Issue 9 - April 2012


Online version of this newsletter:

Welcome to the ninth issue of MetaboNews, a monthly newsletter for the worldwide metabolomics community. In this month's issue,
we feature a Software Spotlight article on YMDB, the Yeast Metabolome Database. This newsletter is being produced by The Metabolomics Innovation Centre (TMIC,, 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 (

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Software/Stat Spotlight

1) Software Spotlight

YMDB Banner

YMDB: Yeast Metabolome Database

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

The Yeast Metabolome Database (YMDB, is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast) (Figure 1). This database covers metabolites described in textbooks, scientific journals, metabolic reconstructions, and other electronic databases. YMDB contains metabolites arising from normal S. cerevisiae metabolism under defined laboratory conditions as well as metabolites generated by S. cerevisiae when used in baking and in the production of wines, beers, and spirits. YMDB currently contains 2002 small molecules with 857 associated enzymes and 138 associated transporters. Each small molecule has 48 data fields describing the metabolite, its chemical properties, and links to spectral and chemical databases (Figure 2). Each enzyme/transporter is linked to its associated metabolites and has 30 data fields describing both the gene and corresponding protein.

YMDB home page

Figure 1.
From the YMDB home page, users can search the database using the search box near the top of the page. In this example, the user conducts a search for glucose-6-phosphate.

Each MetaboCard contains 48
        data fields

Figure 2. Shown here are some of the data fields for glucose-6-phosphate. Each MetaboCard contains 48 data fields describing the metabolite, its chemical properties, and links to spectral and chemical databases.

Users may search through the YMDB using a variety of database-specific tools. The simple text query box, that appears at the top of virtually every page, supports general text queries of the textual component of the database. By selecting either metabolites or proteins in the “search for” field it is possible to restrict the search and the returned results to only those data associated with metabolites or with proteins. Clicking on the Browse button (on the navigation panel that appears at the top of every YMDB page) generates a tabular synopsis of YMDB's content (Figure 3). This browser view allows users to casually scroll through the database or re-sort its contents. Clicking on a given MetaboCard button brings up the full data content for the corresponding metabolite. A complete explanation of all the YMDB fields and sources is given here. Under the Search link (on the navigation panel) users will find a number of search options listed in a pull-down menu. The Chem Query option allows users to draw (using MarvinSketch applet or a ChemSketch applet) or to type (SMILES string) a chemical compound and to search the YMDB for chemicals similar or identical to the query compound. The Advanced Search option supports a more sophisticated text search of the text portion of YMDB. The Sequence Search button allows users to conduct BLASTP (protein) sequence searches of all sequences contained in YMDB. Both single and multiple sequence (i.e., whole proteome) BLAST queries are supported. YMDB also supports a Data Extractor option that allows specific data fields or combinations of data fields to be searched and/or extracted. Spectral searches of YMDB’s reference compound NMR and MS spectral data are also supported through its MS, MS/MS, GC/MS, and NMR Spectra Search links. Users may download YMDB’s complete textual data, chemical structures, and sequence data by clicking on the Download button.

Clicking on the Browse button generates a tabular
          synopsis of YMDB's content

Figure 3.
Clicking on the Browse button generates a tabular synopsis of YMDB's content, allowing users to casually scroll through the database or re-sort its contents by YMDB ID, Name, IUPAC Name, or Formula Weight.

Please let the YMDB authors know what you would like to see in future versions of YMDB. Your feedback and suggestions are very helpful and help to improve YMDB's overall quality and usefulness. Please email your feedback and suggestions to the YMDB authors.

The YMDB is supported by:

Citing YMDB

YMDB is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (YMDB) and the original publication (see below). The YMDB authors ask that users who download significant portions of the database cite the YMDB paper in any resulting publications.

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

Biomarker Beacon

2) 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 metabolomics 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, metabolomics approaches were used to develop biomarker tools for the identification of biomarkers associated with jaundice syndrome and high-altitude pulmonary edema, respectively.
  1. Wang X, Zhang A, Han Y, Wang P, Sun H, Song G, Dong T, Yuan Y, Yuan X, Zhang M, Ning X, Zhang H, Dong H, Dong W. Urine metabolomics analysis for biomarker discovery and detection of jaundice syndrome in patients with liver disease. Mol Cell Proteomics. 2012 Apr 13. [Epub ahead of print] [PMID: 22505723]

    In this paper, the research team used a UPLC-Q-TOF-HDMS (ultra performance liquid chromatography quadrupole time-of-flight high definition mass spectrometer) to identify urine biomarkers for jaundice syndrome (JS) in patients with liver disease. Current diagnostic methods do not accurately detect JS in patients with liver disease and little is known about overall metabolomic changes that occur during JS progression. This research group identified 44 metabolites that permit differentiation of JS patients from healthy patients. In JS patients, the following metabolic pathways were perturbed: glutamate, aspartate, and alanine metabolism, and ketone body synthesis and degradation. These identified metabolites may prove to be useful in the development of a non-invasive diagnostic for JS in patients with liver disease.

  1. Luo Y, Zhu J, Gao Y. Metabolomic analysis of the plasma of patients with high-altitude pulmonary edema (HAPE) using (1)H NMR. Mol Biosyst. 2012 Apr 12. [Epub ahead of print] [PMID: 22498880]

    In this study, the researchers identified plasma biomarkers of patients with high-altitude pulmonary edema (HAPE) using a metabolomics-based approach. Due to a lack of a reliable biomarker, it is currently difficult to perform early diagnosis of patients with HAPE. The research team used (1)H NMR to compare metabolic patterns in 10 patients with HAPE and 10 patients without HAPE. In HAPE patients, while valine, lysine, leucine, isoleucine, glycerol phosphoryl choline, glutamine, glycine, glutamate, creatinine, citrate, and methyl histidine were found at significantly increased levels, alpha- and beta-glucose, trimethylamine, and lipid metabolic products were detected at decreased levels. These initial findings could aid in the development of an early-stage diagnostic for HAPE and shed light on HAPE pathogenesis.

Metabolomics Current Contents

3) Metabolomics Current Contents

Recently published papers in metabolomics:


4) MetaboNews

23 Apr 2012

Cancer Metabolomics: Elucidating the Biochemical Programs that Support Cancer Initiation and Progression [Meeting Review]

Meeting Overview
In the early part of the 20th century, German biochemist Otto Warburg observed that tumor tissues and normal tissues metabolize glucose differently. Instead of relying on the citric acid cycle to extract maximal energy from a molecule of glucose, tumor cells rapidly convert glucose to lactate through glycolysis even when oxygen is abundant.

Known as the Warburg effect, this observation sits at the core of the field now known as cancer metabolomics. But for many years after Warburg's observation, scientists focused on separate mechanisms of oncogenesis without considering that these metabolic differences could drive the formation of new cancers or could speed their growth. More recently, cancer researchers have recognized that these metabolic changes help cancer cells build the macromolecules that support the rapid growth and proliferation of tumors.

Organized by Stephen S. Gross of Weill Cornell Medical College and Jennifer Henry of the Academy, the Cancer Metabolomics: Elucidating the Biochemical Programs that Support Cancer Initiation and Progression symposium held on February 3, 2012, is the latest in a series of meetings about cancer metabolomics. In an initial keynote address, Craig Thompson of Memorial Sloan Kettering Cancer Center gave an overview of the field and of the emerging links between oncogenic and metabolic pathways. Gary Siuzdak of Scripps Research Institute described metabolomics tools and the process of finding new cancer metabolites. As one slice of her research on sirtuin enzymes, Marcia Haigis of Harvard Medical School outlined how mitochondrial forms of these enzymes may be involved in cancer growth and proliferation. Joshua Rabinowitz of Princeton University explained fatty acid metabolism in cancer cells, and Eileen White of the Cancer Institute of New Jersey described autophagy in cancer cells. In a second keynote talk, Lewis Cantley of Beth Israel Deaconess Medical Center and Harvard Medical School discussed biochemical research to understand metabolic signals in cancer. In the final talk, Steven Lipkin of Weill Cornell Medical College described research linking the mechanisms of the primary chemotherapy in colorectal cancer, 5-fluorouracil, and a drug being tested for chemoprevention, difluoromethylornithine.

Presentations available from:
Lewis C. Cantley, PhD (Beth Israel Deaconess Medical Center and Harvard Medical School)
Marcia C. Haigis, PhD (Harvard Medical School)
Steven M. Lipkin, MD, PhD (Weill Cornell Medical College)
Joshua D. Rabinowitz, PhD (Princeton University)
Gary Siuzdak, PhD (The Scripps Research Institute, California)
Craig Thompson, MD (Memorial Sloan-Kettering Cancer Center)

23 Apr 2012

Warwick researchers solve 40-year-old Fourier Transform Mass Spectrometry phasing problem - Scientists at the University of Warwick have developed a computation which simultaneously doubles the resolution, sensitivity and mass accuracy of Fourier Transform Mass Spectrometry (FTMS) at no extra cost.

Researchers in the University’s Department of Chemistry have solved the 40-year-old phasing problem which allows plotting of spectra in absorption mode.

This breakthrough can be used in all FTMS including FT-ICR, Orbitrap and FT-TOF instruments and will have applications in proteomics, petroleum analysis, metabolomics and pharmaceutical analysis among other fields.

Professor Peter O’Connor, who co-developed the method, said: “We have vastly improved the quality of data available at no extra cost.

"FTMS is used extensively in the fields of pharmaceuticals, healthcare, industry, natural resources and environmental management so this breakthrough represents a real step towards improving research across the board in these areas."

The method is detailed in the study Absorption-Mode: The Next Generation of Fourier Transform Mass Spectra published in the journal Analytical Chemistry.

It is co-authored by Professor O’Connor, Yulin Qi, Mark Barrow and Huilin Li from the University of Warwick.

10 Apr 2012

Metabolon Launches Strategic Outsourcing Programs Focused on Disease Metabolism - Metabolon, Inc., a diagnostics and services company offering the industry’s leading biochemical profiling technology, announces the launch of its Disease Metabolism Strategic Outsourcing Program.

Through this program, Metabolon’s partners will collaborate toward shared objectives such as identifying novel targets, establishing high resolution phenotypic screening platforms, elucidating drug mechanism of action, discovering and validating pharmacodynamic biomarkers for translation to the clinic and for patient stratification. Partners will have access to dedicated scientific, technical and IT staff at Metabolon, along with the company’s proprietary disease ontologies, as well as supporting visualization tools for the integration of metabolomics data with existing or data derived from such disciplines as genomics and proteomics.

John Ryals, Metabolon President and CEO, said, "We are excited to launch our Strategic Outsourcing Program as it represents a step change in the way the industry will think about and use metabolomics. This initiative results from years of research and development at Metabolon and has been requested by our industrial clients to fully exploit the potential of our platform. We believe that integrating metabolomic profiling deeply at the various stages of the R&D trajectory will lead to better targets, higher quality molecules, faster time to the clinic and reduced R&D risk and cost."

Metabolon has completed hundreds of projects including those in oncology and metabolic disorders, and has acquired vast institutional knowledge of the metabolic pathways and targets that are involved in the onset of disease and its progression. This new program offers a turnkey metabolism center of excellence that provides pharmaceutical and biotech partners access to the most advanced metabolomics research platforms, which serve to enhance their drug discovery and development efficiency. Metabolon’s platform yields actionable insight into key disease metabolic processes, drug action, and patient response.

Source: MarketWatch

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

Metabolomics Events

5) Metabolomics Events

3-4 May 2012

Canadian Bioinformatics Workshops: Informatics and Statistics for Metabolomics
Venue: Toronto, Ontario, Canada
Lead Faculty (2012): David Wishart
Registration Fee for Applications received before April 4, 2012: $500 + HST
Registration Fee for Applications received after April 4, 2012: $700 + HST
There are travel and registration awards available for students - Apply now!

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 for more information.

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.

Register now as space is limited to 30 participants.

7-8 May 2012

LIPID MAPS Annual Meeting 2012: Lipidomics Impact on Cell Biology, Metabolomics and Translational Medicine
Venue: La Jolla, CA, USA

This is an exciting time for the emerging field of lipidomics. With the development and evolution of sophisticated mass spectrometers linked to highly efficient liquid chromatography systems, individual molecular species of lipids can now be isolated and identified, allowing us to begin to understand lipid metabolism and the treatment of lipid-based diseases (atherosclerosis and inflammatory disease as well as arthritis, cancer, diabetes and Alzheimer's disease). Recent awareness that each category of lipid consists of thousands if not tens of thousands of individual molecular species requires sophisticated informatics to ensure consistent databasing and annotation of the numerous lipid molecular species and analysis of tremendous quantities of experimental data. The goal of this meeting is to bring together biological and biomedical scientists in a wide range of fields to share new findings and methods in the broader lipidomics field and to explore joint efforts to extend the use of these powerful new methods to new applications. Presentations will provide an excellent introduction for scientists new to these methods, and are sure to be of interest to lipidomics veterans to learn about latest techniques and research results.
The meeting program tentatively features the following six sessions:
  • Cancer
  • Inflammation
  • Macrophage Biology
  • Metabolic Disease
  • Metabolomics
  • Translational Medicine
For more information, please visit

20-24 May 2012

60th ASMS Conference on Mass Spectrometry and Allied Topics
Venue: Vancouver, BC, Canada

The conference and short courses will be held at the Vancouver Convention Centre, 1055 Canada Place, Vancouver, BC V6C 0C3, Canada.  All oral sessions, poster sessions, exhibit booths, and corporate hospitality suites will be located in the Convention Centre.

21-23 May 2012

Les 6èmes Journées Scientifiques du Réseau Français de Métabolomique et Fluxomique (JS 6 RFMF)
Venue: Nantes, France

The 6th Scientific Days of the French Network of Metabolomics and Fluxome will be held in Nantes from 21 May 2012 to May 23, 2012, organized by the platform Corsaire, the platform of Metabolomics Biogenouest. Corsair includes eight technical support centers located throughout Western France (Brest, Nantes, Rennes, and Roscoff).
The main topics selected for JS 6 RFMF are:

  • Applications of metabolomics and fluxomics in the areas of the sea, agronomy and health.
  • Technological developments, bioinformatics, and statistical processing

For more information, please visit

18-21 June 2012

Shortcourse: Metabolic Phenotyping in Disease Diagnosis & Personalised Health Care
Venue: Imperial College London, London, UK

We are organising a metabolic profiling short course at Imperial College London with Profs. Nicholson and Holmes.
The course will be held on the 18th-21st June, 2012.

25-28 June 2012

METABOLOMICS 2012: Breakthroughs in plant, microbial and human biology, clinical and nutritional research, and biomarker discovery
Venue: Washington Marriott Wardman Park Hotel, Washington, DC, USA

The annual meeting of the Metabolomics Society brings together metabolomics researchers from around the world to discuss their most recent achievements as they work to harness the power of metabolomics. Gathering together in a hospitable venue is key to developing the collegial interactions that can build a successful community that advances together.
The 2012 meeting promises a program full of practical workshops and parallel sessions covering the broad range of biological and technological metabolomics topics as well as providing rich opportunities for networking. Join us as we gather together to share ideas, insights, advances and obstacles in the multi-faceted world of metabolomics.

For more information, please visit

10 July 2012

Merck Deep Dive: Translational Technologies for Basic and Clinical Scientists
Venue: Ocean Place Resort and Spa, Long Branch, New Jersey, USA

Join us for another in this quarterly unique series that brings together about 150 Merck subject experts and key vendors. Sponsors and Exhibitors can display products and services to a very focused set of the Merck community leaders. Select exhibitors are given an opportunity to privately present upcoming product development and get instant feedback from Merck on where they would like to see development go to meet their upcoming needs. Topic for this event: Translational Technologies for Basic and Clinical Scientists. Molecular BioMarkers (Proteomics/Genomics/Metabolomics) is a key part of this event.

28-31 Aug 2012

NuGOweek 2012 (9th Edition): “Nutrition, lifestyle and genes in the changing environment”
Venue: Helsinki, Finland

NuGOweek 2012: “Nutrition, lifestyle and genes in the changing environment”, will be held from Tuesday afternoon 28 August till Friday 31 August in Helsinki, Finland. This will be the 9th edition of the NuGOweek.

Venue & Accommodation
The conference venue and hotel is the hotel and conference centre Hilton Helsinki Kalastajatorppa .

Scientific & Conference Committee
The members of the Scientific Committee are:
Matti Uusitupa (chair), Jussi Pihlajamäki, Marjukka Kolehmainen, Kaisa Poutanen, Kirsti Husgafvel-Pursiainen, Jim Kaput, Martin Kussmann, Ben van Ommen, Lars Ove Dragsted, Stine Marie Ulven, Antonio Zorzano, Lorraine Brennan

The members of the Conference Organising Committee are:
Marjukka Kolehmainen, Matti Uusitupa, Kaisa Poutanen, Hannu Mykkänen, Jussi Pihlajamäki, Kati Hanhineva, Vanessa de Mello Laaksonen, Fré Pepping, Ingeborg van Leeuwen-Bol.

Further details about the programme will be made available end of February 2012.

Course on Metabolomics
Also this year we will organise a PhD course prior the NuGOweek. From 20-25 August 2012 the Course on Metabolomics 2012 will be held in Kuopio, Finland.

For further information please contact Ingeborg van Leeuwen-Bol or visit

25-27 Sep 2012

Metabomeeting 2012
Venue: Manchester Conference Centre, Manchester, UK

Established in 2005, the Metabomeeting series is now arranging its seventh International meeting in Manchester Conference Centre, Manchester, UK during 25-27th September 2012.

Previous meetings have been held at King's College, Cambridge, Imperial College London, the Norwich Bioscience Institutes, the Ecole Normale Supérieure de Lyon and in Helsinki in collaboration with VTT Research Centre. The Metabomeeting conference focuses on providing a forum for researchers in metabolomics to meet and discuss all aspects of its research, development and application.

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 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.

You are invited to submit abstracts for consideration for podium presentations. All abstracts need to be submitted before May 4th 2012.

More details are available via

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
Conference flyer (PDF): _Montreux_conference_2012.pdf

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 Jobs

6) 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 ( 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
Experimental Officer in Metabolomics University of Birmingham Birmingham, UK 16-Apr-2012 Metabolomics Society Jobs
Experimental Officer in Bioanalytical Chemistry University of Birmingham Birmingham, UK 16-Apr-2012 Metabolomics Society Jobs
Lectureship in Metabolomics / Metabolic Biochemistry University of Birmingham Birmingham, UK 16-Apr-2012 Metabolomics Society Jobs
Postdoc position in metabolomic NMR  University of Freiburg Freiburg, Germany 12-Apr-2012 University of Freiburg
PhD Research Project: Metabonomic evaluation of Lactobacillus salivarius ability to protect against Brachyspira pilosicoli-induced intestinal spirochetosis University of Reading Reading, UK 31-Mar-2012
Post-­doctoral Position CIC bioGUNE Centre Bilbao, Bizkaia, SPAIN 26-Mar-2012 Metabolomics Society Jobs
PhD Studentship in Bioanalytical Chemistry University of Birmingham Birmingham, UK 22-Mar-2012 Metabolomics Society Jobs
PhD fellowship: "Metabolomics of Nicotiana attenuata’s ecological interactions" Max Planck Institute for Chemical Ecology Jena, Germany 21-Mar-2012 Max Planck Institute for Chemical Ecology

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 ( Upon review, a limited number of job submissions will be selected for publication in the Jobs Wanted section.

Note: There are no postings at this time.

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