MetaboNews -- August 2017
MetaboNews Masthead
Published in partnership between
TMIC and the Metabolomics Society
Issue 72 - August 2017

CONTENTS:


Online version of this newsletter:
 http://www.metabonews.ca/Aug2017/MetaboNews_Aug2017.htm
TMIC Services
TMIC Services

npj Molecular Phenomics: Call for Papers
npj Molecular Phenomics: Call for Papers

Welcome to the seventy-second issue of MetaboNews, a monthly newsletter published in partnership between The Metabolomics Innovation Centre (TMIC, http://www.metabolomicscentre.ca/) and the international Metabolomics Society (http://www.metabolomicssociety.org/), 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. MetaboNews represents the one-stop-shop for the very latest and most critical news about the science of metabolomics. In this issue, we feature a Metabolomics Spotlight article from IROA Technologies LLC titled "Metabolomics: Do we really know how many unknowns there are in a data set? (and how to find out)", and a metabolomics interview with Seyed Ali Goldansaz of the University of Alberta.
This issue of MetaboNews is supported by:

Chenomx -- Metabolite Discovery & Measurement

Chenomx Inc.
IROA Technologies

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Metabolomics Society News

CONFERENCE CORNER 

The Metabolomics Society is calling for interested members in the Greater Asia region to express their interest in hosting the 2020 annual Metabolomics Society meeting (http://metabolomics2020.org/). Please send notice of your interest using this form by 15th September 2017. You should name individuals who will be key to forming a Local Organizing Committee (LOC), and outline the scientific plan for the conference. The LOC will report to the Metabolomics Society and assist A-S-K staff to select a suitable venue and organize the conference. The tasks of the LOC are to ensure national and regional support for the conference, to assist the Society in administrative planning and, most importantly, to chair and organize the scientific management of the conference, including forming an International Organizing Committee that has the responsibility for scientific aspects of the meeting. Please complete the application form outlining your ideas to maximize the scientific quality and outreach of the conference. For further enquiries, please contact the Society via A-S-K Associates (metabolomics@askusa.com).


MEMBERS CORNER

 Board of Directors

Words from the Chair
So, we finally got to all (well, nearly all) meet in person! For those not familiar with this section, most of the Board’s work is done through teleconferences, but for the international meeting we hold a Board of Directors meeting at the start of the conference. It was very reassuring that we were already hearing great things about the Sunday workshops at the meeting! At the face-to-face Board meeting we finalized the details for the election of new Board members and members of the Early-career Members Network, so I encourage you to apply to either or both! One agenda point I want to flag is we voted on the split of the Conference and Training Committee into two separate committees. Given the importance of the conference each year, it tends to dominate the current combined committee. By forming a new Training Committee, we hope to prioritize training activities, particularly in regions of the globe where Metabolomics is still developing. If you are involved in a training activity, such as a workshop or summer school, please contact the chair of the committee, Christoph Junot with your ideas. 

Finally, I would like to say a thank you on behalf of the Board to all those that made the conference possible – Melissa and Horst for being the ultimate hosts (and their ice cream), the Local Organizing Committee, the Scientific Organizing Committee, the student volunteers in their purple tops, our Sponsors, A-S-K Associates and everyone else that made the conference so special. Seattle has a lot to live up to!

2017 Board of Directors – Election Opening Soon!
All members of the Metabolomics Society are welcomed and encouraged to participate in the 2017 Board of Directors election, which will open during the first week of August. An email will be sent to all members once the poll is open. Voting will be open through August 25, 2017 at 11:59pm USA CST.

You can find a list of the nominees as well as their biographies and statements of interest on the Election page of the website.

NOTE: All members are required to enter the email address associated with their membership to complete the online voting.

Please contribute to shaping the future of our Society by voting and playing an active role.

Society Membership Survey
Thank you to all who participated in the membership survey. We had a great response and hope the data collected will help the Society effectively plan in the future.

NOT A MEMBER OF THE METABOLOMICS SOCIETY? YOU CAN COMPLETE A SHORT SURVEY FOR A CHANCE TO WIN $200 AMAZON GIFT CARD

The Metabolomics Society would like to know how to better serve non-members and potential new members and we want to know what you think! Take 5 minutes to help the Metabolomics Society by completing a short survey. To complete the survey, click here: https://www.surveymonkey.com/r/MetabolomicsSociety.

Early-career Members Network (EMN)
Join the Early-career Members Network (EMN) committee for 2017–2018

We are inviting 6 early-career researchers to join the Metabolomics Society's Early-career Members Network (EMN) Committee for 2017–2018. Applications are now open, and deadline to submit your application is 15th August, 2017. Eligibility – the applicant must be: (i) a member of the Metabolomics Society; (ii) a masters or PhD student or early-career member within 5 years of receiving your highest degree; (iii) actively engaged in metabolomics science. Time Commitment: we anticipate a contribution of up to two hours per week (on average). Application Procedure: Please send the following, in one document (.docx or .pdf), to the EMN committee (info.emn@metabolomicssociety.org):
  1. One-page CV with relevant experience in developing and leading networking activities (e.g., student rep for other societies) plus your research experience in metabolomics (e.g., presentations, publications, etc.). If you are currently a member, please provide your membership number to us as well.
  2. Up to 300 words on why you fit the role, and up to an additional 300 words (one page in total) on what ideas you are passionate about developing as part of the Early-career Members Network.
Successful candidates will be notified by the end of September 2017 to start in October 2017.
Additional information can be found at the EMN page on the Metabolomics Society website here. Please contact us via info.emn@metabolomicssociety.org if you have any question or need more clarification.


TASK GROUPS CORNER

Data Standards Task Group
Initiative launched to improve the standardisation of metabolomics assays in regulatory toxicology
The European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC) has announced the launch of a new initiative which will accelerate the use of metabolomics technology to improve the safety assessment of chemicals. Metabolomics is the study of the myriad of small molecules in biochemical pathways that sustain life, by generating energy, or building larger molecules such as DNA.

This technology has the potential to transform chemical risk assessment by providing a deeper view of the molecular events underpinning toxicity than is currently possible. However, because it is so new, scientists do not yet have standard procedures for applying metabolomics or reporting its findings, both of which are needed for chemical risk assessment.

The MEtabolomics standaRds Initiative in Toxicology (MERIT) brings together a team of international experts to address this problem by defining best practices and minimum reporting requirements when metabolomics is used in regulatory toxicology. It comprises partners from industry, government agencies, regulators and academia, from across Europe and the USA, including the US EPA, US FDA, EFSA, UK HSL, BASF HE, Syngenta, Unilever, Imperial College London, University of Birmingham, VU University Amsterdam and the Metabolomics Society Data Standards Task Group.

Alan Poole, Secretary General of ECETOC explains that “Omics has enjoyed a great deal of success in research. Nevertheless, the use of omics data in regulatory assessment has been hindered by the different approaches to the acquisition and processing of the data which can lead to different outcomes, even from identical studies. By focusing on gene expression and metabolic phenotyping, we can gather significant complementary information on regulatory processes and downstream function – both critical to understanding mechanisms of toxicity”.

Mark Viant, co-chair of the new group states “We need to address all the roadblocks to translating this highly effective technology of metabolomics into mechanism-based chemical safety science”. Tim Ebbels, also co-chair, added “The MERIT project is a critical step towards that goal”.

For further details, or to express your interest in commenting upon the best practices and reporting requirements, please contact Dr Tim Ebbels (t.ebbels@imperial.ac.uk) or Professor Mark Viant (m.viant@bham.ac.uk).

ECETOC is an Industry-funded, not-for-profit, non-political science based organization with access to chemical industry’s scientific experience and expertise focusing solely on the science of chemical risk assessment for regulatory purposes. ECETOC provides a scientific forum for expert collaboration from world-wide industry, academia and regulatory bodies to develop Tools, Guidance, State of Science on how emerging science builds on existing risk assessment frameworks. It does this through Task Forces, Expert Meetings and Workshops.


INTERNATIONAL AFFILIATES CORNER

 Australian & New Zealand Metabolomics Network (ANZMN)
Visit http://www.anzmn.org
A good knowledge of Chemistry is useful for the analytical and bioanalytical aspects of Metabolomics. ANZMN members Associate Professor Oliver Jones and Associate Professor Michelle Spencer (and a great team of computer science students) have developed a new game-based app called 'Chirality 2' to help teach some fundamental concepts for first-year Organic Chemistry in a fun and innovative way. The app uses drag and drop, touch-screen interfaces for users to solve puzzles, answer questions, earn medals, and sharing results with their friends via social media. The topics covered are functional groups, structure classification, intermolecular forces, isomers, chiral carbons and naming of molecules. There are timed modes and also feature fun facts about structures. You can get instant feedback and track your progress as you go. The app is available on both Android (https://play.google.com/store/apps/details?id=rmit.edu.au.oliverjones) and iTunes (https://itunes.apple.com/us/app/chirality-2/id1251289926?mt=8).


OTHER NEWS

Meeting Report: Metabolomics Society Conference Awards
At the Metabolomics Society meeting in Brisbane we announced a number of awards from the society. The most prestigious of these awards were the 2017 Lifetime Honorary Fellowships granted to outstanding scientists to recognise their exceptional contributions to the field of metabolomics. This year the awards were made to:
and
In addition, we made a number of studentship and early-career members network awards to aid those at the start of their scientific career to attend the meeting.

AGILENT STUDENT TRAVEL AWARD
Metabolites TRAVEL AWARD EARLY-CAREER MEMBERS NETWORK (EMN) TRAVEL BURSARY AWARD
 METABOLOMICS SOCIETY STUDENT PHOTOGRAPHER AWARD
 METABOLOMICS SOCIETY EARLY-CAREER TRAVEL AWARD
 METABOLOMICS SOCIETY STUDENT TRAVEL AWARD
 
 Software Spotlight

Metabolomics Spotlight

Metabolomics: Do we really know how many unknowns there are in a data set? (and how to find out)

 Feature article contributed by Felice de Jong1, Chris Beecher1, Alexander Raskind1, Casey Chamberlain2, Joy Guingab2, Tim Garrett2

Affiliations: 1. IROA Technologies LLC, Bolton, MA USA 01740; 2. University of Florida, Gainesville, FL USA

Summary

The inability to distinguish between noise and true biological data is still a major challenge to metabolomics researchers although there are many more tools becoming available to deconvolute sets of peaks or metabolite features (mass-to-charge, chromatographic retention time, isotopic pattern, fragmentation). The goal here was to construct a specific study using IROA1,2 generated samples and perform an in-depth LC-MS analysis of the peaks in these samples to determine how many unknowns were in the dataset.

The number of unknown (unnamed) compounds in a metabolomics dataset is generally two or three times more than the number of known (named) compounds. How can it be that there are so many unknowns when biochemistry is such a mature science? Years of observations have given us several clues. We often see the same compound more than once. We know this is in defiance of the principles of chromatography and is therefore dismissed as an artifact of the "look-it-up-in-a-database" method of naming things that is the basis of most non-targeted platforms; however, many of these features are structures unique to their molecular formula and we know that metabolites can ionize as several adducts. Sometimes we see visible patterns of peaks in a 2-D overview and we know that chromatography isn’t perfect, so these features are most likely all real. There are also too many unknowns with masses that do not easily translate to molecular formula, and these we tend to dismiss because they are not believable. Using accurate mass databases to identify metabolites is common but unless retention time and isotopic pattern information are considered, specific compound identification is improbable. The interpretation of fragmentation data adds a level of time-consuming complexity if standards are not available.

This study adopted an experimental design in which: 1) all molecules of biological origin may be distinguished from molecules not of biological origin (see Figure 1); 2) due to the nature of the IROA signature, the number of carbons and the formula of any molecule could be determined; and 3) four metabolite features (mass-to-charge, chromatographic retention time, isotopic pattern, and fragmentation) were combined to achieve accurate identification.
The IROA pattern for L-proline

Figure 1. The IROA pattern for L-proline is that of a five-carbon molecule with a C12 base mass at 116.0705.  Note the spacing of peaks is exactly a neutron mass apart, and the peaks are symmetrical.

Complex IROA Internal Standards were generated by growing yeast until fully labeled in media whereby all carbon sources were labeled with either 5%- or 95% -U13C. Equal aliquots of cells were pooled, extracted and subjected to LC-MS to yield perfect mirror-image patterns (Figure 1). The resulting "IROA-Matrix" material, in which every molecule was specifically isotopically labeled, was analyzed in triplicate. Standardized peak picking was performed to determine how many peaks would be found in a “normal” metabolomic dataset. This was followed by a deep annotation of all the IROA peaks using IROA ClusterFinder™ software. The experiment was repeated on multiple instruments. Since all biological peaks were labeled, we knew that all unlabeled peaks were non-biological.

A standard peak-picking process, using mzMine, found 3,200 peaks on average, in each of the "IROA-Matrix" files when analyzed with a minimum peak height of 100,000. The ClusterFinder program at the same setting (minimum = 100,000) found only 781 IROA peaks. Since all the biological peaks yielded an IROA pattern, of the 3,200 peak picked peaks, 2,419 (74%) were artifacts (Figure 2).

Peak-picking yielded peaks of biological (Orange), and non-biological (Blue) origin

Figure 2. Peak-picking yielded peaks of biological (Orange), and non-biological (Blue) origin. Only 24% of the peaks had isotopic signatures and originated from the sample analyzed; the remainder were natural abundance.

Among the peaks of biological origin, there were still a lot of unknown peaks. To see if these could be in-source, or instrument-induced fragmentation, we created a software package that allowed us to select any peak and find all highly correlated peaks (i.e., fragments, adducts and polymeric derivatives) (Figure 3). For any selected peak, correlated peaks were identified and a matrixed table was generated in which the degree of correlation was below the diagonal, and the mass differences were above the diagonal (Figure 4A). From this table and the IROA-derived data, it was generally possible to determine the exact fragmentation sequence (Figure 4B), and once it became obvious that there was a tremendous amount of post-LC fragmentation, it became easy to recognize it as columns of peaks in a 2-D representation of the peaks (Figure 4C).

The positive-mode fragmentation of a few of the amino acids

Figure 3. The positive-mode fragmentation of a few of the amino acids illustrate how many fragments, adducts, or polymerics may be seen for some molecules. The peaks in this table are all in addition to the normal M+H.

4A

Click on the thumbnail below to view a larger version of the image
Figure 4A

4B
Figure 4B


4C

Figure 4C
Figure 4. The correlation table exhibits the mass difference between any two correlated peaks above the diagonal. The fragmentation sequence may be read from the connections seen here.

Conclusion

It was easily determined that a large percentage of peaks found in a basic peak picking routine were artifacts was since these peaks did not exhibit IROA patterning. Of the IROA-patterned peaks, a chemical formula was accurately determined and many compounds were identified by comparison to authentic standards from the MSMLS3. Compounds for which standards were not available were identified tentatively by reference to the Clusterfinder™ embedded databases, and formulae calculations were attempted for all others. Among the biologically derived peaks were 1) known authenticated, and tentatively known compounds; and 2) unknowns either with or without formulae. Many compounds occurred multiple times.

Highlights
  • Many of the compounds occurring multiple times are common fragments of named compounds. They made chemical sense when correlated peaks were identified using algorithms and the fragmentation path was examined.
  • Most of the unknowns examined to date are either fragments, adducts, or polymerics. The formulae calculated from their IROA parameters are generally correct. They are often “named by lookup” and not recognized as a fragment, for instance, indoline will show up for all tryptophan-related compounds.
  • A very limited number of the IROA peaks found could not be either identified directly or assigned relative to another known peak. These are likely the only true unknown compounds of biological origin.

The IROA-Matrix has been developed into a Workflow Kit which includes Standards and software. Further information can be freely found here and the Kit User Manual obtained from the primary author of this article.

References

  1. de Jong F, Beecher C. Addressing the current bottlenecks of metabolomics: Isotopic Ratio Outlier Analysis (IROA®), an isotopic-labeling technique for accurate biochemical profiling. Bioanalysis 2012, 4(18), 2303-14.
  2. Stupp GS, Clendinen CS, Ajredini R, Szewc MA, Garrett T, Menger RF, Yost RA, Beecher C, Edison AS. Isotopic Ratio Outlier Analysis Global Metabolomics of Caenorhabditis elegans. Analytical Chemistry 2013 85(24), 11858-11865. doi: 10.1021/ac4025413.
  3. Mass Spectrometry Metabolite Library of Standards.

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

MetaboInterview
This section 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 Seyed Ali Goldansaz.
Seyed Ali Goldansaz

 PhD Student, Wishart Research Group, University of Alberta, Edmonton, Canada


Seyed Ali Goldansaz
Biography

Seyed Ali obtained his BSc degree in Animal Science from the College of Agriculture & Natural Resources, University of Tehran, I.R. Iran, and his MSc in Nutritional Immunology from the University of Alberta. He is currently conducting research in an interdisciplinary field looking into the identification of predictive biomarkers of sheep feed efficiency, carcass merit, pregnancy and litter size using different "omics" technologies, with a main focus on metabolomics.

Metabolomics Interview (MN, MetaboNews; SAG, Seyed Ali Goldansaz)

 MN: How did you get involved in metabolomics?

SAG: My background is in Animal Science and, generally, metabolomics is very new in this field. When I wanted to start my MSc in 2011, I had the option of choosing between two projects for my thesis work, both of which involved metabolomics. Ultimately, I decided to do my thesis work on the effects of bacterial lipopolysaccharide on prion disease. As part of that project, I collected urine and serum samples from FVB infected-mice at different time points and conducted NMR analyses to identify and quantify the metabolome associated with prion infection. This experiment was conducted in collaboration with The Metabolomics Innovation Centre (TMIC). Over time, my collaborations with TMIC grew further and it was through their metabolomics facilities that I became more and more involved in this field. Upon completing my MSc, I had the opportunity to create a new collaboration between TMIC and Livestock Gentec (LG) at the University of Alberta to start my PhD. Currently, bridging between metabolomics and Animal Science, I am looking at identifying predictive biomarkers of feed efficiency, carcass merit, pregnancy, and litter size in sheep.

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

SAG: One of the exciting aspects of metabolomics is its versatility in biomarker discovery; it can be used for the diagnosis or prognosis of various traits. In my project, we are using metabolomics to identify biomarkers with a predictive value that could be used for early detection of some economical traits. For example, we hope to identify biomarkers of ewe pregnancy and litter size that would enable differentiation between pregnant and non-pregnant ewes and detect the number of fetuses carried by each pregnant animal between 40-50 days into pregnancy. Meanwhile, current practices in larger flocks using ultrasound diagnosis require highly experienced veterinarians/technicians to only detect the pregnancy and not the litter size. Another exciting aspect of my research is developing "pen-side" kits that embed the predictive biomarkers. These kits are designed to be portable, highly accurate, economically affordable, and can be used by anyone, without needing any scientific knowledge or technical capability or instrumentation. These kits are meant to provide a consistent service regardless of the size of the flock, geographical proximity, or farm accessibility.

 MN: What key metabolomics initiatives are you pursuing at your research centre or institute?

 SAG: One of my main objectives in bridging between metabolomics and sheep research is to introduce the opportunities metabolomics could provide for livestock researchers. An example is the collaboration between LG and TMIC, which provides an opportunity to couple genomics and metabolomics technologies for the sake of livestock research. To investigate the application of metabolomics in animal science, we recently published a systematic review looking at five major livestock species (cow, sheep, goat, horse, and pig) reported up to 2016. This systematic review has gathered the livestock metabolome from all publications reporting more than eight metabolites and centralized the information in a freely accessible online database called The Livestock Metabolome Database (LMDB). We identified only 149 articles reporting metabolomics data on these five livestock species. In this manuscript, we review the trends in the application of metabolomics in livestock research and point out some of the opportunities provided through metabolomics. This review and the online database (LMDB) should enable livestock researchers and producers to conduct more targeted metabolomic studies and identify where further metabolome coverage is needed.

MN: What is happening in your country in terms of metabolomics?

SAG: The Metabolomics Innovation Centre at University of Alberta is one of the leading centres in metabolomics with great research capacity and a multitude of collaborations with researchers in various fields. For more information on TMIC developments, please visit www.metabolomicscentre.ca.

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

 SAG: I think biomarker discovery for predictive measurements of production traits using portable kits is going to be a breakthrough for the livestock industry. We hope to take a big step towards achieving this goal by designing experiments with longitudinal sample collection to discover the predictive biomarkers, validate the results using a larger scale sample size, and implement the validated biomarkers in a pen-side kit. Farmers would also benefit from a management perspective by using these kits to predict animal performance, e.g., feed efficiency, meat yield, the number of fetuses a ewe carries, before entering the production system or very early in the trial. This additional information allows the farmers to decide whether they want to keep the animal and, if they do, how to change their management practices to be efficient and meet the needs of the animal. An example is reducing costs on overfeeding ewes that have not yet been detected as pregnant and adjusting feed for ewes carrying multiple fetuses, compared to those with only one fetus.

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

SAG: As we have described in our systematic review, metabolites are the canaries of the genome. Metabolomics can provide a sensitive indicator of how changes are being regulated at the proteomic and genomic levels. Phenotypic changes can be identified and quantified using metabolomics. Consolidating the omics technologies for a system-level understanding of how various biological processes happen is another important issue. Metabolomics data, especially when studying metabolite kinetics, can reveal some of the unknown physiological pathways and point out the important regulators of these pathways.

 MN: What do you see as the greatest barriers for metabolomics? 

SAG: I think one of the greatest barriers in metabolomics, especially for scientists new to the field, is how to apply metabolomics. Our systematic review showed that quite a few publications have done a poor job designing and conducting their metabolomics analyses. Some examples are using a low number of animal replicates or sample sizes, reporting metabolites as biomarkers while not conducting the right statistical analyses and validation for it, and not using the appropriate analytical platforms for their experiments. Another barrier for metabolomics is the dearth of quantitative data. Most publications report the metabolites they have identified, however, they do not provide any quantitative values comparing control vs treatment group concentrations, or how the concentrations have changed as a result of the treatment, or what the minimum/maximum concentrations are for the given metabolites. Another limitation may be the accuracy of metabolomics instruments and the need for method development for sensitive metabolites such as vitamins or those below the detection limit.
 
MN: What improvements, technological or otherwise, need to take place for metabolomics to really take off? 

SAG: Science is endless and, as such, the need for improvement in all aspects of any field including metabolomics is constant. One of the aspects that has and will further improve metabolomics is the availability of online databases that are freely accessible and serve as a hub for the research community and industry. Imagine if you no longer had to browse through multiple web pages, all in the same field, to find the information you need but rather, one centralized web page has all that you are looking for and can provide the information anytime, anywhere at the mercy of a click or a simple search! Another improvement needed in this field is to develop instruments and/or methodologies that allow more sensitive and reproducible detection of metabolites.

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

SAG: It seems that in general, research funding around the globe has declined in recent years. However, more and more are becoming interested in performing and funding metabolomics research. This won’t last long if metabolomics researchers do not make a difference for the industries and governments supporting them by saving them money or increasing their profitability.

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

SAG: Despite all the fantastic research everyone does, I think we should remember that research and doing good science is just one aspect of our lives. We shouldn’t forget who we are, why we are doing what we’re doing, and where we are heading. I’ve come to learn by experience that regardless of how excellent your research is, it will one day become old and people may forget about it; however, if you want to become eternal, you should capture not only the minds, but hearts too. Increasing our knowledge should increase our humility too, or else, you would be no different than a hard disk, which only carries loads of scientific material. Just like any fruit tree; the more fruitful the tree, the more curved (humble) the branches get!


Please note: We are open to suggestions for our MetaboInterviews section. Please send suggestions for future interview candidates to Ian Forsythe at metabolomics.innovation@gmail.com.
Metabolomics Current Contents

Metabolomics Current Contents

Recently published papers in metabolomics:
Metabolomics Events

Metabolomics Events
23-24 Aug 2017
Swedish Metabolomics Conference 2017: Metabolomics and Health
Venue: Chalmers University of Technology, Gothenburg, Sweden
Confirmed speakers:
  • David Wishart, University of Alberta
  • Elaine Holmes, Imperial College London
  • Claudio Luchinat, University of Florence
  • Tuulia Hyötyläinen, Örebro University
  • Craig Wheelock, Karolinska Institutet
  • Peter Spégel, Lund University
  • Ali Moazzami, SLU
  • Tove Fall, Uppsala University
  • Henrik Annti, Umeå University
Information and registration: http://www.chalmers.se/en/conference/Swedish-Metabolomics-2017/Pages/default.aspx
11-15 Sep 2017
School on "Cloud-based Metabolomics Data Analysis and Collaboration"
Venue: Building 2 of the Technology Park of Sardinia Pula, Sardinia, Italy
We are happy to announce that registrations are now open; visit http://cloudmet2017.crs4.it/ to register now.

Metabolomics is a well established -omics science whose growth is bringing about new challenges. Systematic studies and integration with other data sources are resulting in ever larger dataset sizes; production applications require superior computational scalability of analysis techniques; complex, multi-step workflows make study reproducibility more challenging.

At the same time, cloud computing technologies are extending their functionality and provide practical solutions for many of these problems.

In this School students will have the opportunity to learn about current topics in metabolomics, with a slant on the integration of cloud computing technologies where they are beneficial to the effectiveness and efficiency of research and analysis work. Top-level lecturers in the field will provide their insight and will be available for the entire duration of the school, with ample opportunity for interaction with the students. Importantly, the School will also include practical sessions where students can put their new knowledge into practice under the guidance of tutors and run analyses using the new PhenoMeNal cloud-based metabolomics platform.

To register and for more information, visit http://cloudmet2017.crs4.it/.
20-23 Sep 2017
MOVISS: Bio and Data
Venue: Vorau, Austria
A problem driven meeting aimed at bioinformaticians, biochemists, statisticians and those who handle and interpret metabolomics data
When: Sept 20-23, 2017
Where: Vorau, Austria
To register and for more information, go to www.MOVISS.eu, and follow us on Twitter @MOVISSmeet
 
Not just an ordinary conference, where people present work they have already done, MOVISS is centered on identifying and problem solving current challenges relating to metabolomics data handling by getting everyone in the room discussing it. Want to be at the forefront of solving some of the major bottlenecks in the Metabolomics Revolution – see you at MOVISS!

A follow up R Summer School will be held on September 25-27, 2017 in Vorau, Austria.
25-27 Sep 2017
Joint OpenMS and MetFrag User Meeting
Venue: Martin-Luther University, Halle, Germany
Speakers include:
  • W. Weckwerth (Uni Vienna)
  • G. Landrum (KNIME)
  • I. Grosse (MLU Halle)
  • Steffen Neumann (IPB Halle)
For more information and registration, please visit http://www.openms.de/um2017/.
2 Oct 2017
Metabolomics: Understanding Metabolism in the 21st Century
FREE online course
Metabolomics is an emerging field that aims to measure the complement of metabolites (the intermediates and products of metabolism) in living organisms. In this course, we provide an introduction to metabolomics and describe the current challenges in analysing the complement of metabolites in a biological system.
 
The course is targeted towards final year undergraduate students from biology / chemical disciplines and medical students, but will also provide a valuable introduction to the metabolomics field for MSc and PhD students, and scientists at any stage in their careers.
 
Register at: https://www.futurelearn.com/courses/metabolomics
or email: bmtc@contacts.bham.ac.uk for more information.
12-13 Oct 2017
Quality Assurance and Quality Control in Metabolomics
Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK
This two-day course will provide a comprehensive overview of the application of quality assurance (QA) and quality control (QC) in metabolic phenotyping. The course is aimed at students and researchers who are actively working in the field. Experts who have developed the application of QA and QC procedures within the field will lead the course. It will include both theoretical and practical components to:
  • Introduce QA and QC in metabolic phenotyping
  • The application of QA and QC in untargeted and targeted studies
  • Preparation of QCs and data acquisition
  • Data processing and reporting standards
The course will finish with a question and answer session with a panel of experts.

Bursaries are now available for PhD students funded by the BBSRC, MRC, or NERC.

For further information and registration details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/quality-phenotyping.aspx or contact bmtc@contacts.bham.ac.uk.
12-13 Oct 2017
Mayo Clinic Metabolomics Symposium
Venue: Leighton Auditorium, Siebens Building, Mayo Clinic, Rochester, Minnesota, USA
Mayo Clinic will host a Metabolomics Symposium from October 12 to October 13 on the Rochester, Minn., campus. The event will feature presentations on the practice and theory of metabolomics applications, the latest research in metabolomics and networking opportunities. The workshop is open to beginning and established researchers, students and postdoctoral fellows.

A focused workshop is available to a limited group of individuals based on availability.

Scholarships for scholars and junior faculty are available.

For more information, please visit http://matrix.conferenceataclick.com/metabolomics_2017/home_live1.htm.
18-20 Oct  2017
Workshop in Environmental Omics, Integration and Modelling
Venue: CosmoCaixa, Barcelona, Spain
The aim of this workshop is to review the state-of-the-art and broaden the knowledge on high-throughput analytical methods, data integration and modelling in Environmental Omics and Toxicology.

The main workshop topics will be the following:
  • Transcriptomic and Genomic studies
  • Metabolomic and Lipidomic studies
  • Development of Chemometrics and Analytical Tools
  • Data Integration and Modelling
We are pleased to invite you to participate in this workshop that will promote knowledge exchange and creation of new relationships and future collaborations.

For more information, please visit http://wenvomics2017.info/.
6-8 Nov 2017
Metabolomics with the Q Exactive
Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK
This three-day course will introduce you to using the Q Exactive mass spectrometer in your metabolomics investigations. The course is aimed at students and researchers with minimal previous experience of applying LC-MS in metabolomics. The course will be led by experts in the field and include lectures, laboratory sessions and computer workshops to provide:
  • An introduction to metabolomics and using the Q Exactive mass spectrometer in your studies
  • Polar and non-polar sample preparation for profiling and targeted studies
  • Data acquisition for profiling and targeted studies
  • Data processing and data analysis
  • Introduction to metabolite identification
The course will finish with a question and answer session with a panel of experts.

Bursaries are now available for PhD students funded by the BBSRC, MRC, or NERC.

For further information and registration details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/q-exactive.aspx or contact bmtc@contacts.bham.ac.uk.
1 Dec 2017
Introduction to Metabolomics for the Clinical Scientist
Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK
This one-day course in partnership with the Phenome Centre Birmingham will provide clinicians with an overview of the metabolomics pipeline, highlighting the benefits of the technique to the medical field. The course will provide an:
  • Introduction to experimental design and sample collection
  • An overview of both the analytical and computational methods applied in the field
  • Case studies and panel discussions with the experts
Bursaries are now available for PhD students funded by the BBSRC, MRC, or NERC.

For further information and registrations details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/introduction-metabolomics.aspx or contact bmtc@contacts.bham.ac.uk.
6-8 Dec 2017
Multiple biofluid and tissue types, from sample preparation to analysis strategies for metabolomics
Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK
This 3-day course will provide a comprehensive overview of dealing with complex biological samples for LC-MS analysis. The course is targeted towards students and researchers who are actively applying metabolomics in their research. The course will be led by experts in the field and include:
  • An overview of quenching and extraction strategies for different biological samples
  • Hands-on sample preparation using different sample types
  • Hands-on HILIC and reversed phase LC-MS data acquisition
  • Solid phase extraction clean up methods
  • An overview of data analysis and metabolite identification
  • An opportunity to ask questions and seek advice to prepare samples in your own research
Bursaries are now available for PhD students funded by the BBSRC, MRC, or NERC.

For further information and registration details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/sample-analysis.aspx or contact bmtc@contacts.bham.ac.uk.
11-13 Dec 2017
MetaboMeeting 2017
Venue: University of Birmingham, UK
Make plans to attend the 10th successful MetaboMeeting conference. The meeting will bring together research scientists and practitioners from all areas of application and development of metabolic profiling, covering a wide range of experience from early career scientists to experts from throughout the international metabolomics field. MetaboMeeting 2017 continues to highlight the work of its attendees through both oral platform presentation and poster sessions.
The deadline for oral presentation abstracts is 15th July 2017.
The deadline for poster abstracts is 1st October 2017.

For further information, visit http://metabomeeting2017.thempf.org/.
14-15 Dec 2017
Metabolite identification with the Q Exactive and LTQ Orbitrap
Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK
This two-day course will provide a hands-on approach to teach the latest techniques and tools available to perform metabolite identification. We will apply these tools on the Q Exactive and LTQ Orbitrap mass spectrometry family. The course is targeted towards students and researchers who are actively applying metabolomics.

The course will be led by experts in the field and include significant hands-on experience using both the Q Exactive and LTQ Orbitrap instruments to perform:
  • Data dependent acquisition
  • Data independent acquisition
  • MS/MS and MSn data acquisition
The course will finish with a session on the tips and tricks from the experts and an opportunity to ask questions.

Bursaries are now available for PhD students funded by the BBSRC, MRC, or NERC.

For further information and registration details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/metabolite-identification.aspx or contact bmtc@contacts.bham.ac.uk.

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

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 four issues (eight weeks) unless the position is filled prior to that date.

Jobs Offered

Job Title Employer Location Posted Closes Source
Two PhD positions
 Robert Koch-Institute Berlin, Germany 27-Jul-2017 7-Aug-2017 Robert Koch-Institute
One PhD position (two years at the Robert Koch-Institute, Berlin, Germany, and one year at ANU, Canberra, Australia)
 Robert Koch-Institute and ANU
 Berlin, Germany and Canberra, Australia 27-Jul-2017 13-Aug-2017 www.allianceberlincanberra.org
Seeking qualified applicants for a Postdoctoral Researcher in Developing High-throughput Metabolomics Methods for Populations-based Phenotyping Karolinska Institutet Gunma University, Japan 18-Jul-2017 31-Aug-2017 Karolinska Institutet
Postdoctoral Researcher in the functional metabolomics of lipid mediators in inflammation Karolinska Institutet Solna, Sweden 6-Jul-2017 31-Jul-2017 Naturejobs
Postdoc Position in Computational Metabolomics  Friedrich Schiller University Jena Jena, Germany 4-Jul-2017 Until filled Friedrich Schiller University Jena
Postdoctoral Fellow / Research Associate in the field of (Bioinformatics / Metabolomics) McGill University Montreal, Canada 25-Jun-2017 1-Oct-2017 McGill University
Early Stage Researcher (ESR/PhD)
 Biocrates Life Sciences AG Innsbruck, Austria
 13-Jun-2017
Biocrates Life Sciences AG
Analytical Scientist (PhD or Master) for Mass Spectrometry based Metabolomics
 Biocrates Life Sciences AG Innsbruck, Austria 13-Jun-2017
Biocrates Life Sciences AG


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.

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