Issue 20 - April 2013
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1) Software Spotlight
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
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
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
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) .
|| Professor in
Food Science and Technology, Director, Foods for Health
Institute, University of California, Davis (http://ffhi.ucdavis.edu/)
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.
3) Biomarker Beacon
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.
6) Metabolomics Events
|8-10 Apr 2013||
Conference and Exhibition on Metabolomics
& Systems Biology
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
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||
Joint symposium on Metabolomics: Translational
approaches in metabolomics - Spa, Belgium
“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’”.
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
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
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!
Chair, Local Organising Committee
Metabolomics Glasgow 2013
For more information, visit http://www.metabolomics2013.org/.
|2-4 Jul 2013||
3rd European Lipidomic
For more information, visit http://mab.uochb.cas.cz/iochb/ELM2013/.
|4-5 Jul 2013||
Informatics and Statistics
for Metabolomics (2013)
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 firstname.lastname@example.org 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
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
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.
The three day event will bring together international experts in nutrition, genomics, bioinformatics and milk research to discuss and share the latest breakthroughs and their implications.
The Annual Symposium is our flagship event that features scientific research related to milk and human health done throughout the world. The symposium draws from the diversity of its memberships to cover the breath of genomics themes that reflect the interest of the Consortium. The goal of the Consortium is to bring together the research and dairy communities to share, translate, and interpret data that are happening within the fields of the "-omics" science.
For more information, visit http://milkgenomics.org/symposia/the-10th-international-symposium-on-milk-genomics-and-human-health-october-1-3-2013.
7) 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 (email@example.com).
Job postings will be carried for a maximum of 4
issues (8 weeks) unless the position is filled prior to
for ‘simultaneous’ Quantitative & Qualitative
Based Metabolomics Position
||University of Colorado at
||Aurora, CO, United States||29-Mar-2013||15-Apr-2013||naturejobs.com|
Liaison and Administrative Coordinator
||Charleston, SC, United States||27-Mar-2013||1-May-2013||naturejobs.com|
in Metabolomics or Applied Mass Spectrometry
||University of Manchester
||Manchester, United Kingdom||27-Mar-2013||26-Apr-2013||naturejobs.com|
/ Specialist Mitochondrial Function
||The Nestlé Institute of
Fellowship in Diabetes Research – Metabolomics and
||Lund University||Malmö, Sweden||11-Mar-2013||12-Apr-2013||naturejobs.com|
||The Nestlé Institute of Health Sciences||Lausanne, Switzerland||7-Mar-2013||7-May-2013||naturejobs.com|
/ Lipidomics Analyst
||The Nestlé Institute of Health Sciences||Lausanne, Switzerland||7-Mar-2013||7-May-2013||naturejobs.com|
studentship in parasite metabolomics
||INRA center of Toulouse (French National Institute for Agricultural Research)||Toulouse, France||2-Mar-2013||11-Apr-2013
Representative / Business Developer (m/f)
||Metabolomic Discoveries GmbH||Potsdam, Germany
Development of suitable plugins for the knowledge
||Metabolomic Discoveries GmbH||Potsdam, Germany
Ian J. Forsythe, M.Sc.MetaboNews
Department of Computing Science
University of Alberta
221 Athabasca Hall
Edmonton, AB, T6G 2E8, Canada
This newsletter is produced by The Metabolomics Innovation Centre (TMIC, http://www.metabolomicscentre.ca/) for the benefit of the worldwide metabolomics community.
A single source destination for fee-for-service metabolic profiling including comprehensive metabolite identification, quantification, and analysis