MetaboNews Masthead

MetaboNews
Issue 20 - April 2013

CONTENTS:


Online version of this newsletter:
http://www.metabonews.ca/Apr2013/MetaboNews_Apr2013.htm

Welcome to the twentieth issue of MetaboNews, a monthly newsletter for the worldwide metabolomics community. In this month's issue, we feature a Software Spotlight article on MSClust, software that bridges the gap between untargeted mass peak alignment and metabolite identification. 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 Bruce German, Professor in Food Science and Technology, Director, Foods for Health Institute, University of California, Davis, USA. 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).

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

 Software Spotlight

1) Software Spotlight

 Wageningen UR Logo

MSClust: Bridging the gap between untargeted mass peak alignment and metabolite identification

Feature article contributed by Yury Tikunov, Wageningen UR Plant Breeding, Wageningen, The Netherlands

Ion-wise alignment of GC-MS and LC-MS chromatograms is widely used in metabolomics studies as a primary data processing approach. A few software implementations of this approach, e.g., MetAlign and XCMS, enable a comprehensive comparative analysis of complex metabolic mixtures by aligning quantitative values of individual mass peaks across samples analyzed. In principle, resulting data matrices can be directly subjected to comparative analysis using various statistical tools. However, conducting such analysis, getting structural information from these data matrices, and making biological interpretations are rather challenging for several reasons:
  1. The resulting mass peak alignment matrices are often extremely large with a disproportionate variable-to-sample ratio, as the amount of variables (i.e., detected mass peaks) may reach tens of thousands.
  2. Up to 90% of the variables may be redundant, since each metabolite will be represented by a number of different mass peaks, including molecular fragments, adducts, molecular fragments and isotopes thereof. Moreover, this redundancy may vary between profiling platforms and metabolites, depending upon their concentration, ionization efficiency, and specific chemical nature. This leads to an unequal representation of metabolites in the dataset and complicates subsequent multivariate or statistical analyses.
  3. A direct interpretation of the experimental results is hardly possible, because the structural information of a metabolite, such as a mass spectrum in the case of GC-MS and in-source fragments in the case of LC-MS, is not provided directly as a result of the alignment.

MSClust is a software tool that was created to bridge two different sides of the metabolomics data analysis workflow: untargeted mass peak alignment on one hand and metabolite identification followed by data interpretation on the other hand (Figure 1). MSClust helps to go from thousands of fragments produced by mass spectrometry to a few hundred MSClust clusters of aligned mass peaks, which represent putative metabolite mass spectra, thereby i) reducing the signal redundancy per metabolite into single representative variables, and ii) reconstructing original mass spectra, thus providing structural metabolite information.

MSClust GUI & a general workflow of a comparative metabolomics data analysis

Figure 1. MSClust GUI (on the left) and a general workflow of a comparative metabolomics data analysis that is based on a mass peak alignment approach (on the right). MSClust receives a mass peak alignment data matrix of size M x S, where M is the number of mass peaks (often tens thousands) aligned across the number of samples profiled, represented by S. As a result it produces a reduced data matrix of size C x S, where C is the number of putative compounds represented by a single mass peak (normally a few hundred) aligned with the same number of samples profiled (S). In addition, it extracts a mass spectra for each of the compounds C, that, in the case of GC-MS data, is compatible with the NIST MS Search compound identification software.


MSClust clusters mass peaks using two features of the ion-wise aligned data: (i) retention time of mass peaks, and (ii) similarity between mass peak abundances across samples analyzed. The unsupervised algorithm of MSClust combines: (i) a potential density method to estimate a number of putative compounds present in the data, so that no prior knowledge about the number of compounds in the data is required, and (ii) a subtractive fuzzy clustering method, which enables more efficient deconvolution of co-eluting compounds with similar mass spectra. Mass peak clusters produced are converted into a putative compound mass spectra list that in the case of GC-MS is directly compatible with the NIST mass spectra library search tool.

A single representative mass peak is selected from each putative mass spectrum based on its abundance and cluster membership, so that each putative compound extracted from the biological sample can be represented by one representative variable in further multivariate statistical analysis. Therefore a 10-fold and 100-fold data reduction can be achieved without a loss of information when processing LC-MS and GC-MS data, respectively.

MSClust software as well as a user manual can be freely downloaded from the MetAlign website: www.metalign.nl. More information about MSClust's performance was published in Tikunov et al., 2012, Metabolomics 8(4) [1].

References
  1. Tikunov YM, Laptenok S, Hall RD, Bovy A, de Vos RC. MSClust: a tool for unsupervised mass spectra extraction of chromatography-mass spectrometry ion-wise aligned data. Metabolomics. 2012 Aug;8(4):714-718. Epub 2011 Oct 15. [PMID: 22833709]


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 Bruce German of the University of California, Davis, USA.


Bruce German

 Professor in Food Science and Technology, Director, Foods for Health Institute, University of California, Davis (http://ffhi.ucdavis.edu/)
Bruce German 
Biography
Bruce German received his PhD from Cornell University, joined the faculty at the University of California, Davis in 1988, in 1997 was named the first John E. Kinsella Endowed Chair in Food, Nutrition and Health is currently Director of the Foods for Health Institute and professor, at University of California, Davis. His research interests include the structure and function of dietary lipids, the role of milk components in food and health, and the application of metabolic assessment to personalizing diet and health.

The goal of his research is to build the knowledge necessary to improve human health through personalized health measurements and foods. Research projects directed to this goal are studying how individual human lipid metabolism responds to the chemical composition and structural organization of foods. Each person has slightly different responses to diet based on their genetics, their life stage and lifestyle, their metabolism, and their nutrition status. It is thus necessary to understand the molecular basis of these differences, how to measure them and design food strategies to complement them. We are working on analytical strategies to enable individuals to monitor how their body reacts to various foods and to modify their consumption to maintain good health. With health targets established, it is the equally important task of the research to understand how to provide superior choices in foods that integrate the compositional, structural, and nutritional functionalities of biomaterials. The model being used of how to proceed is milk, the product of millennia of constant Darwinian selective pressure to produce a food to nourish, sustain, and promote healthy infant mammals to be healthier (http://www.imgconsortium.org/). Milk is the only bio-material that has evolved for the purpose of nourishing growing mammals. Survival of offspring exerted a strong selective pressure on the biochemical evolution of lactation as a bioguided process. Just as evolution of any biological organism, the strong survive, which leads to the appearance of new traits that promote health, strength, and ultimately survival. This evolutionary logic is the basis of the research program to discover physical, functional, and nutritional properties of milk components and to apply these properties as principles to foods (http://fgp.ucdavis.edu/prog/fg).

Bruce and colleagues have published more than 350 papers on lipids and food, metabolism, metabolite measurements, food functions, and patented various technologies and applications of bioactive agents. The research articles from the lab rank in the top 10 most cited in Agriculture available at www.ISIhighlycited.com and Google scholar http://scholar.google.com/citations?hl=en&user=0Zkd2dwAAAAJ. For a list of Bruce German's selected publications, please refer to http://www.metabonews.ca/Apr2013/interviews/Bruce_German/B_German_Selected_Publications.pdf.


Metabolomics Interview (MN, MetaboNews; BG, Bruce German)

MN: How did you get involved in metabolomics?

BG: We were studying lipid metabolism in humans with the goal to understanding how best to guide diets and agricultural production and it became increasingly clear that a) individual humans were different and hence a "one size fits all solution" to diet couldn't succeed, b) differences in humans could not be captured as single markers but were apparent at various points within metabolic pathways, and c) the analytical platforms necessary to measure entire subsets of metabolism were ostensibly at hand, they just had to be configured to keep track of all analytes instead of focusing on one or two. These three perspectives led us to the inescapable conclusion that we would need to measure people comprehensively and quantitatively and that surprisingly that challenge was becoming possible analytically. As we began to publish and present the approaches that we were pursuing with lipids and diet/nutrition, we began to run into a similar minded group of people advocating the measurement of comprehensive subsets of metabolites from biological samples for toxicological, pharmacological, medical, and agricultural reasons. The field of metabolomics thus seemed to emerge as more like biology dragging scientists kicking and screaming into reality, rather than scientists advancing a new way of pursuing their hypotheses. Those first meetings around metabolomics (when even the name wasn't clear) were genuinely delightful as scientists from various fields began to talk excitedly amongst each other sharing about the realization of these common themes of measuring metabolites comprehensively and quantitatively to address very disparate goals.

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

BG: The concept of measuring entire pathways of metabolites as the means to understand biology has been an enabling principle for much our research since the field crystallized many years ago. Lipid metabolism is one of the most complex areas of biology and we are continuing to develop and apply metabolomics technologies to try and understand its functions and dysfunctions and apply what we learn to diagnostics and dietary interventions. Certainly, one of the most exciting events was the decision by one of the leading innovators in metabolomics, Steve Watkins, to take the lipid metabolomics concepts from the academic laboratory and, together with Ryan Davis and Jeremy Ching from the lab, start the company Lipomics Technologies Inc. This small company that Steve built has been a major asset to the study of lipids in the academic and industrial settings ever since. The company has recently joined Metabolon and is building diagnostic platforms for a wide range of diseases and predispositions. From a more biological perspective, we have been interrogating milk and lactation with the same metabolomics approaches and toolsets. Milk has become our 'Rosetta Stone' to understand how nourishment and prevention can be achieved through diet—after all, evolution had to answer the same questions. This unifying theme—lactation—has been a powerful guide through the complexities of human health intervention through diet and metabolomics as an enabling toolset.

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

BG: The University of California, Davis is by many accounts the heart of metabolomics. With key leaders such as Bruce Hammock, Oliver Fiehn, Carlito Lebrilla, John Newman, Carolyn Slupsky, as examples of the programs creating astonishing breadth and depth of metabolomics research at UC Davis it would take books to describe all of the ongoing research here. Nonetheless, some initiatives are genuinely key to the entire field. With the recent funding of the West Coast Metabolomics Center, Oliver Fiehn is bringing metabolomics to the larger California scientific community. Bruce Hammock's remarkable assembly of the ensemble of signaling oxylipid pathways is revealing the pivotal role of epoxy lipids in physiologic signaling and guiding the development of SEH inhibitors as next generation anti-hypertensives, anti-inflammatories, and analgesics. Carolyn Slupsky's exciting work on urinary metabolites has revealed diagnostic patterns of infectious diseases and their resolution in humans. Perhaps most remarkable has been the brilliant work of Carlito Lebrilla in disassembling glycobiology as a metabolomic entirety. In a tour de force demonstration of translation, Carlito has shown that human milk contains a full spectrum of glycan metabolites as a complex class of perplexingly undigestible free oligosaccharides. In gorgeous parallel collaborative research, David Mills, an inspiring and innovative microbial ecologist, has documented that these oligosaccharides are digestible only by a rare group of bifidobacteria species whose genomes provide a dazzling array of genes beautifully matched to the enzymatic disassembly of milk's oligosaccharide linkages. If the exquisite evolutionary relationship between oligosaccharide metabolism of mothers with the metabolic capability of the uniquely beneficial bacteria that colonize and dominate their breast-fed babies doesn't warm your heart, you have no future in metabolomics! As proof of principle, Neonatologist Mark Underwood is using the evolutionary strategy of combining human milk oligosaccharides and the infant-isolated Bifidobacteria to test if he can effectively colonize and protect the premature infants in the neonatal intensive care unit at the University Hospital. A dynamic young group of investigators are now extending this work in various directions; Angela Zivkovic into lipid metabolism, Jennifer Smilowitz gestational diabetes, and Daniela Barile into oligosaccharide biology are just a few of the exciting initiatives that are taking metabolomics principles to address diet and health.

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

BG: The tools of metabolomics are beginning to inform translation into various applications from diagnostics to interventions, but the over-arching theme that we see is to bring a more individual approach to health and diet, i.e., personalization. Once again, milk and lactation have been inspiring. We have learned that milk is: personal, active, dynamic, and structured, in ways that we never would have imagined. It is clear that the future of health and diet will be much more personal and immediate. Bringing such an individual approach to practice will require that people are measured more accurately and more often. This means for us scientifically, that we have to understand metabolism well enough to know what to measure, when, where, and how accurately, in order to predict variations in individual health. Only metabolomics approaches are able to bring the combination of comprehensive coverage, chemical identity, and quantitative accuracy to guide the selection of targets for personal health 'diagnostics'. Similarly metabolomics is bringing the same comprehensive analysis and biological interpretation to describe diets in detail. However much the media enjoys demonizing some foods and lionizing others, the truth is that nothing about health is interpretable, much less solvable, without quantitative estimates of individual metabolic needs and input dosages. Metabolomics will guide a revolution in food analysis as the knowledge base of personal diets.

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

BG: To me the greatest strength of metabolomics is the basic idea of integrating biology into measured, interpreted metabolic systems rather than attempting to reduce it into single components. While genomics and proteomics certainly share this integrative view of biology, theirs is a more static and predictive view of biology, while metabolomics is genuinely a dynamic and immediate view of life as it functions. Nonetheless, as a field, metabolomics is just a baby. The practice of metabolomics is still assembling the basic analytical toolsets and we have made discouragingly little progress in matching analysis of metabolites with the computational mapping of those metabolites to pathways and the much more relevant and exciting process of annotating variations in quantities of metabolites to actual processes, functions, and dysfunctional states. The strengths of the toolsets to date are the increasingly accurate and sensitive analytical platforms to measure large numbers of metabolites, the libraries of different metabolites being constructed around the world from these platforms, and the robotic capabilities to achieve high throughput. We are beginning to see the future in which metabolomics platforms can address our great questions.

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?

BG: The greatest barrier is computation. The field has achieved great success in measuring metabolites and we now need to bring computational tools to interpret them—automatically. We are like the world wide web without search engines, lots of data, no ways to turn it into information and knowledge. I am optimistic that we are close, but realistically we need to recruit some very innovative minds to the challenge of building comprehensive, dynamic models of metabolism. It shouldn't be that difficult, after all, Google converts the roads in every city into a dynamic, quantitative traffic system in real time! The other barriers are largely our inability to interrogate biology in the structural complexity at which it functions. If I take our particular barriers in lipids, the biological membrane is clearly far more complex and diverse than the simple models of a homogeneous fluid bilayer. Without tools to examine this complexity at the length scale at which it functions, metabolomics at best can only provide a crude average composition of entire pools of membranes. Even the most obvious particles of lipids are difficult to isolate in meaningful integrity: HDL (high-density lipoprotein), one of the most attractive lipid 'domains' for study, cannot be routinely broken up into the functional diversity that we already know exists. The field of nanoscience would add greatly to the progress of metabolomics both in descriptive and mechanistic research, and in applications from diagnostics to surveillance.

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

BG: Given the increasingly competitive funding environment for science in general, metabolomics ought to be in a relatively advantageous position because of the breadth of the fields it impacts, the pragmatic relevance of those fields and the translational opportunities to improve human health and safety. Nonetheless, scientists in this field should be constantly looking to build the collaborations across disciplines that bring metabolomics to practice. As a field, metabolomics has great strength in chemistry and analytics and it is now time to realize its potential for growth in applications across the biological disciplines. Although we don't tend to think of metabolomics in a modular sense, future growth, particularly into funding opportunities in larger programmatic projects, can take advantage of metabolomics if we diversify into modules. This strategy is proving to be valuable in several programs around the United States.

 MN: What role can metabolomics standards play?

BG: As a user and developer in the field, I would wholeheartedly endorse a formalized initiative on metabolomics standard development and validation. Having said that, I am very aware of the investment that will be required to get there and the difficulty of obtaining that investment with current funding constraints. Again in my opinion, now is the time, when the field is relatively small and manageable, that this aspect of analytical precision and accuracy can be achieved. In our own areas of research and application for example, quantitation of metabolites is absolutely essential to the entire value proposition of the approach. This simply cannot be achieved in the platforms available without standards. For mass spectrometry this means not only quantitative standards of metabolites themselves but that at least a subset are selectively and quantitatively enriched with stable isotopes. Perhaps an industrial consortium could be assembled to address this enabling opportunity for the entire field.

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

BG: I would very much like to see the field of metabolomics serve as a conceptual model of biology for educating students at their earliest exposures to science. With young minds thinking in ways that only they can, the challenges of informatics, visualization of pathways, and interpretation of pathways as integrating systems can be solved by the next generation of scientists who will truly change human health potential. Just as the genetic code is our truly universal language, metabolism is our universal music. Let's teach the next generation of young scientists how to play.
Biomarker Beacon

3) Biomarker Beacon

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


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

In the following two recent studies, metabolomic approaches were used to develop tools for the identification of biomarkers associated with Alzheimer's disease and pediatric septic shock, respectively.
  1. Fukuhara K, Ohno A, Ota Y, Senoo Y, Maekawa K, Okuda H, Kurihara M, Okuno A, Niida S, Saito Y, Takikawa O. NMR-based metabolomics of urine in a mouse model of Alzheimer's disease: identification of oxidative stress biomarkers. J Clin Biochem Nutr. 2013 Mar;52(2):133-8. doi: 10.3164/jcbn.12-118. Epub 2013 Mar 1. [PMID: 23526113]

    In this paper, the research team sought to identify novel biomarkers for Alzheimer's disease (AD) using a mouse model. The investigators used nuclear magnetic resonance-based metabolomics coupled with multivariate statistics to evaluate urine samples from transgenic AD mice expressing mutant tau and β-amyloid precursor protein. The authors of this study discovered that three oxidative stress biomarkers, 3-hydroxykynurenine, homogentisate, and allantoin, were present at significantly higher levels in AD mice compared to control mice. These metabolites may serve as key biomarkers in the early-stage assessment of risk for developing AD.

  1. Mickiewicz B, Vogel HJ, Wong HR, Winston BW. Metabolomics as a Novel Approach for Early Diagnosis of Pediatric Septic Shock and its Mortality. Am J Respir Crit Care Med. 2013 Mar 7. [Epub ahead of print] [PMID: 23471468]

    A reliable early-stage diagnostic for pediatric septic shock (PSS) could help reduce morbidity and mortality in children. In this study, the researchers used 1H-NMR to identify serum biomarkers for PSS. The investigators looked at three patient groups (60 septic shock patients, 40 pediatric intensive care unit patients with systemic inflammatory response syndrome, and 40 healthy children) and discovered three metabolites that were significantly elevated in septic patients compared to healthy controls: 2-hydroxybutyrate, 2-hydroxyisovalerate, and lactate. These metabolite biomarkers could help advance the development of an early-stage diagnostic for septic shock in children.
Metabolomics Current Contents

4) Metabolomics Current Contents

Recently published papers in metabolomics:
MetaboNews

5) MetaboNews
Winter 2013
Alberta Innovates Food for Thought

Dr. David Wishart and his research team are analyzing the micronutrients of more than 70 Alberta foods to help both consumers and producers
It’s a familiar refrain many health-conscious people take to heart: “You are what you eat.” But, what exactly are you eating?

Legislated food labels offer basic information, such as calories, grams of fat, and fibre, but many of the chemical constituents of food that affect our health aren’t included. Micronutrients—amino acids, phytosterols, anti-oxidants, and omega-3 fatty acids, for instance—aren’t included on packaging. Dr. David Wishart, a researcher with the University of Alberta’s Biological Sciences and Computing Sciences departments, thinks this information should be readily available to everyone. “Food isn’t just a source of calories. It can be used to enhance health and prevent diseases. I think that’s been largely forgotten,” he says.

His latest research project, funded by an Alberta Innovates Bio Solutions’ Quality Food for Health grant, promises to change this. Dr. Wishart’s team has been awarded $500,000 over the next three years to analyze the chemical constituents in about 70 Alberta foods. In addition to micronutrients, he will examine the compounds that give foods their taste and colour. “Those are things that are obviously important to what we choose and why we buy certain foods,” he says. “Hopefully, it will help us understand what makes food taste good and why.”

Even though the project focuses only on Alberta-produced foods (like cereal crops, pulses, beef, vegetables, fruit, poultry, and cheese), the project is an ambitious undertaking. Each food has a unique combination of about 3,000 to 5,000 chemical compounds. But this doesn’t faze Dr. Wishart, who is known internationally for his work on the human metabolome project, which catalogued and characterized 19,000 metabolites, 1,500 drugs, and 18,000 food components found in the human body.

Eventually, the data Dr. Wishart’s team is gathering will be placed in the FoodDB online database, which will be accessible to consumers, producers, food testing agencies, healthcare providers, and other professional users. However, the primary users will be Albertan consumers (to help them make more educated food-buying decisions) and local producers (to assist in marketing the health benefits of their products). “It’ll have pictures of raw foods and detailed information on their chemical compositions,” he says. “People can read about the health effects of different foods, too.”

The research will also be communicated via another website geared solely toward the general public, which will include food fact sheets highlighting information about certain key foods. “That’ll be aimed at the public and not very scientific, but colourful and accessible,” says Dr. Wishart. He also hopes to reach out to producers and see if they’d be open to putting QR codes on their products, which allow consumers to scan labels at a grocery store with their smart phones and quickly link to useful nutritional information on the producer’s website. “We’d like to reach out and make use of the web and modern technology so people can get informed about what they’re eating and buying.”
 
29 Mar 2013
New Metabolite-Based Diagnostic Test Could Help Detect Pancreatic Cancer Early

A new diagnostic test that uses a scientific technique known as metabolomic analysis may be a safe and easy screening method that could improve the prognosis of patients with pancreatic cancer through earlier detection.

Researchers examined the utility of metabolomic analysis as a diagnostic method for pancreatic cancer and then validated the new approach, according to study results published in Cancer Epidemiology, Biomarkers & Prevention, a journal of the American Association for Cancer Research.

"Although surgical resection can be a curative treatment for pancreatic cancer, more than 80 percent of patients with pancreatic cancer have a locally advanced or metastatic tumor that is unresectable at the time of detection," said Masaru Yoshida, M.D., Ph.D., associate professor and chief of the Division of Metabolomics Research at Kobe University Graduate School of Medicine in Kobe, Japan. "Conventional examinations using blood, imaging and endoscopy are not appropriate for pancreatic cancer screening and early detection, so a novel screening and diagnostic method for pancreatic cancer is urgently required."

Using gas chromatography mass spectrometry, the researchers measured the levels of metabolites in the blood of patients with pancreatic cancer, patients with chronic pancreatitis and healthy volunteers. They randomly assigned 43 patients with pancreatic cancer and 42 healthy volunteers to a training set and 42 patients with pancreatic cancer and 41 healthy volunteers to a validation set. They included all 23 patients with chronic pancreatitis in the validation set.

Analysis of the metabolomic data generated from the training set indicated that levels of 18 metabolites were significantly different in the blood of patients with pancreatic cancer compared with the healthy volunteers. Further investigation led the researchers to develop a method to predict a pancreatic cancer diagnosis using assessment of the levels of just four metabolites. In the training set, the approach demonstrated 86 percent sensitivity and 88.1 percent specificity. When tested again in the validation set, which included patients with chronic pancreatitis, the method demonstrated 71.4 percent sensitivity and 78.1 percent specificity.

"Our diagnostic approach using serum metabolomics possessed higher accuracy than conventional tumor markers, especially at detecting the patients with pancreatic cancer in the cohort that included the patients with chronic pancreatitis," Yoshida said. "This novel diagnostic approach, which is safe and easy to apply as a screening method, is expected to improve the prognosis of patients with pancreatic cancer by detecting their cancers early, when still in a resectable and curable state."

 
18 Mar 2013
New Partnership between AB SCIEX and LECO Corporation - Offering Combined Solutions for GC/MS and LC/MS

LECO Corporation, a global leader in accurate mass technologies and GC/MS instrumentation, and AB SCIEX, a global leader in LC/MS technology, have announced a co-marketing agreement to cooperatively offer bundled liquid chromatography (LC) and gas chromatography (GC) mass spectrometry-based solutions to metabolomics researchers who require both types of separation capabilities.

Metabolomics researchers often require the use of both GC/MS and LC/MS technologies to provide comprehensive coverage of the analytes in their biological systems as part of the Systems Biology approach. The new AB SCIEX/LECO bundled solutions will provide these researchers with high speed, accurate mass capabilities with LC and GC, along with robust nominal mass GC/MS and triple quadrupole mass spectrometry.

Researchers will have at their disposal pairings of time-tested nominal mass systems as well as industry-leading high performance GC-TOF and LC-QTOF MS systems.  The application support and service teams of both companies will work together to ensure that users get the support they need to run their comprehensive experiments. 

“As the industry leader in LC/MS, we interact with metabolomics researchers all over the world, and we understand that there are times when metabolomics researchers want to use both GC/MS and LC/MS,” said Aaron Hudson, Senior Director, Academic and Omics Business.  “Representing a virtual one-stop shop for metabolomics mass spectrometry, the joint bundles from AB SCIEX and LECO provide users with greater flexibility in chromatography while obtaining the rich information that MS/MS delivers.”

“Bringing together leaders in GC/MS and LC/MS and facilitating the availability of our systems as complementary technologies helps ensure that metabolomics researchers can approach their work  to obtain the very best data and information available,” said Jeffrey Patrick, Director of Marketed Technologies for LECO. “Our leadership in GC/MS technologies is a perfect complement to the offerings of AB SCIEX and puts the combined power of our product portfolios, expertise, services, and support to work for these researchers.” 

The joint bundles from AB SCIEX and LECO will be available in North America and Europe.

Source: AZoM.com

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
8-10 Apr 2013

2nd International Conference and Exhibition on Metabolomics & Systems Biology
Venue: Hilton Suites Chicago/Northbrook, USA

OMICS Group invites you to attend the 2nd International Conference and Exhibition on Metabolomics & Systems Biology which is going to be held during April 08-10, 2013 at Hilton Suites Chicago/Northbrook, USA.

Metabolomics-2013 is a remarkable event which brings together a unique and International mix of large and medium pharmaceutical, biotech and diagnostics companies, leading universities and clinical research institutions making the conference a perfect platform to share experience, foster collaborations across industry and academia, and evaluate emerging technologies across the globe.

2nd International Conference and Exhibition on Metabolomics & Systems Biology will serve as a catalyst for the advances in the study of Metabolomics & Systems Biology by connecting scientists within and across disciplines at sessions and exhibition held at the venue, creates an environment conducive to information exchange, generation of new ideas, and acceleration of applications that benefit research in Metabolomics & Systems Biology.

For more information, visit http://omicsgroup.com/conferences/metabolomics-systems-biology-2013/.
14-19 Apr 2013

54th ENC Conference
Venue: Asilomar Conference Grounds, Pacific Grove, California, USA

Come immerse yourself in cutting-edge NMR science at the beautiful Asilomar conference grounds by the sea!
  • Jan 11, 2013: Deadline for abstracts to be considered for short talks and early decision.
  • Jan 11, 2013: Deadline for student travel and Ritchey Award materials
  • March 8, 2013: Deadline for late poster abstracts
  • March 15, 2013: Deadline for Asilomar lodging and advance conference registration
General Information: http://enc-conference.org/Conference/GeneralInformation/tabid/144/Default.aspx
Preliminary Program: http://www.enc-conference.org/ConferenceDetails/Program/tabid/63/Default.aspx

For more information, visit http://www.enc-conference.org/.
13-14 May 2013

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

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

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

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

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

Two educational sessions are scheduled  for the PhD students.

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

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

For more information, visit http://www.metabolomicscentre.nl/news/first-belgian-netherlands-joint-symposium-metabolomics-translational-approaches-metabolomics-sp?goback=%2Egde_2414599_member_224905745.
1-7 June 2013

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

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

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

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

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

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

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

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

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

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

We look forward to welcoming you to Glasgow in 2013!

Dave Watson
Chair, Local Organising Committee
Metabolomics Glasgow 2013

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

3rd European Lipidomic Meeting
Venue: Pardubice, Czech Republic

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

For more information, visit http://mab.uochb.cas.cz/iochb/ELM2013/.
4-5 Jul 2013

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

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

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

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

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

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

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
Postdoc for ‘simultaneous’ Quantitative & Qualitative metabolomics
 Leiden University
 Leiden, Netherlands 1-Apr-2013 8-Apr-2013 naturejobs.com
MS Based Metabolomics Position
 University of Colorado at Boulder
 Aurora, CO, United States 29-Mar-2013 15-Apr-2013 naturejobs.com
Conference Liaison and Administrative Coordinator
 Metabolomics Society
 Charleston, SC, United States 27-Mar-2013 1-May-2013 naturejobs.com
Lecturer in Metabolomics or Applied Mass Spectrometry
 University of Manchester
 Manchester, United Kingdom 27-Mar-2013 26-Apr-2013 naturejobs.com
Scientist / Specialist Mitochondrial Function
 The Nestlé Institute of Health Sciences
 Lausanne, Switzerland 25-Mar-2013 24-May-2013 naturejobs.com
Postdoctoral Fellowship in Diabetes Research – Metabolomics and Proteomics
 Lund University Malmö, Sweden 11-Mar-2013 12-Apr-2013 naturejobs.com
Omics Data Analyst
 The Nestlé Institute of Health Sciences Lausanne, Switzerland 7-Mar-2013 7-May-2013 naturejobs.com
Metabolomics / Lipidomics Analyst
 The Nestlé Institute of Health Sciences Lausanne, Switzerland 7-Mar-2013 7-May-2013 naturejobs.com
PhD studentship in parasite metabolomics
 INRA center of Toulouse (French National Institute for Agricultural Research) Toulouse, France 2-Mar-2013 11-Apr-2013
 naturejobs.com
Sales Representative / Business Developer (m/f)
 Metabolomic Discoveries GmbH Potsdam, Germany
 27-Feb-2013
metabolomicdiscoveries.com
Internship/Thesis: Development of suitable plugins for the knowledge base
 Metabolomic Discoveries GmbH Potsdam, Germany
 27-Feb-2013
metabolomicdiscoveries.com


Jobs Wanted

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


General Notices
  • The Metabolomics Society is seeking support to help to grow and manage the business of the Society. While the planning and running of the annual international conference is of high priority, many other administrative tasks require support as detailed in the ‘call for response’ documents. To request these documents, please contact treasurer@metabolomicssociety.org for more information.

    Responses using the standardized Response Form (provided upon request) should be submitted before May 1, 2013.

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