldwide metabolomics community. In this month's issue, we feature a Database Spotlight article on Phenol-Explorer, a database on dietary polyphenols and their metabolites. As of the May 2012 issue, we introduced a new section called MetaboInterviews that features interviews with metabolomics experts from around the world. This issue includes an interview with Dr. Gary Siuzdak of the Scripps Center for Metabolomics. This newsletter is being 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/Stat Spotlight

1) Database Spotlight

 Phenol-Explorer Logo

Phenol-Explorer, a database on dietary polyphenols and their metabolites

Feature article contributed by Augustin Scalbert, Head of Biomarkers Group, International Agency on Research on Cancer (IARC), Lyon, France

Foods are derived from various animal and plant species and each species is characterized by the presence of large number of chemical constituents. Some of these constituents have received considerable attention due to their established or suggested role in nutrition and health. These include polyphenols abundant in wine, tea, coffee, fruits, wholegrain cereals, and many other foods of plant origin. They have become very popular because of their antioxidant properties and their possible role in the prevention of diseases, such as cardiovascular diseases, diabetes, cancers, osteoporosis, and neurodegenerative diseases.

Polyphenols constitute one of the largest families of phytochemicals with over 500 compounds described in various foods. We developed Phenol-Explorer, the first comprehensive database on dietary polyphenols, which describes 502 polyphenols in 452 foods (1) (http://www.phenol-explorer.eu/). The database has been used to measure polyphenol intake in populations and to study associations between intake and disease risk (2).

Once ingested with our diet, polyphenols are rapidly absorbed and metabolized, either by the gut microbiota or in our tissues. A detailed knowledge of the bioavailability of the various polyphenols and the nature and concentrations of the metabolites formed in the body is also essential to understand their effects on health. We recently released the second version of Phenol-Explorer (Phenol-Explorer 2.0) which now includes 375 polyphenol metabolites described in the literature (http://www.phenol-explorer.eu/metabolites) together with detailed pharmacokinetic data (3) (Figure 1). It contains descriptions of the animal or human studies (food or polyphenol ingested, dose administered, composition of the administered food, etc.) where the compounds were observed, with links to the original literature source.

Screenshot of the Phenol-Explorer database showing metabolites formed after ingestion of green tea

Screenshot of the Phenol-Explorer database showing pharmacokinetics properties after ingestion of green tea

Figure 1. Screenshots of the Phenol-Explorer database showing metabolites formed after ingestion of green tea (above) together with their pharmacokinetic properties (below).


Each metabolite is described with its molecular formula, chemical structure, molecular weight, and links to other databases such as CAS, ChEBI, and PubChem (Figure 2).

Screenshot of the Phenol-Explorer database showing the structure of a metabolite formed upon tea ingestion

Figure 2. Screenshot of the Phenol-Explorer database showing the structure of a metabolite found after tea ingestion.


Various queries can be made in Phenol-Explorer 2.0 to identify all metabolites formed from a particular polyphenol. For example, the database allows users to retrieve the 27 metabolites formed from chlorogenic acid, the main polyphenol present in coffee, in rat and human feeding studies (http://www.phenol-explorer.eu/metabolism/polyphenol-metabolites/948), or polyphenol metabolites identified in urine or plasma after consumption of coffee (http://www.phenol-explorer.eu/metabolism/metabolites/1089). All data and results of query searches can be exported as CSV or Excel files.

This information on polyphenol metabolites is now used in our lab to identify in complex urine fingerprints from free-living subjects all polyphenol metabolites, which may serve as biomarkers of polyphenol exposure for future epidemiological studies (Figure 3).

Urinary profile obtained by high-resolution mass spectrometry (UPLC-QTof-MS)

Figure 3. Urinary profile obtained by high-resolution mass spectrometry (UPLC-QTof-MS) showing 85 putative polyphenol metabolites identified with the Phenol-Explorer database.


Phenol-Explorer is the first database describing in a systematic way all metabolites formed from a particular class of food compounds. This database can be particularly useful to identify metabolites formed from dietary polyphenols in human biofluids which constitute altogether a significant fraction of what we have called the 'food metabolome' (4).

Acknowledgments

Phenol-Explorer 2.0 has been developed at INRA, Clermont-Ferrand (J. Rothwell, C. Manach, A. Scalbert) and IARC, Lyon (Will Edmands, A. Scalbert) in collaboration with the University of Barcelona (M. Urpi-Sarda, M. Boto-Ordonez, R. Llorach, C. Andres-Lacueva), the University of Alberta, Edmonton (D. Wishart, V. Neveu), and Insiliflo, Edmonton (C. Knox), with the financial support of Danone Research and the Institut National du Cancer, Paris, France.

References
  1. Neveu V, Perez-Jiménez J, Vos F, Crespy V, du Chaffaut L, Mennen L, Knox C, Eisner R, Cruz J, Wishart D, Scalbert A. Phenol-Explorer: an online comprehensive database on polyphenol contents in foods. Database (Oxford). 2010;2010:bap024. Epub 2010 Jan 8. [PMID: 20428313]
  2. Pérez-Jiménez J, Fezeu L, Touvier M, Arnault N, Manach C, Hercberg S, Galan P, Scalbert A. Dietary intake of 337 polyphenols in French adults. Am J Clin Nutr. 2011 Jun;93(6):1220-8. Epub 2011 Apr 13. [PMID: 21490142]
  3. Rothwell JA, Urpi-Sarda M, Boto-Ordoñez M, Knox C, Llorach R, Eisner R, Cruz J, Neveu V, Wishart D, Manach C, Andres-Lacueva C, Scalbert A. Phenol-Explorer 2.0: a major update of the Phenol-Explorer database integrating data on polyphenol metabolism and pharmacokinetics in humans and experimental animals. Database (Oxford). 2012 Aug 9;2012:bas031. [PMID: 22879444]
  4. Manach C, Hubert J, Llorach R, Scalbert A. The complex links between dietary phytochemicals and human health deciphered by metabolomics. Mol Nutr Food Res. 2009 Oct;53(10):1303-15. Review. [PMID: 19764066]
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 Dr. Gary Siuzdak of the Scripps Center for Metabolomics.


Gary Siuzdak
Professor of Chemistry and Molecular Biology and Director of the Scripps Center for Metabolomics at The Scripps Research Institute in La Jolla, California
Dr. Gary Siuzdak 
Biography
Gary Siuzdak is Professor of Chemistry and Molecular Biology and Director of the Scripps Center for Metabolomics at The Scripps Research Institute in La Jolla, California (http://masspec.scripps.edu/). He is also Faculty Guest at Lawrence Berkeley National Laboratory and served as Vice President of the American Society for Mass Spectrometry. His research interests include developing novel mass spectrometry-based approaches in metabolomics and nanostructure-based imaging. He has written two books, "Mass Spectrometry for Biotechnology" and the "The Expanding Role of Mass Spectrometry in Biotechnology". He is also in the process of writing a third book on Metabolism and Mass Spectrometry with Gary J. Patti (Assistant Professor at Washington University in St. Louis).


Metabolomics Interview (MN, MetaboNews; GS, Gary Siuzdak)

MN: How did you get involved in metabolomics?

GS: My first untargeted metabolomic experiments, reverse phase liquid chromatography combined with ESI QqQ mass spectrometry, were focused on identifying novel metabolites involved in sleep (Science 1995). For me, this study illuminated the need of MS/MS data for characterizing metabolites and I can trace the origins of METLIN to those initial experiments. Since then the analytical and informatic technologies have dramatically improved, and what took me almost a year to accomplish back in 1995 would only take weeks now, or, maybe, even a day.


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

GS: 2012 has highlighted both our most exciting applied and informatic results. For example untargeted metabolomics of chronic pain (Nature Chem. Biol. 2012) allowed us to identify a novel endogenous metabolite (dimethylsphingosine) that is related to a previously unexplored pathway in pain response.

   
Dimethylsphingosine

From an informatics perspective we are extremely excited about our cloud-based XCMS/METLIN platform, as it is facilitating research around the globe, and that tens of thousands of scientists are making use of METLIN's metabolite and tandem mass spectrometry database (Nature Biotechnology 2012 & Analytical Chemistry 2012). Developing technology is one thing yet seeing so many scientists applying it to a very diverse set of problems is especially rewarding.

XCMS Online
  
 



https://xcmsonline.scripps.edu/


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

GS: The applications are synergistic with our analytical and informatic developments, with primary foci on cancer, aging, microbes, and microbial communities.

Related to the development of XCMS Online and METLIN data repository, we are now implementing multi-group analysis (Analytical Chemistry 2011, Nature Protocols 2012), working to increase the speed of data processing, performing real-time tandem mass spectrometry searching, developing XCMS pathway analysis tools, and, of course, always increasing the size of METLIN. In fact, our partnerships with SIGMA, ChromaDex, Cayman, Agilent, Joint BioEnergy Institute (Berkeley) and the Dale Boger (Scripps) and William Gerwick (UCSD) labs have allowed the METLIN tandem mass spectrometry database to make significant leaps over the last nine years. This has been especially apparent in the last two years (below).
METLIN tandem mass spectrometry database

http://metlin.scripps.edu/

From an analytical perspective, I'm particularly intrigued by surface-based mass spectrometry technology and that is why we are putting significant effort into our next generation of nanostructure-based metabolite tissue imaging platform.


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

GS:  On a daily basis we observe how the cloud-based XCMS Online/METLIN platform is being applied, with over 100,000 jobs performed so far in cancer, immune response, stem cell analysis, biomarker discovery, neonatal diseases, and disease biochemistry. Beyond this, the applications also include almost every other area conceivable such as food safety/science, forensics, sports medicine, clinical analysis, drug discovery, and more. Given that the XCMS metabolomic platform is already broadly applied, we are interested in continuing to identify and enhance particular XCMS features that are being widely used. For example tandem mass spectrometry is clearly becoming indispensable for metabolite identification, and, another area which has been more of a surprise, is the number of users who are using XCMS as a data repository and as a resource for data sharing.

Ways the cloud-based XCMS Online/METLIN platform is being applied


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

GS: The relatively low number of steps required in the sample analysis process makes performing large numbers of analyses possible with high quantitative reproducibility. For example, thousands of clinical samples are possible to process and analyze in a reasonable amount of time. Another strength is the coupling of untargeted and targeted approaches: once untargeted analyses are performed on a small sample set and specific metabolites identified, validation, and verification is relatively straightforward on a larger set of samples using QqQ targeted analyses. Robert Gerszten and Stanley Hazen have already demonstrated the large-scale analysis capabilities of metabolomics in landmark papers with the analyses of thousands of samples.

 
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?

GS: One barrier is sample preparation. For example quenching enzyme activity as soon as possible (and consistently) is a critical aspect of any metabolomic experiment.

Standardized methods of chromatographic techniques, ionization approaches (ESI, APCI, EI), metabolite extraction, and tandem mass spectrometry databases to identify metabolites are also areas where considerable work needs to be done. 

Separately, metabolite imaging using mass spectrometry is a very powerful technology, (Nature 2007 & Neuroscience 2010) as shown below with an image of intact cholesterol metabolites generated from a brain tissue slice. Yet a significant challenge for mass spectrometry-based imaging is that the current techniques, whether it is NIMS or MALDI, only allow for the observation of hundreds of metabolites. This needs to be improved to obtain a more comprehensive view of the metabolome in these images, especially in comparison to the thousands of metabolites that are observed with LC/MS-based approaches.

An image of intact cholesterol metabolites generated from a brain tissue slice


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

GS: Science in general is a challenging career area at the moment. Funding is uncertain and will likely be for a while. However, there are a growing number of funding bodies that are incorporating metabolomics into their repertoire including those from the NIH developed as Common Fund initiatives. Journal editors are also requesting manuscripts to include metabolomic research; this proof-of-principle will in turn improve the prospects for funding in the future. Even given the current funding uncertainty, this is one area that I'm excited about and believe that it will continue to unveil interesting biochemical insight. I would without reservation encourage young scientists to pursue it.


 MN: What role can metabolomics standards play?

GS: Creativity is the driver behind innovative science, and it is that creativity that has allowed this field to mature to where it is today in terms of mass spectrometry and informatic technologies. Yet the role of standardization is still evolving; now that the field has matured, standardization is becoming even more important to achieve the ultimate goal of cross-validation between platforms and labs.


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

GS: I believe the 'butterfly effect' analogy is especially relevant to metabolomics and helps explain why metabolites are "…the ultimate molecular arbiters of biological function" (J. Perkel). Very small changes on the genome or proteome can have a significant downstream effect on metabolism, allowing for a readout of the entire system. Those metabolic changes can be translated back to their genetic or protein origin using powerful experimental/bioinformatic techniques such as flux analysis, meta-analysis, or multiple group analysis (figure below, Analytical Chemistry 2011, and Nature Reviews 2012) to deconvolve the information down to the most meaningful biochemical pathways.

Meta-Analysis or Multiple Group Analysis

To the young metabolomic scientists: there is no doubt that a broader understanding of metabolism will have a substantial effect on our understanding of the fundamental biochemistry behind living systems and their perturbations. Perhaps more importantly, I would encourage those going into this area to take steps beyond searching for biomarkers, and delve deeper into the meaning that these dysregulated metabolites represent... finding a testable connection to the enzymes responsible for metabolic perturbations is the ultimate validation of your metabolomic research.
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. More than 95% of today's 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 biomarker tools for the identification of biomarkers associated with: 1. Hepatocellular carcinoma in patients with liver cirrhosis, and 2. Hepatitis B virus-infected cirrhosis and alcoholic cirrhosis, respectively.
  1. Ressom HW, Xiao JF, Tuli L, Varghese RS, Zhou B, Tsai TH, Nezami Ranjbar MR, Zhao Y, Wang J, Di Poto C, Cheema AK, Tadesse MG, Goldman R, Shetty K. Utilization of metabolomics to identify serum biomarkers for hepatocellular carcinoma in patients with liver cirrhosis. Anal Chim Acta. 2012 Sep 19;743C:90-100. Epub 2012 Jul 20. [PMID: 22882828]

    In this paper, the research team sought to identify serum biomarkers for hepatocellular carcinoma (HCC) in patients with liver cirrhosis. The investigators performed ultra performance liquid chromatography coupled with a hybrid quadrupole time-of-flight mass spectrometry (UPLC-QTOF MS) to compare serum metabolite levels in 78 HCC patients with 184 cirrhotic controls. The researchers found that metabolites involved in two pathways in particular, sphingolipid metabolism and phospholipid catabolism, were up-regulated in the HCC patients. The up-regulated metabolites included sphingosine-1-phosphate (S-1-P) and lysophosphatidylcholine (lysoPC 17:0). Metabolites that were down-regulated included glycochenodeoxycholic acid 3-sulfate (3-sulfo-GCDCA), glycocholic acid (GCA), glycodeoxycholic acid (GDCA), taurocholic acid (TCA), and taurochenodeoxycholate (TCDCA). Metabolite biomarkers, such as those identified in this study, may serve in the development of an early-stage diagnostic for HCC in patients with liver cirrhosis.


  1. Qi S, Tu Z, Ouyang X, Wang L, Peng W, Cai A, Dai Y. Comparison of the metabolic profiling of hepatitis B virus-infected cirrhosis and alcoholic cirrhosis patients by using (1) H NMR-based metabonomics. Hepatol Res. 2012 Jul;42(7):677-85. doi: 10.1111/j.1872-034X.2011.00964.x. Epub 2012 Mar 8. [PMID: 22404306]

    In this study, the researchers aimed to identify metabolites associated with hepatitis B virus-infected cirrhosis and alcoholic cirrhosis. This group used (1) H nuclear magnetic resonance (NMR)-based metabonomics to profile serum metabolites from three groups: 21 HBV-infected cirrhosis patients, 20 alcoholic cirrhosis patients, and 20 healthy controls. An orthogonal partial least-squares-discriminant analysis (OPLS-DA) model consisting of five metabolites, creatine, acetoacetate, isobutyrate, glutamine, and glutamate, was used to differentiate between HBV-infected cirrhosis and alcoholic cirrhosis. This research team used NMR-based metabonomics combined with multivariate analysis (i.e., principal component analysis, OPLS-DA) to build a potentially useful discriminator between one disease state and another.
Metabolomics Current Contents

4) Metabolomics Current Contents

Recently published papers in metabolomics:


MetaboNews

5) MetaboNews
10 Aug 2012
EasyLCMS: An asynchronous web application for the automated quantification of LC-MS data

Downstream applications in metabolomics, as well as mathematical modelling, require data in a quantitative format, which may also necessitate the automated and simultaneous quantification of numerous metabolites. Although numerous applications have been previously developed for metabolomics data handling, automated calibration and calculation of the concentrations in terms of mumol have not been carried out.

Moreover, most of the metabolomics applications are designed for GC-MS, and would not be suitable for LC-MS, since in LC, the deviation in the retention time is not linear, which is not taken into account in these applications. Moreover, only a few are web-based applications, which could improve stand-alone software in terms of compatibility, sharing capabilities and hardware requirements, even though a strong bandwidth is required. Furthermore, none of these incorporate asynchronous communication to allow real-time interaction with pre-processed results.

Findings: Here, we present EasyLCMS (http://www.easylcms.es/), a new application for automated quantification which was validated using more than 1000 concentration comparisons in real samples with manual operation. The results showed that only 1% of the quantifications presented a relative error higher than 15%.

Using clustering analysis, the metabolites with the highest relative error distributions were identified and studied to solve recurrent mistakes.

Conclusions: EasyLCMS is a new web application designed to quantify numerous metabolites, simultaneously integrating LC distortions and asynchronous web technology to present a visual interface with dynamic interaction which allows checking and correction of LC-MS raw data pre-processing results. Moreover, quantified data obtained with EasyLCMS are fully compatible with numerous downstream applications, as well as for mathematical modelling in the systems biology field.

Paper: Fructuoso S, Sevilla Camins A, Bernal C, Lozano AB, Iborra JL, Canovas M. EasyLCMS: An asynchronous web application for the automated quantification of LC-MS data. BMC Res Notes. 2012 Aug 11;5(1):428. [Epub ahead of print] [PMID: 22884039]
 
2 Aug 2012
Waters and Nonlinear Dynamics to Co-Develop Next Generation Research Solutions for Large-Scale, Complex Data Sets

Firms to Combine Complementary Expertise in Analytical Science and Informatics to Advance Proteomics and Metabolomics Research

Waters Corporation (wat:NYSE) and Nonlinear Dynamics Ltd. have entered into an agreement to co-develop a new analytical solution that derives information from complex data sets generated by large-scale proteomics and metabolomics experiments.

Waters and Nonlinear Dynamics collaborated on the development of the Waters Omics Research Platform with TransOmics™ Informatics first introduced in May during the ASMS Conference on Mass Spectrometry and Allied Topics in Vancouver combining both Waters® SYNAPT® G2-S HDMS and TransOmics Informatics developed by Nonlinear Dynamics' under an exclusive worldwide OEM agreement.

With the launch of Waters Omics Research Platform, Waters introduced two new solutions powered by Waters TransOmics Informatics:
  • Proteomics solution combining Waters nanoACQUITY UPLC® and Waters SYNAPT® G2-S HDMS mass spectrometer for the bottom-up analysis of complex mixtures.
  • Metabolomics solution built around the Waters ACQUITY® UPLC I-Class and Waters SYNAPT G2-S HDMS mass spectrometer for routine screening of large sample cohorts.
Waters first introduced ion mobility to mass spectrometry with the introduction of the SYNAPT® High Definition Mass Spectrometer™ (HDMS™) in 2007.

Used in small molecule research, protein characterization, metabolite identification and bio-pharmaceutical applications, the Synapt HDMS system is still the only mass spectrometer to employ high efficiency ion-mobility based measurements and separations to enable the analysis of sample ions differentiated by size, shape and charge as well as mass. The added dimension of shape-selective separation increases the analytical specificity and sample definition so that scientists can extract more information from their samples, including the detection of components previously unseen by conventional mass spectrometers.

"The complexity of biological samples is so great that the sensitivity and specificity of analytical techniques required for biological discovery presents scientists with significant challenges when it comes to managing experimental data," said James Langridge, Ph.D., Director of Pharmaceutical & Life Sciences Discovery, Waters Division. "We believe that through our partnership with Nonlinear Dynamics we can address this situation and advance the pace of discovery."

"I'm delighted to see this exciting partnership bring together the latest MS technology with world-renowned data analysis software," said Will Dracup, Executive Chairman, Nonlinear Dynamics. "Researchers today are faced with large, complex data sets and they need to be able to visualize this and extract reliable results. The software Nonlinear has developed specifically addresses these issues, unlocking the potential of the valuable, content-rich, omics data that Waters' ion mobility technology generates."

A common goal of any omics studies - whether proteomics or metabolomics - is to gain a clear understanding of the interplay between molecules at the protein and metabolite level leading to a better understanding of the underlying biology of an organism or a specific disease state. The Waters Omics Research Platform Solution facilitates research across multiple discovery areas for researchers in the pharmaceutical and life sciences, food, and clinical research areas.

Waters intends to commence shipments of its UPLC®/SYNAPT G2-S HDMS-based instrument solutions with TransOmics Informatics announced at ASMS during the fourth quarter of 2012.


Source: MarketWatch
 
1 Aug 2012
Metabolon Strengthens Metabolomics Leadership With Acquisition of Lipomics Technologies

Gains proprietary lipids technology platform and further opportunities for diagnostics, personalized medicine and commercial services

Metabolon, Inc. announces the completion of its acquisition of Lipomics Technologies, Inc. This transaction combines Metabolon’s world-leading metabolomics technology platform for commercial services and diagnostics with Lipomics’ world-leading TrueMass® Profiling lipids technology platform.
 
Lipomics’ laboratory facilities will remain at its headquarters in Sacramento, California while Metabolon’s headquarters and laboratories will remain in Research Triangle Park.  Steven M. Watkins, Ph.D., Lipomics’ founder, will join Metabolon’s executive team as chief technology officer. Financial terms of the transaction were not disclosed.
 
Michael Milburn, Ph.D., chief scientific officer of Metabolon, stated, “Metabolon has pioneered metabolomics technology and is the largest provider of solutions globally to the pharmaceutical, healthcare, consumer products, nutrition and agricultural industries, as well as to hundreds of academic institutions. Lipomics is the leader in technology to analyze lipids, including metabolites of fatty acids, acylcarnitines, sterols, amino acids, bile acids and eicosanoids. Together we have an unprecedented suite of technologies and capabilities to benefit our expanding customer base. The combined technologies will deliver new and improved diagnostic products and personalized medicine solutions for unmet needs, particularly in metabolic disease and cancer.”
 
“For the past 10 years Lipomics has taken pride in providing the best technology and science for understanding the role of lipids in human disease, principally in metabolic diseases associated with obesity and the lipid remodeling aspects of cancer,” said Dr. Watkins. “The prospect of combining our approach with Metabolon’s global platform is extremely exciting. Integrating the technologies will provide a deep and coherent understanding of biological systems and allow us to produce unparalleled services and products for years to come.”
 
John Ryals, Ph.D., chief executive officer of Metabolon, expressed his support of the acquisition saying, “By combining Metabolon and Lipomics, we have created the undisputed technology leader in the emerging field of metabolomics. We have product offerings that span from global metabolomics to complex lipid analysis to targeted analysis of many different classes of molecules.  By combining our two companies, we have more than 140 employees and 450 clients, have completed 2,000 commercial projects and have 200 scientific papers either published or under review. We are not aware of another company or institution with this record of scientific and commercial achievement in the field of metabolomics.
 
“We are the leader in the commercialization of metabolomics with a profitable commercial life sciences service business and have launched the world’s first metabolomics-based diagnostic test for type 2 diabetes risk based on biomarkers that measure insulin resistance. We expect that in 2013 we will be marketing additional diagnostic products aimed at diseases related to obesity and cancer, and are committed to maintaining our position as the world’s leader in metabolomics.”


Source: Metabolon Press Release

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
3-7 Sep 2012

4th Australasian Metabolomics Symposium and Workshop
Venue: Kuala Lumpur, Malaysia

Moving Forward to Integrate Systemic Biology into Post-Genomics Era

Metabolomics is a new emerging field of "omics" research which has attracted attention and focus of academia, industry and government sectors. As for year 2011, there are more than 700 papers being published on this subject. Metabolomics is a comprehensive characterization of the small molecule metabolites in biological systems which provide an overview of the metabolic status and global biochemical events associated with a cellular or biological system. It is an interesting tool which allows researchers to understand the changes in networks and pathways and provide insights into physiological and pathological states. Systems Biology and the ability to integrate genomics, transcriptomics, proteomics, and metabolomics data is evolving at a rapid pace. Metabolomics has the potential and has promised to enable detection of disease states and their progression, monitor response to therapy, stratify patients based on biochemical profiles, and identify targets for drug design. Together with internationally recognized metabolomics experts, we would like to invite you to participate in the Australasian Symposium and Workshop in Metabolomics organised by the Malaysian Metabolomics Society and Pharmacogenomics Centre (PROMISE), UiTM. The event would be held in Shah Alam, Malaysia.

For the symposium, a series of plenary lectures will be held by prominent speakers who have been working on metabolomics. There will be also sessions for oral presentation by selected participants. This workshop will be a combination of lectures and practical sessions focusing on LC-MS data acquisition, data extraction and statistical analysis of large datasets. At the end of the course participants should be familiar with sample preparation, LC-MS data acquisition, LC-MS data interpretation, statistical analysis of metabolomics data sets and challenges associated with all of the above.

For further information, please visit http://metabolomics.my/



18-20 Sep 2012

Metabolomics in Drug Discovery & Development
Venue: Boston, USA

The world’s first and only pharmaceutical focused metabolomics meeting

The last decade of exciting academic research in metabolomics is now being applied by drug developers to determine and validate tox and safety biomarkers. Investment from drug developers is huge as the pharmaceutical industry is now using metabolomics to find novel targets, enhance experimental design, and ensure clinical success. However, statistical challenges and inherent variability in data sets must be overcome to realize the full potential of this exciting technology.

Metabolomics in Drug Discovery and Development is the only meeting where you can hear cutting edge case studies from drug developers who are already reaping the benefits of metabolomics.

The 19 expert speakers include…
  • Rick Beger, Director at the Centre of Excellence for Metabolomics, FDA
  • Bjoern Riefke, Head of Metabolic Profiling & Clinical Pathology, Bayer Healthcare
  • Thomas Ruddy, Director of Analytical Chemistry, Merck
  • David Wishart, Professor, University of Alberta
  • Jeff Trimmer, Executive Director, Pfizer
  • Reza Salek, Scientific Investigator, European Bioinformatics Institute
  • Thomas Hankemeier, Director, Netherlands Metabolomics Facility
  • Shashi Ramaiah, Drug Safety Biomarker & Precision Medicine Lead, Pfizer
Visit the event website to see the full speaker line up and exactly what will be covered.

Quote ‘METABO’ when registering for 10% off standard prices.

There is a special rate of $599 for those representing not-for-profit organizations

www.metabolomics-drugdevelopment.com

Conference brochure
20-21 Sep 2012

Metabolomics Data Analysis Workshop: Analysis of LC-MS focused metabolomics data with IDEOM and mzMatch
Venue: Bioinformatics Research Centre, Joseph Black Building, University of Glasgow, Glasgow, UK

We kindly invite you to attend a workshop "Analysis of LC-MS focused metabolomics data with IDEOM and mzMatch".
  • IDEOM workshop: Thursday 20th September 2012 (£ TBA)
  • mzMatch workshop: Friday 21st September 2012 (£ TBA)
Times: 10am to 5pm
Catering: Lunch and Tea/Coffee provided
Computers: Bring own laptop or book a desktop

Registration
Places are limited and booking is mandatory.

Outline

  • Introduction to LC-MS focused metabolomics
  • Practical tutorials to get familiar with the software
  • Explanation of tips and tricks for non-experts in the field
  • Demonstration of advanced features
  • Discussions for future development of data processing software

More details are available via http://mzmatch.sourceforge.net/workshop.php
25-27 Sep 2012

Metabomeeting 2012
Venue: Manchester Conference Centre, Manchester, UK

The Metabolic Profiling Forum is pleased to announce that Metabomeeting 2012 will be held at the Manchester Conference Centre, Manchester, UK from September 25-27th 2012.

The conference centre is located within the University of Manchester campus, close to major transport links and one of the most cosmopolitan centres in the UK. The meeting is the seventh of the Metabomeeting conferences and continues the series of highly successful events held across Europe since 2005. The program will focus on the increasingly diverse range of applications as well as the latest developments to enhance the practise of metabolomics.

Confirmed speakers for the meeting include:
  • Professor Robert Hall, Plant Research International, The Netherlands, who will present the plenary lecture.
  • Professor Rainer Breitling, University of Glasgow, UK.
  • Professor Hannelore Daniel, Technical University of Munich, Germany.
  • Dr Jules Griffin, University of Cambridge, UK
  • Dr George Harrigan, Monsanto, USA
  • Dr Jerome Jansen, Raboud University, Nijmegen, The Netherlands.
  • Dr Nick Lockyer, University of Manchester, UK.
  • Professor George Nychas, Agricultural University of Athens, Greece.
  • Professor Ian Wilson, AstraZeneca, UK.
  • Dr Asaph Aharoni, Weizmann Institute of Science, Israel
Submission of abstracts for poster presentation has now opened. All abstracts for poster presentation must be submitted before August 10th 2012.

More details are available via http://thempf.org/mpf_cms/index.php/conferencesworkshops/forthcoming-mpf-events/78-metabomeeting-2012.
1-3 Oct 2012

2nd International Workshop on Metabolomics & Proteomics
Venue: CIC bioGUNE, Bilbao, Spain

Metabolomics and Proteomics constitute two key technologies that have paramount importance in the Systems Biology era. Each of the techniques allows tackling the huge complexity that a living systems displays at metabolome and proteome level.
 
Proteomics was born after the sequences of genomes were released and by the hand of the great advances performed in mass spectrometry and bioinformatics. This way, with the genomics sequences available, hundreds of proteins can be identified in the same experiment and latest developments also allow systematic quantification of the gene products. These developments allow studying variations suffered by the proteins within a cell in a perturbed condition (e.g. disease, drug treatment etc.). Proteins constitute the major catalytic entities in cell and knowing the details of dynamics, modifications and interactions of proteins will help getting insights about basic molecular mechanisms that rule the fate of the cell. Moreover, since most of drugs are targeted against proteins, it is clear the interest in getting as much information as possible that will eventually render new insights into clinics.

Metabolomics can be defined as the quantitative and qualitative analysis of all metabolites (molecules with a molecular weight of less than 1.500 Da) in a given organism. This results in the construction of a metabolome or metabolic fingerprint, analogous to the genome or the proteome. Since the set of all metabolites is directly linked to the actual state of a cell, tissue or an organism and thus to the phenotype, the metabolome is optimally suited for the determination of biomarkers that are typical for certain genotypes or pathologies, and to identify key cellular pathways involved in the development and progression of diseases.
 
CIC bioGUNE has prepared a very interesting scientific program in which leading academics speakers will tell us about the state-of-the-art in metabolomics and proteomics including technological aspects related to the different platforms (RMN, GC-MS, LC-MS and protein arrays). The workshop will also cover recent breakthroughs in each of the disciplines as single-cell and high-throughput metabolomic approaches, protein characterization and large scale protein quantification, along with the applications that these technologies have found in environmental and disease biomarker discovery areas. Importantly, the scientific program will be completed with poster sessions and presentations from equipment manufacturers.  In summary, the participants will have the opportunity to learn, meet and interact with experts in different metabolomic and proteomic related areas obtaining a deep and broad vision on these  powerful technologies
  • Workshop Invitation: [PDF]
  • Workshop Agenda: [PDF]
For further information, please visit http://metabolomicsandproteomicsworkshop2012.cicbiogune.es/
16-17 Oct 2012

Metabolic Profiling & Lipidomics
Venue: Madrid, Spain (Part of Systems Biology Europe)

Welcome to the Metabolic Profiling & Lipidomics track of the Systems Biology Europe conference and exhibition.

This conference aims to discuss the latest developments in the rapidly evolving area of metabolic profiling with particular emphasis on the break out field of Lipidomics. Recent HPLC-MS advances now allow for individual molecular species of lipids to be isolated and identified. This meeting will detail the cutting edge research taking place as a result of these developments with emphasis on understanding not only lipid metabolism but also ascertaining the role of lipids in conditions such as atherosclerosis, inflammatory disease, arthritis, cancer, diabetes and Alzheimer's disease, with a view to improving treatment. As a whole focus will be drawn to the key technological developments being made in both the separation and detection analytical fields used in profiling as well as the area’s other key applications including toxicity assessment, functional genomics and nutrigenomics.

Other conference tracks at this event include Cancer Proteomics, Exosomes/Markers in Biological Fluids, and Informatics. Registered delegates will have access to all four meetings ensuring a very cost-effective trip.

In addition the event will also host two cutting edge business courses which can be viewed here.

For further information, please visit http://selectbiosciences.com/conferences/index.aspx?conf=MPL2012
7-9 Nov 2012

29th LC/MS Montreux Symposium
Venue: Montreux, Switzerland

Short Courses: November 5-6, 2012
The Montreux LC/MS 2012 conference: Special highlights on Metabolomics and Clinical Chemistry

The field of LC/MS is continuously growing as is reflected by the participation of over 30 nationalities and by scientific contributions from a variety of research and development domains such as pharmaceutical, biotechnological, food, environmental and research on novel instrumentation and new LC/MS fields such as nanotechnology and microfluidics, UPLC, low flow rate spray techniques, proteomics, and systems biology.

In collaboration with the Metabolomics Society, a special joint parallel program for this rapidly emerging field is organized addressing the technology as well as novel systems-based biology approaches in pharma, nutrition, clinical chemistry, plant sciences, and medical biology. A parallel program is organized together with various Clinical Chemistry societies focusing on current and future LC/MS options in clinical diagnosis. Accreditation by related societies for the program as well as the short course has been applied for.
For more information, visit http://www.lcms-montreux.com/.

27 Jan-1 Feb 2013

Gordon Research Conference on Plant Lipids: Structure, Metabolism & Function
Venue: Galveston, Texas, USA

The third Gordon Research Conference on "Plant Lipids: Structure, Metabolism, and Function" promises to be an exciting event where the latest research on plant lipids is presented and discussed. For the first time, the conference will be preceded by a Gordon Research Seminar on Plant Lipids, providing excellent opportunities for graduate students and postdoctoral researchers to share research, to develop research and social networks in a supportive environment, and to discuss careers and mentoring. We encourage young scientists to participate in the Gordon Research Seminar, and we encourage broad participation in the Gordon Research Conference. Presenters will discuss the latest advances in plant and algal lipid metabolism, oil synthesis, lipid signaling, lipid visualization, lipid biotechnology and its applications, the physiological and developmental roles of lipids, and plant lipids in health. The conference will be a great chance for old and new members of the international plant lipid research community to interact. Applications to attend this conference are open to all researchers interested in plant lipids.

Application Deadline
Applications for this meeting must be submitted by December 30, 2012. Please apply early, as some meetings become oversubscribed (full) before this deadline. If the meeting is oversubscribed, it will be stated here. Note: Applications for oversubscribed meetings will only be considered by the Conference Chair if more seats become available due to cancellations.

Related Meeting Information
The Plant Lipids: Structure, Metabolism & Function Gordon Research Conference will be held in conjunction with the Plant Lipids: Structure, Metabolism & Function Gordon Research Seminar. Those interested in attending both meetings must submit an application for the GRS in addition to an application for the GRC. Please refer to the Plant Lipids: Structure, Metabolism & Function GRS web page for more information.


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


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 Date Posted Source
Post-doctoral research fellow: Food metabolomics
 European Commission, Joint Research Centre, Institute for Reference Materials and Measurements Geel, Belgium 30-Aug-2012 Naturejobs.com
Associate Professor Georgia Health Sciences University Augusta, GA, United States
 29-Aug-2012 Naturejobs.com
Biochemistry and Molecular Biology Faculty Position University of California, Los Angeles (UCLA) Los Angeles, CA, United States
 23-Aug-2012 Naturejobs.com
Clinical Laboratory Director Metabolon Durham, NC, USA 15-Aug-2012 Metabolomics Society
Senior Bioanalytical Chemist Metabolon Durham, NC, USA 15-Aug-2012 Metabolomics Society
Metabolomics Data Analyst
 Stemina Biomarker Discovery
 Madison, WI, USA
 15-Aug-2012 Stemina Biomarker Discovery
Postdoctoral researchers: "Biostatistician for functional genomics data integration" The Biosystems Data Analysis group Amsterdam, Netherlands
 9-Aug-2012 Naturejobs.com
Research Scientist (Plant Metabolomics) Hudson Shribman Scientific Recruitment Ltd East Anglia, United Kingdom
 27-Jul-2012 Naturejobs.com
Computer Scientist University of Manchester Manchester, United Kingdom
 16-Jul-2012 Naturejobs.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.
  • Position Sought: Seeking a position in drug research and development and biomarker discovery. [Candidate's CV]

Scientific Journal Announcements
  • Special issue of Electrophoresis on the subject of Metabolomics: see invitation [PDF]

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