MetaboNews Masthead
Published in partnership between
TMIC and the Metabolomics Society
Issue 51 - November 2015

CONTENTS:


Online version of this newsletter:
 http://www.metabonews.ca/Nov2015/MetaboNews_Nov2015.htm
TMIC Services
TMIC Services

Welcome to the fifty-first 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 on a metabolomics approach to implementing personalised medicine in the diabetes clinic and a metabolomics interview with Arjen Lommen of RIKILT Wageningen UR.
This issue of MetaboNews is supported by:

Metanomics Health
    
Chenomx -- Metabolite Discovery & Measurement    
mzCloud
Metanomics Health GmbH
Chenomx Inc.
mzCloud

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Metabolomics Society Logo

Metabolomics Society News

CONFERENCE CORNER

12th Annual International Conference of the Metabolomics Society
Location: Dublin, Ireland
Date: June 27-30, 2016
Website: http://metabolomics2016.org/
Stay tuned to the conference website for updates about the 2016 Metabolomics Society Conference. The 2016 conference will provide opportunities for researchers in all fields of metabolomics science to present their work and network with leaders in the field. Four general themes will feature in Dublin including:
-    Metabolomics in Nutrition and Food Research
-    Metabolomics in Health and Disease
-    Advancing the Field
-    Environmental, Plant and Model Organisms (including joint sessions with the Plant Metabolomics Platform).

LAST CALL: Open Call to Metabolomics Society Members for Scientific Sessions and Workshops


We are in the process of planning workshops and scientific sessions and we welcome you to submit proposals for these important meetings. 



Additional details can be found by clicking on the links below.
Do not delay – the proposals are due by October 30, 2015. 

 Please follow the format shown here:
For the scientific session proposals:
Title:
Content: (expected content in bullet point form)
Potential Keynote speaker:
Rationale: (can incorporate the bullet points listed above also).
For workshop proposals:
Title:
Topic Outline/Content (i.e. content in bullets):
Target Audience:
Potential Speakers:
Rationale:

Support for local conferences
The Society is glad to support national and regional conferences conducted by our affiliated organisations. This includes support for the first meeting of the Swiss Metabolomics Society in Basel on December 1st 2015 (http://www.swiss-metabolomics.ch/Events-and-Courses.php), and the first ANZMET conference in Melbourne from March 30th – April 1st 2016 (www.anzmet.org).
For more information about support for local meetings, see http://metabolomicssociety.org/events/event-funding.

Free Online Access to Videos from Metabolomics Conference Workshops
Recordings of the workshops from this year's Metabolomics Conference in San Francisco are now available for viewing on the Metabolomics Society website
The presenters are kindly acknowledged for agreeing to make their presentations freely accessible to the public. Additional videos from the scientific sessions of the conference will soon be available to Society members.
Videos from previous conferences and webinars are also available to view at any time on the Metabolomics Society Website. Remember to keep your Metabolomics Society membership up-to-date to ensure access to the most current material.


MEMBERS CORNER

 Early-career Members Network (EMN)
The EMN is dedicated to and run by early-career scientists who are members of the Metabolomics Society and are from academia, government, or industry. The network aims to provide a forum for metabolomics researchers at the start of their professional career.

EMN Elections
With the EMN having been active for over two years we have recently been recruiting new committee members whilst at the same time having to say goodbye to six of the founding members. Out-going are Sastia Prama-Putri (Chair), David Leisenfeld (Secretary), Vincent Asiago (Treasurer), Gabriel Valbuena, Thomas Payne and Eva Daskalaki. Every one of them has contributed a great deal of their free time to establish the EMN and we are eternally grateful for all their efforts.

To replace them we welcome in seven new faces that will help guide our network over the upcoming years: Aoife O’Gorman (Ireland), Baljit Kaur Ubhi (USA), Devin Benheim (Australia), Fidele Tugizimana (South Africa), Jan Stanstrup (Denmark), Nicola Gray (UK) and Stacey Reinke (Sweden). These new recruits join the continuing committee team of Nicholas Rattray (new-Chair), Justin van der Hooft, Ralf Weber, Biswapriya Misra, Agneta Kiss, Jennifer Reid with Sastia Prama-Putri (Past-Chair) and Krista Zanetti acting as EMN advisors. With all members coming from a broad range of countries, this geographical diversity will hopefully allow the EMN to reach out to new members from all over the world.

With our new committee members in place, we are currently allocating roles and working groups that will continue developing our webinar series, conference workshops and outreach activities. Please have a look at the EMN pages within the Metabolomics Society website for further updates: http://metabolomicssociety.org/members-center/early-career-members-network

Please feel free to contact us via info.emn@metabolomicssociety.org if you have any suggestions or comments regarding our planned activities this year (i.e., online webinars and workshops). If you think you have a great idea for a new activity we should organise then please do share with us; the EMN can only be a success with your support and ideas!


Membership News for 2015
EARLY-BIRD Registration will be delayed this year; please stay tuned for more information coming soon!
TASK GROUPS CORNER

 Industry Engagement Task Group
The IETG is looking for corporate and institutional partners to expand the interactions between the Metabolomics Society and instrument vendors, service providers, suppliers, publishers and other institutions. If your business would like to learn more about this exciting opportunity, especially for Metabolomics2016 in Dublin, Ireland, please visit our information portal.


INTERNATIONAL AFFILIATES CORNER

Australian & New Zealand Metabolomics Network (ANZMN)
Visit www.anzmn.com.au
This month the ANZMN celebrates the success of some of its members. First up is ANZMN committee member Dr Devin Benheim of Latrobe University who was recently elected to the Early-career Members Network (EMN) Committee of the Metabolomics Society. If you are an early-career ANZMN researcher and/or have ideas about how to increase networking and training opportunities for young metabolomicists in the Asia-Pacific region, please contact Devin (D.Benheim@latrobe.edu.au) to discuss them, as he is keen to hear from you. The ANZMN also congratulates committee member Dr Daniel Dias on his recent appointment as an early-career fellow at RMIT University; as well as our vice president, Dr Darren Creek on his re-election to the board of the metabolomics society and recent promotion to senior lecturer. Well done to all.

Réseau Français de Métabolomique et Fluxomique (RFMF)
Visit www.rfmf.fr/
French Metabolomics and Fluxomics network will organise its annual conference in Montpellier (south coast of France) from May 30th to June 2nd 2016. Around 250 people are expected with four international invited speakers (list to be announced soon). To facilitate integration of young scientists in the community, some talks will be held in French (slides in English). Nevertheless, we warmly welcome English-speaking contributions. Last but not least, the French society mantra will remain: "good food, good science"!
Note that RFMF members voted for this new logo:
RFMF Logo
PUBLICATIONS CORNER

 Metabolomics journal, Vol. 11, Issue 6, December 2015
See the latest issue of our journal at: http://link.springer.com/journal/11306/11/6/page/1

In addition to the many excellent research papers, this issue contains the following contributions on the Metabolomics Society pages.
Stay abreast of the latest metabolomics news via the Twitter feed on the front page of the website. Also you can follow us on Twitter: Metabolomics Society @MetabolomicsSoc and Metabolomics journal @Metabolomics. And you can visit us on Facebook.


OTHER FEATURES THROUGH THE YEAR

2015 ELECTIONS ANNOUNCEMENT
We are pleased to re-announce that the following have been elected to the Board of Directors of the Metabolomics Society for 2015:

Dr Darren Creek, Monash Institute of Pharmaceutical Sciences, Australia (re-elected for 2nd term)
Dr Sastia Prama Putri, Osaka University, Japan (newly elected)
Dr Krista Zanetti, National Cancer Institute, USA (newly elected)
Dr David Broadhurst, University of Alberta, Canada (newly elected)

We congratulate all the new directors on their election and look forward to working with them over their two-year term starting in October. The Board would particularly like to thank all those who stood for election to the Board this year, and would encourage everyone—whether on the Board or not—to engage with the Society’s mission, for example by joining a task group. (See Board & Committees page of the Metabolomics Society website)

Tim Ebbels, Chair, Nominations and Elections Committee

 
 Software Spotlight

Metabolomics Spotlight

Implementing personalised medicine in the diabetes clinic – a metabolomics approach

Tuulia Hyötyläinen1, Martin Ridderstråle1, and Matej Orešič1

1Steno Diabetes Center A/S, DK-2820 Gentofte, Denmark

About the authors
Tuulia Hyötyläinen: Principal Investigator, Metabolomics and Head of Metabolomics Laboratory, Steno Diabetes Center A/S
Martin Ridderstråle: Vice President, Head of Clinic, Steno Diabetes Center A/S
Matej Orešič: Principal Investigator, Systems Medicine, Steno Diabetes Center A/S

Personalised medicine (PM) refers to a medical model using characterization of individuals’ phenotypes and genotypes for tailoring the right therapeutic strategy for the right person at the right time, and/or to determine the predisposition to disease, and/or to deliver timely and targeted prevention1. PM is widely considered as an alternative to the currently established evidence-based medicine (EBM), which is based on the treatment-failure approach. Alternatively, PM should be viewed as a means of improving the precision of EBM. Owing to the growing recognition that the current healthcare systems are unsustainable together with innovation in biomedical sciences and in information and communications technologies (ICT), several initiatives have been established aimed to support research and pilot studies in PM2,3.

Can metabolomics contribute to PM? We certainly believe so, and this view is widely shared in the metabolomics community.

Steno Diabetes Center is a world-renowned diabetes clinic, which treats about 6000 diabetes patients, among whom there are 3500 patients diagnosed with type 1 diabetes, 2500 patients with type 2 diabetes complicated by micro-and macro-vascular disease, and referred patients with dysregulated metabolism. Given its historic dedication to the advancement of diabetes care, Steno is an ideal setting to test the PM approach in practice. In addition to pursuing metabolomics research to study diabetes and its co-morbidities, our aim is also to introduce metabolomics into the clinic as a key profiling platform used to predict patients’ responses to different treatments—and thus offer decision support tools for patients and clinicians used for selecting or recommending optimal treatment regimens (to be used in the broad sense of the word, thus including also lifestyle changes). The expectation is that by using the ‘personalised profiles’, we will be able to circumvent the commonly applied treatment-failure approach and thus ultimately contribute to better patient outcomes (Figure 1).

Personalised medicine approach using metabolomics

Figure 1. Personalised medicine approach using metabolomics as compared to treatment-failure EBM approach in clinical practice. ‘Personalised profile’ based on metabolomics as well as other clinical and lifestyle data will be used to predict the patients’ responses to specific treatments and thus help select the best treatment regimens.

Several practical challenges lie ahead when translating metabolomics into the clinic. Firstly, while many metabolite biomarkers have been identified which associate with diabetes progression, it is not yet clear if they are informative in the context of patient outcomes in response to different treatments. Longitudinal data is needed from individuals over the course of the disease and its treatments, which can be used as a reference to build the predictive models. Secondly, in current clinical practice most of the blood testing is done on fasting samples. Many ‘personalised’ features of the metabolome are however revealed in response to specific challenges4. Introduction of challenge tests may therefore be needed as part of the patient assessment. Thirdly, data must be quantitative and sufficiently simple to evaluate. Every clinician understands the meaning of a fasting glucose of 6.5, even when the units are not stated. The same is needed for other metabolites measured in the clinic. At Steno, metabolite profiles will be measured at every patient’s visit, so it is essential that the data is comparable between different measurements taken over months to years. Fourthly, metabolomic assays need to be inexpensive. Even if some patient benefit is observed by using metabolic profiles as part of patient assessment, it is unlikely that such an approach will be accepted in clinical practice if it is too expensive.

In response to the above challenges, we have been setting up a quantitative metabolomics assay comprising approximately 50 metabolites, which will be piloted in the diabetes clinic. The panel includes several amino acids, selected phospholipids and bile acids, TCA cycle metabolites, metabolites of the kynurenine pathway as well as selected other metabolites—selected based on the current knowledge of the pathways underlying the development of diabetes and its complications. Software tools are also being developed for automated quality control and to facilitate interpretation of the data.  Only time will tell if the panel is useful for selection of optimal treatments, and if the panel needs to be developed further—without compromising quality and cost. Ultimately, metabolomics will have to be put to the test. In order for metabolomics to be accepted as part of clinical practice, the PM approach using metabolomics (and other relevant clinical and lifestyle data) will need to be compared to the currently established EBM approach (Figure 1)—considering both the health outcomes as well as health economics.

In summary, many challenges lie ahead on the path to implementation of PM in clinical practice. We believe that metabolomics, among many ‘omics’ techniques, has the best chance to make an impact on transforming medicine in the foreseeable future, at least in diabetes prevention and care.

References
  1. EU Horizon 2020 Advisory Group for Societal Challenge 1. Advice for 2016/2017 of the Horizon 2020 Advisory Group  for SOCIETAL CHALLENGE 1, “HEALTH, DEMOGRAPHIC CHANGE AND WELLBEING". 2014. http://www.eurida-research.com/downloads/ag_report-health.pdf. Accessed August 30, 2015.
  2. Collins FS, Varmus H. A new initiative on precision medicine. N Engl J Med. 2015;372(9):793-795.
  3. The PerMed SRIA. Shaping Europe’s Vision for Personalised Medicine. 2015. http://www.permed2020.eu/_media/PerMed_SRIA.pdf. Accessed August 30, 2015.
  4. Krug S, Kastenmuller G, Stuckler F, et al. The dynamic range of the human metabolome revealed by challenges. FASEB J. 2012;26(6):2607-2619.

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 Arjen Lommen.
Arjen Lommen

 Senior Scientist, RIKILT Wageningen University & Research Centre, Wageningen, Netherlands
Arjen Lommen
Biography

Arjen Lommen is a senior scientist at RIKILT Wageningen UR. RIKILT is a government-oriented institute  mainly doing research in food safety (http://www.wageningenur.nl/en/Expertise-Services/Research-Institutes/rikilt.htm). Starting out by studying protein biochemistry, molecular genetics, and technical microbiology (Molecular Sciences, 1985, WUR), he got his PhD in NMR studies on a bacterial protein. During a brief postdoc period at the Dutch National NMR facilities in 1990 (3D NMR on savinase), he taught himself programming in C. In 1991, he accepted his current job at RIKILT (part of Wageningen University and Research Center) and has gradually moved from metabolic profiling using NMR to researching and programming data analysis for high-end MS technology. During his 25 years at RIKILT, he authored and co-authored many papers in high-ranking journals in data analysis as well as applications. He is the author of a number of software packages and programs, amongst others metAlign, metAlignID, Search_LCMS, Search_GCMS, HR3—see also http://www.metabonews.ca/Dec2012/MetaboNews_Dec2012.htm. 


Metabolomics Interview (MN, MetaboNews; AL, Arjen Lommen)

 MN: How did you get involved in metabolomics?

AL: In 1990, I was a postdoc at the Dutch National NMR facility doing 600 MHz 3D heteronuclear NMR studies on a protease called savinase. In those days, 3D NMR was so new that no software was available for the third dimension. I taught myself programming in C to be able to tackle the data on a 50 MHz SUN Unix workstation. In 1991, I started working at RIKILT Wageningen UR (food safety research) as the NMR expert for a new 400 MHz NMR. I realized then—although I was certainly not the first—that NMR had the potential for what was then called “metabolite profiling” or “chemical fingerprinting”. Because data analysis software was not meant for comparing profiles in those days, I started developing C-programs to preprocess and align NMR data. The first major application was in the second half of the 90’s in a big EU-project, which was about utilizing new technology to compare transgenic tomatoes to what was already on the market (Journal of Biotechnology, 2000). This NMR software was later on adapted to Windows C++ for GC-MS and ultimately LC-MS data (metAlign software, www.metalign.nl).

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

AL: Within a one kilometre radius on the Wageningen UR campus, I get to work with lots of experts in mass spectrometry, plant sciences, residue and contaminant analysis, bioinformatics and statistics. All my personal challenges lie in providing software tools for others to solve bottlenecks in metabolomics data analysis. The most exciting aspects were having my alignment software being used in some very early key publications in untargeted MS-based metabolomics: A. For data from a monolithic capillary separation (Anal. Chem, 2003), B. in GC-MS for tomato volatile analysis (Plant Physiology, Breakthrough Technologies, 2005), and C. in plant genetics (Nature Genetics, 2006). Together with Ric de Vos and Sofia Moco of PRI, I am first author of an article in Nature Protocols (2007) that describes how to do untargeted large scale plant metabolomics. After having proven the value of software in many projects, I managed to get metAlign published in 2009 in Analytical Chemistry as sole author. In 2012, metAlignID (J. of Chrom A, 2012) was published, which does extremely fast-targeted analysis of LECO GC-GC-MS data; since then metAlignID has been the primary tool in GC-GC-MS screening for residue and contaminant analysis at RIKILT. In 2015, I was happy to have another sole author publication in Analytical Chemistry on ultrafast PubChem searching and improved filtering rules for elemental composition analysis, based on the outstanding work of Kind and Fiehn, which fits nicely with LC-Orbitrap-MS and metAlign-based post-processing mass precision enhancement and fast LC-MS searching.
MN: What key metabolomics initiatives are you pursuing at your research centre or institute?

 AL: At RIKILT, it is all about logistics in data analysis. The time needed for data analysis is often the bottleneck and the most expensive factor in a full-cost scenario. RIKILT is interested in large-scale targeted analysis using profiling techniques; we call this instrumental screening. Another upcoming field is activity-based screening followed by compound identification.

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

AL: The big development funding boom is over. The focus is now on making technology available to other parties and industry.

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

 AL: During the last few years at RIKILT, our software for metabolomics has been adapted to residue and contaminant analysis. The focus for the future will be on high-end systems like our current LC-Orbitrap-MS and demo GC-Orbitrap-MS. The sub-ppm mass precision, after post-processing of ions and fragments, will limit the number of elemental compositions and possible IDs. My current research is focused on fragment and retention prediction together with fast database searching as well as creation of dedicated databases.




This will be used together with metabolomics-type clean-up strategies for certain chemical classes of compounds (for instance, metabolized compounds). Together this may help in finding “known unknowns” and even pinpointing “unknown unknowns” relevant to residue and contaminant analysis.

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

AL: For us, it is not the metabolomics itself, but the data analysis tricks learned from the metabolomics surge that may drive research.

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

 AL: Identification is currently the biggest bottleneck as well as the lack of standards needed for quantification. Furthermore, ion suppression in LC-MS (soft ionization) is a much underestimated problem. Stable hard ionization techniques for LC-MS are not available. The alternative is to increase the separation. This on the other hand will create data sets which are so big they cannot be handled anymore in an acceptable time frame. For example, LC-LC-ion mobility-accurate mass MS (full scan together with all kinds of fragmentation) is, in principle, technically possible, but the computers or practical software to handle the data are not. Even GC-GC-accurate mass-MS is a question mark.
MN: What improvements, technological or otherwise, need to take place for metabolomics to really take off?

AL: Metabolomics as an untargeted (or broad targeted)  profiling technique is always about many parameters/compounds and statistics. Therefore, we need to do many experiments. Important are very stable, highly-automated sample clean-up and measurement together with highly-automated analysis. Getting perfect data for a reasonable price will probably have to be the basis.

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

AL: In Holland, currently, it is not metabolomics itself that is funded, but applications of the technology. Applications are often small scale, because it is still a relatively expensive technology.

 MN: What role can metabolomics standards play?

 AL: Metabolomics standards are crucial. We have to minimize ambiguity in identification.

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

AL: It has always been a pleasure to have the opportunity to work with so many experts from different disciplines. I have learned so much from them in the past decades. A highly interdisciplinary field like metabolomics depends on a willingness to learn from other experts. Furthermore, I have been very lucky to have been asked/involved in seven consecutive multi-year research programs (Global, EU, national funding, etc.)
 
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
3-6 Nov 2015

Data Analysis for Metabolic Phenotyping
Venue: Imperial College London, South Kensington, London, UK

This 3.5-day course aims to provide a comprehensive overview of data analysis for metabolic phenotyping studies, using data acquired from both mass spectrometry and NMR spectroscopy.

It combines lectures and tutorial sessions to ensure a thorough understanding of the theory and practical applications.
  • Pre-processing of data acquired via LC-MS and NMR.
  • Basic chemometrics and unsupervised analysis including PCA.
  • Supervised analysis and advanced chemometrics - OPLS and O2PLS
  • Pathway analysis and statistical spectroscopy.
Online booking: https://fomcoursebookings.ic.ac.uk/data_metabolic_profiling_11_2015.html

Please visit our website at http://www1.imperial.ac.uk/iiptc/ or contact Dr Tim Ebbels (iptc@imperial.ac.uk) for further information.
7-9 Dec 2015

MetaboMeeting 2015
Venue: Robinson College, Cambridge, UK

SELECTBIO are delighted to announce that we are once again partnering with the Metabolic Profiling Forum (MPF) to host the Metabomeeting 2015. The MPF will focus on the conference program while SELECTBIO will take care of logistics, promotion and exhibition/sponsorship activities. We are expecting up to 270 attendees offering a unique opportunity to network with key researchers who are making innovative discoveries within this field.   We are also delighted to announce that this year the registration price includes a wonderful dinner reception which will be held on Tuesday 8th December in the Magnificent Kings College Dining Hall.

Agenda Topics
  • Advancing Biological Knowledge from Single Cells to Whole Organisms
  • Applying Metabolomics to Nutritional Support and Food Analysis
  • Clinical Development in Metabolomics
  • Enhancing Analytical Approaches in Metabolomics
  • Modelling and Data Analysis
  • New Developments in Plant Metabolomics
  • Next Generation Metabolomics - Where will the Revolution will Happen Next
  • Structure and Reporting of Metabolomics: Data to Knowledge
For further details, visit http://selectbiosciences.com/conferences/index.aspx?conf=Metabo2015
10-12 Dec 2015

3rd ICAN Conference Series on Omics
Venue: Saint James Albany Hotel Spa, Paris, France

On behalf of the steering committee, the Institute of Cardiometabolism And Nutrition (ICAN) is delighted to invite you to attend the 3rd ICAN CONFERENCE SERIES on Omics which will take place in Paris, France, from December 10-12, 2015.

ICAN Conference Series is an educational organization directed and managed by ICAN and the scientific community. Since its inception in 2012, ICAN organized two ICAN conference in 2013 and 2014, and they both were a real success!

ICAN conference Series convene dynamic, open, peer-reviewed conferences on the exciting new frontiers of life science. Whether you are a geneticist, an immunologist or virtually any other type of life science investigator, and whether you are from academia, industry or the government/non-profit sector, we think you will find the experience of attending a ICAN Conference Series meeting valuable and memorable.

As in the previous editions, we aim to warrant high quality scientific programme and facilitate interactions especially between speakers and young investigators and researchers. To that aim ICAN CONFERENCE SERIES scientific board will select young researchers abstracts eligible for Junior researchers registration rate and limit the total number of participants. Moreover, this year, certain young researchers will have the opportunity to be one of the two chairs of each session.

For further details, visit http://www.ican-series.com/home.
11-12 Feb 2016

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 comprehensive theoretical and hands-on approach to teach the latest techniques and tools available to perform metabolite identification applying mass spectrometry in non-targeted metabolomics studies. The course is targeted towards students and researchers who are actively applying metabolomics and want to fully understand the mass spectrometry tools and software applied for metabolite identification.

The course will be taught by experts in the fields of metabolomics and chemical analysis and will include significant hands-on experience using both the Q Exactive and LTQ-Orbitrap mass spectrometers and related software/databases/libraries. The course will focus on:
  • Conversion of raw data to molecular formula and associated difficulties
  • Data Dependent Acquisition (DDA) and Data Independent Acquisition (DIA)
  • MS/MS and MSn data acquisition to construct spectral trees
  • Current software, databases, and libraries applied in metabolite identification
The course will finish with a session on the tips and tricks from the experts and an opportunity to ask questions.

For further information and registration details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/metabolite-identification.aspx or contact Dr Cate Winder (C.L.Winder@bham.ac.uk).
14-19 Feb 2016

EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists
Venue: European Bioinformatics Institute, CB10 1SD, United Kingdom (Google Maps)

This course will provide an overview of key issues that affect metabolomics studies, handling dataset and procedures for the analysis of metabolomics data using bioinformatics tools. It will be delivered using a mixture of lectures, computer-based practical sessions and interactive discussions. The course will provide a platform for discussion of the key questions and challenges in the field of metabolomics, from study design to metabolite identification.

We will have lively and interactive discussion throughout the course in addition to the hands-on data analysis and processing. We encourage you to bring your data, problems you might have with a particular data set or study for group discussion.  You will be asked to present your work and participate in the discussions from day one.

Who is this course aimed at: This course is aimed at PhD students, post-docs and researchers with at least two or three year’s experience in the field of metabolomics who are seeking to improve their skills in metabolomics data analysis.

Topics covered:
  • Metabolomics study design, workflows and sources of experimental error, difference between target and un-target approaches.
  • Metabolomics data processing tools: hands on open source R based programs, XCMS, MetFrag, MetFusion, rNMR, BATMAN
  • Metabolomics data analysis: Using R Bioconductor, understanding usage of univariate and multivariate data analysis, data fusion concepts and data clustering
  • Metabolomics downstream analyses: KEGG, BioCyc, MetExplore and Cytoscape for metabolic pathway and network analysis with visualisation of differential expression, understanding metabolomics flux analysis.
  • Metabolomics standards and databases: data dissemination and deposition in EMBL-EBI MetaboLights repository, collection and ever growing metabolomics online resource, COSMOS data standards, MSI
For further details, visit http://www.ebi.ac.uk/training/course/embo-practical-course-metabolomics-bioinformatics-life-scientists-0.
23-24 Feb 2016

Quality Assurance and Quality Control in Metabolic Phenotyping
Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK

This two-day course will provide a comprehensive theoretical overview of the application of quality assurance (QA) and quality control (QC) in metabolic phenotyping and hands-on training in the analytical laboratory and bioinformatics laboratory. The course is aimed at students and researchers who are actively working in the field and want to learn how to apply the important processes of quality assurance and quality control in their research. Experts who have developed the application of QA and QC procedures within the metabolomics field will lead the course. It will include both theoretical and practical components focused on:
  • Theoretical aspects of QA and QC in metabolic phenotyping
  • The application of QA and QC in untargeted and targeted studies
  • Preparation of QC samples and appropriate data acquisition
  • Data processing and QA/QC reporting
The course will finish with a question and answer session with a panel of experts.

For further information and registration details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/quality-phenotyping.aspx or contact Dr Cate Winder (C.L.Winder@bham.ac.uk).
30 Mar to 1 Apr 2016

The Australian & New Zealand Metabolomics Conference (ANZMET 2016)
Venue: La Trobe Institute for Molecular Science, Melbourne, Victoria, Australia

The inaugural ANZMET conference is an exciting, peer-driven event! It is designed to foster an all-inclusive, engaging and rich interpersonal process through a blend of traditional presentations, rapid-fire postgraduate presentations, poster sessions, a roundtable discussion, and topical peer sessions.

Its aim is to promote collaboration, innovation, and community-building in metabolomics across private and government sectors by open engagement of all researchers and institutions throughout Australia and New Zealand. The conference is actively supported by the Australia & New Zealand Metabolomics Network (ANZMN), in conjunction with the Metabolomics Society and Metabolomics Australia. Several keynote speakers will present at the conference, including Professor David Wishart amongst others.
For further details, visit http://www.anzmet.org/.
4-6 Apr 2016

Metabolomics with the Q Exactive
Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK

This three-day hands-on 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 liquid chromatography-mass spectrometry (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, LC-MS and using the Q Exactive mass spectrometer in your studies
  • Sample preparation for analysis of polar and lipid metabolites in metabolic profiling and targeted studies
  • Instrument methods and 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.

For further information and registration details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/q-exactive.aspx or contact Dr Cate Winder (C.L.Winder@bham.ac.uk).
18 Apr to 26 May 2016

Copenhagen School of Chemometrics - 2016 (CSC-2016)
Venue: Copenhagen, Denmark

  • CSC-2016 is FREE of charge for students at any level.
  • PhD students can obtain a maximum of 12 ECTS.
  • We will count with highly recognized chemometricians as lecturers/teachers: Frans van den Berg, Riccardo Leardi, Thomas Skov, Tormod Næs, Rasmus Bro, Age Smilde, Åsmund Rinnan, Evrim Acar, Federico Marini and Jose M. Amigo.
  • Bonus track: There is the possibility to attend the “Introduction to Matlab for Multivariate Data Analysis” PhD course (see flyer for more information).
The maximum number of participants will be 20 participants per seminar. Therefore, it's strongly recommend to contact Jose Amigo (jmar@food.ku.dk) as soon as possible for keeping your seat!

How to enroll in the CSC-2016? Please, send an e-mail to Jose Amigo (jmar@food.ku.dk) with the information requested in this flyer.
20-22 Apr 2016

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 three-day course will provide a comprehensive overview of dealing with complex biological samples for liquid chromatography-mass spectrometry (LC-MS) analysis. The course is targeted towards students and researchers who are actively applying metabolomics in their research and want to learn more about robust sample preparation and data acquisition. The course will be led by experts in the field and  will include:
  • An overview of sampling, 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 and liquid-liquid extraction
  • An overview of data analysis and metabolite identification
  • An opportunity to ask questions and seek advice to prepare samples in your own research.
For further information and registration details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/sample-analysis.aspx or contact Dr Cate Winder (C.L.Winder@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
Field Application Specialist Metabolomics/Mass spectrometry
 Biocrates Life Sciences
 East Coast, USA
 21-Oct-2015
Biocrates Life Sciences
An academic position in Metabolomics (1 EFT)
 Université Catholique de Louvain Louvain-la-Neuve, Belgium
 19-Oct-2015
Université Catholique de Louvain
Bioinformatics (Metabolomics-specific) Research Fellow 1
 University of Birmingham
 Birmingham, UK 15-Oct-2015
University of Birmingham
Scientist, Section of Nutrition and Metabolism/Biomarkers Group
 International Agency for Research on Cancer Lyon, France
 9-Oct-2015
 4-Nov-2015 International Agency for Research on Cancer
Postdoctoral research position in chemical ecology / (imaging) mass spectrometry
 Max Planck Institute for Chemical Ecology
 Jena, Germany 2-Oct-2015
Max Planck Institute for Chemical Ecology
Four Tenure-Track Faculty Positions in the School of Integrative Plant Science
 Cornell University Ithaca, NY, USA 14-Sep-2015
 Until filled Metabolomics Society Jobs
Assistant/Associate Professor in Plant Metabolomics
 Cornell University Ithaca, NY, USA 11-Sep-2015
 Until filled Metabolomics Society Jobs
Postdoctoral Position in Metabolomics Bioinformatics
 University of North Carolina Charlotte, NC, USA 9-Sep-2015
 Until filled Metabolomics Society Jobs


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.
  • There are currently no positions being advertised.

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