Issue 1 - August 2011


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Welcome to the first issue of MetaboNews, a monthly newsletter for the worldwide metabolomics community. In this issue we feature a Software Spotlight article on MetATT, a web-based tool designed for analyzing two-factor (including time-series) metabolomic data. 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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1) Software Spotlight


Feature article contributed by Jianguo Xia, Postdoctoral Research Fellow, Biostatistician, Dept of Computing Science, University of Alberta, Edmonton, Canada

Researchers in metabolomics have long recognized that an individual’s metabolic profile is very sensitive to multiple factors such as age, gender, diet, etc. It is natural, sometimes necessary, to include these additional factors during metabolomic data analysis. MetATT ( is a user-friendly, web-based tool designed for analyzing two-factor (including time-series) metabolomic data, e.g., to consider the gender effect in a case-control study, or to investigate temporal profiles under different experimental conditions.

To use MetATT, users first need to convert their data into the proper format. MetATT accepts a data table with samples in rows and features (spectral bins, peaks, compounds) in column (or in transposed format). The first column must contain sample names, while the next two columns must contain group labels of the two factors. For time-series data, the column of different time points must be labeled as Time, and samples from the same subjects must appear as blocks. More detailed instructions can be obtained on the website (Fig.1).

MetATT home page 

Figure 1. MetATT home page. This page gives an overview of the methods implemented in MetATT. Experienced users can directly click the "Click here to start" link to start analysis. First-time users should follow the "Data Formats" link or the "FAQs" link to become familiar with the basic requirements and features of the program. The "Resources" link provides the R scripts for users who want to run the analysis on their local computers from the command line of R.

MetATT contains five carefully selected methods to help researchers understand their data. In particular, MetATT provides two visualization techniques to facilitate data exploration and pattern discovery – interactive 3D principal component analysis (PCA) and two-way clustered heat map. The PCA visualization supports rotation, zooming, and highlighting. Pointing and clicking on any data point will display the characteristic variables of the corresponding sample (Fig. 2). The two-way clustered heat map presents all the data points in the form of colored heat maps based on their (usually normalized) values. Users can highlight and re-arrange the heat map data any way they wish (Fig. 3). MetATT also supports the classical univariate two-way ANOVA method, along with two recent multivariate extensions – ANOVA-simultaneous component analysis (ASCA) and multivariate empirical Bayes time-series data analysis (MEBA). The two-way ANOVA supports within- and between- subjects analysis for time-series/repeated samples and two-factor independent samples, respectively. The results are summarized as a Venn diagram (Fig. 4) in addition to a detailed data table. The ASCA method first decomposes the variation in the entire data set into individual variations induced by major experimental factors (and their interactions), and then applies PCA to each variation to obtain a simple and interpretable result. MetATT’s implementation of ASCA also incorporates two recent improvements for variable selection and model validation. The MEBA method compares the average temporal changes of individual variables among different biological conditions. The result is a ranked list of variables with distinctive temporal profiles (Fig. 5).

Interactive 3D
          PCA visualization

Figure 2. Interactive 3D PCA visualization. The colors of these data points are based on the factor labels. Users can change the colors according to any of the two factor labels. Users can also rotate or zoom the 3D plot. Clicking on any data point will display the top 20 characteristic variables of the corresponding sample on the right hand side of the screen.

Two-way clustered

Figure 3. Two-way clustered heat map. The samples are sorted by their factor labels. Users can change the hierarchical clustering algorithms, the color schema, as well as the order of the samples to suit their preferences.

Venn diagram summary of two-way ANOVA results

Figure 4.
Venn diagram summary of two-way ANOVA results.

The top four variables with distinctive
              temporal profiles

Figure 5.
The top four variables with distinctive temporal profiles. The temporal profiles are presented as line graphs coloured based on the two conditions (WT and MT) under study.

The complex procedures are implemented in a simple, stepwise manner through a user-friendly web-interface. At the end of session, a detailed analysis report will be generated which integrates the background introduction of each method used together with the corresponding graphical and text outputs.

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 Rupasri Mandal, Research Associate, Mass Spectrometry/Separations, 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), the use of metabolomics allows information about multiple compounds to be used together to make better medical decisions. Global metabolic profiling has now been used to determine clinical biomarkers in assessing the pathophysiological health status of patients.

In the following two recent clinical studies, metabolomics approaches were used to predict the risk for cardiovascular disease (CVD) and the development of diabetes, respectively.

1. Z. Wang, E. Klipfell, B.J. Bennett, R. Koeth, B.S. Levison, B. DuGar et al., Gut Flora Metabolism of Phosphatidylcholine Promotes Cardiovascular Disease, Nature, 2011, vol 472, pp. 57-63.

Metabolic profiles of plasma in an independent large clinical cohort were used to predict risk for cardiovascular disease (CVD). Three plasma metabolites of the dietary lipid phosphatidylcholine (PC) - choline, trimethylamine N-oxide (TMAO) and betaine - were identified as predictive biomarkers for CVD. Stable isotope dilution LC/MS/MS was used for quantification of those metabolites. This is the first study to identify a direct link between intestinal microflora, dietary PC and CVD risk. This knowledge could be used for the development of new diagnostic tests and may help to inform therapeutic strategies for CVD.

2. T.J. Wang, M.G. Larson, R.S. Vasan, S. Cheng, E.P. Rhee, E. McCabe et al., Metabolite Profiles and The Risk of Developing Diabetes, Nature Medicine, 2011, vol 17, pp. 448-454

Plasma metabolic profiles of 2,422 subjects from the Framingham Offspring Study were performed using an MS-based metabolomics platform (LC-MS/MS). The objective was to investigate whether metabolite profiles could predict the development of diabetes. Amino acids, amines and other polar metabolites were profiled. From these groups, five metabolites of interest were identified: isoleucine, leucine, valine, tyrosine and phenylalanine. These branched-chain and aromatic amino acids were identified as predictors of the future development of diabetes. This study suggests that amino acid profiles could be used in diabetes risk assessment.

Metabolomics Current Contents

3) Metabolomics Current Contents

Recently published papers in metabolomics:

4) MetaboNews

Jul 2011

KEGG has gone commercial - Due to a lack of funding, one of Biology's most popular databases has moved to a subscription model. Minoru Kanehisa, a bioinformatics professor at Kyoto University, has led this project since its beginning in 1995. The KEGG website will continue to be freely available. However, academic and commercial users wanting access to KEGG's FTP site will now have to pay for access. Kanehisa and his colleagues have started a non-profit organization, NPO Bioinformatics Japan, as a means for raising funds to pay for KEGG's operations. Academic users will pay $2,000 per year for individual users and $5,000 per year for organizations. Kanehisa estimates that if they can get just 10% of the current FTP users (totalling 3,000 users per month), then they will have enough money to survive. A lot of work goes into making KEGG the high quality database that academic and commercial users have come to rely on during the last 15 plus years. As a result, KEGG employs a large team of 25 full-time staff and 5-10 part-time employees. To support KEGG and all of its efforts to date, consider a KEGG FTP subscription.

Sources: KEGG and GenomeWeb
Jul 2011

Metabolomics Society meeting summary - The Seventh International Conference of the Metabolomics Society was held in Cairns, Australia, June 27-30, 2011, following relocation from Japan due to possible power shortages following tsunami.  Despite the logistic challenges of such a last-minute move, the Australian hosts put together a great event with more than 140 posters and 80 speakers from around the world. The program was packed with presentations covering a wide variety of topics in metabolomics: everything from biomarker discovery, pathways and disease, plants, microbes and the environment, to pharmacology and nutrition. New technologies, fluxomics, bioinformatics, and systems biology were also hot topics. The emphasis on new capabilities in quantitative lipidomics was especially noteworthy.  Another highlight was the presentation from Dr. Marasu Tomita, who is the director of the Institute for Advanced Biosciences, Keio University and was one of the original organizers for the conference. His talk emphasized the growing prominence of metabolomics in Japan, as reflected by the impressive metabolomics facilities in Tsuruoka city and their remarkable analytical capabilities. The south pacific, including Japan, Australia and New Zealand was generally very well represented at the conference, showing the growing global importance of metabolomics as an omics science. Japan will host the conference in 2014. Conference proceedings are available on the Metabolomics Society website at

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

12-14 Sep 2011

CIC bioGUNE International Workshop on Metabolomics
Venue: Bilbao, Spain

In the "Global Systems Biology" era, metabolomics constitutes one of the most powerful technologies to integrate the biological pathways and understand how a living organism interacts with its environment. Metabolomics can be defined as the quantitative and qualitative analysis of all metabolites (molecules with a molecular weight of less than 1,500 Da) in a given organism. This results in the construction of a metabolome or metabolic fingerprint, analogous to the genome or the proteome. Since the set of all metabolites is directly linked to the actual state of a cell, tissue or an organism and thus to the phenotype, the metabolome is optimally suited for the determination of biomarkers that are typical for certain genotypes or pathologies, and to identify key cellular pathways involved in the development and progression of diseases.

CIC bioGUNE has prepared a very interesting scientific program in which leading academics speakers will tell us about the state-of-the-art in metabolomics including technological aspects related to the different platforms (RMN, GC and LC). The workshop will also cover recent breakthroughs in single-cell and high-throughput metabolomics approaches along with the applications that this technology has found in environmental and disease biomarker discovery areas. Importantly, the scientific program will be completed with poster sessions and presentations from equipment manufacturers. In summary the participants will have the opportunity to learn, meet and interact with experts in different metabolomics-related areas obtaining a deep and broad vision on this powerful technology.

For more information, please visit

25-28 Sep 2011

Metabomeeting 2011
Venue: Helsinki, Finland

The Metabolic Profiling Forum (MPF) is pleased to announce Metabomeeting 2011, to be held in collaboration with the VTT Research Centre of Finland at the Helsinki Congress Paasitorni. The conference centre is located in Siltasaari, in the heart of Helsinki, on the shore-front and next to the Hakaniemi market
The MPF is also pleased to be organising Metabomeeting 2011 in conjunction with the inaugural Nordic Metabolomics meeting, which for this first meeting will be focusing on the latest developments/enhancements in data analysis and modelling.

30 Sep-4 Oct 2011

ASMS Asilomar Metabolomics meeting
Venue: Pacific Grove, California, USA

The upcoming ASMS Asilomar Metabolomics meeting will promote an in-depth discussion of current problems and perspectives of mass spectrometry-based metabolomics. The meeting is endorsed by the Metabolomics Society.

We will challenge ideas and concepts throughout the conference and have allocated ample time for discussions, e.g., during evening receptions. In addition to invited speakers, there will be poster sessions and oral contributions based on abstract submissions. We will focus on a range of hot  topics, including:  databases; metabolite/gene annotations; fluxes; compound identifications; metabolite imaging; secondary metabolism; metabolomics in human diseases; and quality control for high-throughput metabolomic quantifications.

Download conference brochure

8-9 Nov 2011

7th annual Advances in Metabolic Profiling
Venue: Dublin, Ireland

Welcome to the 7th annual Advances in Metabolic Profiling conference and exhibition. This year's event will be held in the dynamic city of Dublin, economic and cultural centre of Ireland.

The conference will be co-located with Mass Spec Europe. Registered delegates will have access to both meetings ensuring a very cost-effective trip.

For more information, please visit

13-16 Nov 2011

International Conference on Natural Products (ICNP2011) - Metabolomics A New Frontier in Natural Products Science
Venue: Palm Garden Hotel, Putrajaya, Malaysia

On behalf of the Organising Committee you are invited to participate in the next International Conference on Natural Products (ICNP2011) - Metabolomics A New Frontier in Natural Products Science.

The conference is being organised by the Universiti Putra Malaysia and Malaysian Natural Products Society. The conference will be held at Palm Garden Hotel, IOI Resort, PUTRAJAYA from 13th -16th November 2011.

For more information, please visit

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 Metabolomics Society is pleased to announce the location and dates for our next annual meeting 'METABOLOMICS 2012'. We will host a program full of practical workshops and parallel sessions covering the broad range of biological and technological metabolomics topics as well as provide rich opportunities for networking. Prominent scientists will speak on the state-of-the-art in a number of leading disciplines to kick off each session, after which, we will have a full agenda of innovative speakers with specific oral presentation opportunities provided for younger researchers. We invite you to reserve the above dates in your calendar and follow our website for further details,

Local Organisers: Dan Bearden, Rick Beger, Rima Kaddurah-Daouk, Lloyd W. Sumner, Don Robertson, Padma Maruvada and Donna Kimball.

For more information, please visit

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
Postdoctoral Research Associate position to analyze plant composition
Iowa State University
Ames, Iowa
Metabolomics Society Jobs
Postdoctoral Fellow in Metabolomics
Duke University
Durham, NC
Metabolomics Society Jobs
Scientist, Proteomics/Metabolomics
Merck Sharp & Dohme (MSD) Singapore
Post-Doctoral Fellow: Biomarkers of Disease in Dairy Cows
University of Alberta
Edmonton, AB
University of Alberta

Jobs Wanted
Very highly qualified individuals (e.g., lab managers, professors, directors, executives with extensive experience) seeking employment in metabolomics are encouraged 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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