MetaboNews Masthead
Published in partnership between
TMIC and the Metabolomics Society

Issue 56 - April 2016

CONTENTS:


Online version of this newsletter:
http://www.metabonews.ca/Apr2016/MetaboNews_Apr2016.htm

TMIC Services
TMIC Services

Welcome to the fifty-sixth 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 titled "The rising of ambient-ionization mass spectrometry for metabolomics and lipidomics applications", and a metabolomics interview with Philip Britz-McKibbin of McMaster University.


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

2016 Metabolomics Society Conference, Dublin

June 27 June 30, 2016

ABSTRACT SUBMISSION DEADLINE has been extended!  There is still time to submit an abstract for the Conference, until Tuesday, April 5 at 6 pm Central European Time. The Early Bird Registration fee has also been extended to April 5.

The annual Conference of the international Metabolomics Society will be held in the friendly city of Dublin, and will showcase the latest advances in metabolomics technology and novel biological insights that are emerging from metabolomics science. The conference will feature six diverse workshops including two workshops from the EMN and sessions that explore the following major themes:

There is an exciting list of plenary and keynote speakers with expertise ranging across the full spectrum of metabolomics development and applications.

The EMN has a series of events planned for the conference with more details at http://metabolomics2016.org/program/early-career-member-network-reception

Register at www.metabolomics2016.org and book your accommodation at http://metabolomics2016.org/venue/hotel-information to secure a room at conference special rates.

Student and Early Career members of the Society are eligible for travel awards. See http://metabolomics2016.org/submission/awards for application details.

Videos from previous conferences and webinars:
If you can’t wait until June for another dose of cutting-edge metabolomics, or you want a sneak peak of what to expect at an international conference of the Metabolomics Society, a range of videos are available online to view at any time at http://metabolomicssociety.org/resources/videos. These videos include keynotes and workshops from previous conferences, in addition to EMN Webinars from last year. Some content is limited to members only, which includes everyone that has registered for the Dublin 2016 conference!


2016 HONORARY FELLOWS ANNOUNCED

An Honorary Fellowship is a significant lifetime award granted by the Board of Directors of the Metabolomics Society to recognize exceptional members of the community who have either made outstanding contributions to the Metabolomics Society over a sustained period of time, and/or made a pioneering and sustained contribution to the science of metabolomics at an international level. With up to two lifetime fellowships awarded each year, the Board is pleased to recognize the following individuals as the lifetime Honorary Fellows of the Metabolomics Society for 2016:

Professor Roy Goodacre: In recognition of his pioneering work in establishing the Metabolomics Society (Director 2005-2015) and establishment of the journal Metabolomics (2005) as the premier journal in the field. His sustained record of academic contributions and service as a goodwill ambassador for the area of metabolomics has materially advanced the role of metabolomics in the scientific community.

Professor Matej Orešič: in recognition of his groundbreaking development of metabolomics data processing tools and powerful analytical methods that have enabled systems-level investigations of processes that lead to obesity and diabetes, with a specific focus on type 1 diabetes.

We congratulate both of these esteemed scientists and look forward to their continued contributions in the years to come.


MEMBERS CORNER

Membership News for 2016
Please remember that when you register for the 2016 Metabolomics Society Conference, Dublin as a non-Member, you will automatically become a member of the Society for the rest of the calendar year. Please follow the instructions provided after you register as a non-member.

Publications News
The Society’s Request For Proposals (RFP) for establishing a new Official Journal of the Metabolomics Society is receiving a very favorable response from reputable publishers and the Publications Committee of the Board will soon be reviewing these proposals. We look forward to some exciting news soon.

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.

The EMN is present at Metabolomics2016 in Dublin (Ireland)
The early-career members network (EMN) committee is working hard to prepare its events during the Metabolomics2016 conference in Dublin, Ireland, from June 27 - June 30. We hope to see many early-career metabolomics researchers at the conference and during our events. We will host a social mixer prior to the conference on June 26 from 6 pm – 8 pm in a pub not too far from the conference location. We will also hold a more formal event after the poster session on Tuesday afternoon, where we will discuss your and our future ideas on the role and function of the EMN with the entire EMN community. Finally, the EMN will chair the early-career session during the conference. When in Dublin, keep an eye out for our conference stand where you can find more information and a nice and useful EMN gadget.

We would appreciate it if you indicate your presence during the conference registration so we know roughly how many of you to expect. This will allow us to prepare nice events for you! If you have any ideas or suggestions for the EMN committee, feel free to send a message to [email protected].

EMN webinar series
The EMN organized and hosted another webinar in March, this time with Dr Reza Salek from the EMBL-EBI on the tools and infrastructure that has been developed over the last years to store and share metabolomics data from different analytical platforms. The webinar generated a good Q&A session at the end and active participation was encouraged by polling questions during the webinar. Stay tuned for more EMN webinars in the coming months!

Please feel free to contact us via
[email protected] if you have any suggestions or comments regarding our planned activities this year. 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!!


TASK GROUPS CORNER

Model Organism Metabolomes Task Group
The MOM task group has published its first paper, “The Time Is Right to Focus on Model Organism Metabolomes”, which proposes a grand challenge for metabolomics studies of model organisms: to identify and map all metabolites onto metabolic pathways, to develop quantitative metabolic models for model organisms, and to relate organism metabolic pathways within the context of evolutionary metabolomics. This paper is freely available at http://www.mdpi.com/2218-1989/6/1/8

International Affiliates Task Group Meeting in Dublin
The Metabolomics Society has last year established a new task group, uniting all the international Affiliates. Affiliates are national a regional Metabolomics Societies or Foundations, which meet with each other to exchange ideas how to best organize themselves and to offer services to their members, as well as to lobby for funding. The Task Group will be meeting during the Metabolomics Society meeting in Dublin (date will be confirmed). The meeting is also open to individuals or groups that have an intention to set up a national or regional organisation, but haven't yet affiliated themselves with the Society, or are in the process of setting up a legal entity.

If you are interested in joining the meeting or knowing more about the task group you can contact Merlijn van Rijswijk, Chairman of the International Affiliates Task Group ([email protected]) or Ute Roessner of the Metabolomics Society Board of Directors ([email protected]).


INTERNATIONAL AFFILIATES CORNER

Australian & New Zealand Metabolomics Network (ANZMN)
Visit http://www.anzmn.org

ANZMN members were hard at work at the 2016 Agilent Young Scientist Forum (http://www.agilent.com/en-us/promotions/ysf-2015-ap?cid=13045) held at the Florey Institute of Neuroscience and Mental Health (University of Melbourne) in March. ANZMN president Oliver Jones, past president Ute Roessner, and committee members Dave De Souza, Damien Callahan, Devin Benheim, Dedreia Tull, Zofia Felton, and Dan Dias were among the mentors listening to the next generation of Australian life scientists discuss their work. Metabolomics and proteomics featured highly and the standard of presentations was outstanding. The ANZMN congratulates all those who took part and thank Agilent Technologies and the University of Melbourne for organising it.

Korea Metabolomics Society (KoMetS)
Visit http://komets.or.kr/english05.html

Korea Metabolomics

          Society

The 2016 annual symposium and general meeting has been scheduled. The symposium will be held in Konkuk university campus, Seoul from Apr. 7-8. The program consists of 6 sessions, Drug discovery & pharmacology, Food, nutrition & environment, Microbial metabolomics, Human diseases, Emerging technology, and Plant metabolomics. Prof. Akihiko Kondo (Kobe Univ., Japan), and Prof. Eiichiro Fukusaki (Osaka Univ., Japan), Prof. Dong-Yup Lee (Nat. Univ. of Singapore, Singapore), and Dr. Geum-Sook Hwang (Korea Basic Science Institute., Korea) will be invited as keynote lecturers.

Netherlands Metabolomics Centre (NMC)
Visit www.metabolomicscentre.nl/



 
Software Spotlight

Metabolomics Spotlight


The rising of ambient-ionization mass spectrometry for metabolomics and lipidomics applications

Feature article contributed by Bindesh Shrestha1 and Giuseppe Astarita1,2

1 Waters Corporation, Milford, MA 01757, USA
2 Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20007, USA

Ambient ionization mass spectrometry (AIMS) consists of a developing group of mass spectrometry (MS) ionization techniques. With minimal sample preparation, these techniques perform direct-sampling analyses at atmospheric pressure (ambient conditions). Sampling and ion-generation take place in concert, typically facilitating high analytical throughput. Since the introduction of desorption electrospray ionization (DESI) in 2004, at least 25 different AIMS ion sources have been introduced, each with a unique combined approach to either sampling or ionization. Recent advances in AIMS technology have been discussed in detail.1-3 In terms of the number of peer-reviewed publications, DESI has led the pack among these AIMS techniques. A simple citation search of “desorption electrospray ionization” returns more than 1100 peer-reviewed articles (Web of Science, Thomson Reuters, New York, NY, accessed January 4, 2016). Articles published each year from 2004 to 2015 are shown in Figure 1 (top) with typical citations per article (bottom). Some popular peer-reviewed journals that are publishing DESI-related articles are tabulated in Table 1.

Number

          of articles published per year

Figure 1. Number of articles published per year, from 2004 to 2015, on the topic “desorption electrospray ionization” (upper graph) and a trend of citation received per article (lower graph). Based on Web of Science database (Thomson Reuters, New York, NY).

Journal Name
Impact Factorα Number of Publications
Analytical Chemistry
5.636
203
Analyst
4.107
84
Journal of the American
Society for Mass Spectrometry
2.945
79
Rapid Communications in Mass
Spectrometry
2.253
76
Analytical and Bioanalytical
Chemistry
3.436
57
Journal of Mass Spectrometry
2.379
52
International Journal of Mass
Spectrometry
1.972
32
Analytica Chimica Acta
4.513
21
Analytical Methods
1.821
20
Proceedings of the National
Academy of Sciences
9.674
19
α Based on Journal Impact Factor (2014) from Thompson Reuters, New York, NY.

Table 1.
Top peer-reviewed journals with papers on the topic of “desorption electrospray ionization”.

AIMS techniques have been employed to detect metabolites and lipids directly from biofluids, mammalian tissue sections, microbial colonies, cell cultures, etc.4-6 AIMS offers straightforward metabolomics and lipidomics workflows, doing so with almost no reagent use and without time-consuming sample extraction and other preparation steps. Samples are analyzed outside the high-vacuum conditions of a mass spectrometer, making AIMS conducive to the survival of live specimens and thus creating the possibility of in vivo analysis. Often only a sample-staging step, such as the sectioning of tissue on microscope slides, is required. In small subsets of AIMS, such as rapid evaporative ionization mass spectrometry (REIMS),7 sample staging is less critical or unnecessary. In REIMS, for example, analytes can be extracted directly from the surface of a sample, a tumor lesion from a rodent, for example, or the skin of a fruit. Via long flexible tubing, the samples are then transported to a mass spectrometer for detection. Such an application demonstrates the ability of AIMS to generate, in real time, molecular fingerprints that can be used to discriminate among phenotypes.

In situ detection of lipids and metabolites from tissue is also possible using other, conventional methods such as matrix-assisted laser desorption/ionization (MALDI). However, typical MALDI instrumentation requires the application of organic molecules as a matrix and the introduction of the sample into a vacuum. Like MALDI, AIMS techniques are constrained by their incapacity to separate isobaric species and by ion suppression effects. To circumnavigate this limitation, AIMS has been used in combination with ion mobility separation, as a post-ionization separation tool prior to MS detection, improving the specificity of analyte identification and the signal-to-noise ratio.8-10 Figure 2 shows the power of ion mobility separation for discriminating classes of biomolecules during molecular analysis of mouse brain tissue using one of the AIMS techniques, laser ablation electrospray ionization (LAESI).

Utility of ion

          mobility separation in combination with ambient ionization

          mass spectrometry

Figure 2. The utility of ion mobility separation in combination with ambient ionization mass spectrometry (AIMS). Without ion mobility separation, many ions from different groups of biomolecules can be difficult to separate. Mass spectra discriminating just a group of molecules, such as lipids, can be easily produced by selecting a defined m/z and drift time range (Adapted from Shrestha et. al., Analytical Chemistry 2014).11

Molecular MS imaging is among the most remarkable applications of AIMS. Briefly, in a typical MS-imaging experiment, a focused laser beam or stream of charged droplets scans along a sample section of surface tissue, obtaining a mass spectrum at each defined pair of x and y coordinates. The intensities of detected ions in those mass spectra can be plotted, to obtain maps of corresponding metabolites and lipids in those tissue sections. In terms of spatial resolution, DESI is capable of resolving features in the tens of micrometers. Figure 3 depicts an example of DESI image produced from a coronal section of a mouse brain.

Molecular image of phospholipids

          in a coronal section of mouse brain

Figure 3. Molecular image of phospholipids in a coronal section of mouse brain obtained using DESI is presented alongside an optical image of a concurrent section. A typical positive mass spectrum of brain tissue using DESI is also shown (Adapted from Waters Technical note# 720005297en).
 
Until recently, the majority of the AIMS-related applications reported in the literature used home-built AIMS systems. These home-built ion sources were typically coupled to the inlet of a commercial mass spectrometer, usually in lieu of an electrospray ion source. Several of the AIMS methods have been commercialized, notable among them DESI, by Prosolia, LAESI, by Protea, and direct analysis in real time (DART), by IonSense. Usually those ion sources are retro-fitted onto commercial mass spectrometers manufactured by Agilent, Bruker, Thermo, Waters, JEOL, and others. In most cases, these bolted-on ion sources require additional external software for instrument control and data analysis workflow. Waters, however, has licensed the DESI technology from Prosolia and also has acquired all assets relating to REIMS technology from MediMass. Currently, both DESI and REIMS are readily available as integrated options in both the Waters SYNAPT and Xevo family of instruments. This commercial solution, allowing for seamless instrument control and data analysis, will encourage additional researchers to adopt AIMS for their applications.

References
  1. Nemes, P., Vertes, A. TrAC Trends in Analytical Chemistry 2012, 34, 22.
  2. Monge, M. E., Harris, G. A., Dwivedi, P., Fernández, F. M. Chemical Reviews 2013, 113, 2269.
  3. Huang, M.-Z., Yuan, C.-H., Cheng, S.-C., Cho, Y.-T., Shiea, J. Annual review of analytical chemistry 2010, 3, 43.
  4. Wiseman, J. M., Ifa, D. R., Song, Q., Cooks, R. G. Angewandte Chemie International Edition 2006, 45, 7188.
  5. Shrestha, B., Nemes, P., Nazarian, J., Hathout, Y., Hoffman, E. P., Vertes, A. Analyst 2010, 135, 751.
  6. Jackson, A. U., Tata, A., Wu, C., Perry, R. H., Haas, G., West, L., Cooks, R. G. Analyst 2009, 134, 867.
  7. Schäfer, K. C., Dénes, J., Albrecht, K., Szaniszló, T., Balog, J., Skoumal, R., Katona, M., Tóth, M., Balogh, L., Takáts, Z. Angewandte Chemie International Edition 2009, 48, 8240.
  8. Paglia, G., Kliman, M., Claude, E., Geromanos, S., Astarita, G. Analytical and bioanalytical chemistry 2015, 1.
  9. Stopka, S. A., Shrestha, B., Maréchal, É., Falconet, D., Vertes, A. Analyst 2014, 139, 5946.
  10.  Inutan, E., Trimpin, S. Journal of the American Society for Mass Spectrometry 2010, 21, 1260.
  11.  Shrestha, B., Vertes, A. Analytical Chemistry 2014, 86, 4308.


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 [email protected].

 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 Philip Britz-McKibbin.

Professor at the Department of Chemistry and Chemical Biology and Cystic Fibrosis Canada Researcher at McMaster University in Hamilton, Canada
Philip

                Britz-McKibbin

Biography

Philip Britz-McKibbin is a Professor at the Department of Chemistry and Chemical Biology and Cystic Fibrosis Canada Researcher at McMaster University in Hamilton, Canada. His research interests in bio-analytical chemistry and metabolomics include the design of novel analytical strategies to quantify and identify metabolites in biological samples, as well as characterization of their interactions with protein. Philip’s laboratory aims to discover new biochemical markers that support early detection and treatment of human diseases relevant to population health and preventative medicine.

Metabolomics Interview (MN, MetaboNews; PBM, Philip Britz-McKibbin)

MN: How did you get involved in metabolomics?

PBM: I was first introduced to the paradigm of discovery-based metabolomics research as a postdoctoral fellow in Japan from 2001 to 2003. At that time, I visited the Institute for Advanced Biosciences at Keio University, which recently established their metabolomics facility with a unique focus on capillary electrophoresis-mass spectrometry (CE-MS). When returning to Canada to start my first faculty position in 2003, our research group focused on expanding the performance of CE-MS for metabolomics. This was an interesting time period when metabolomics research and technology development were still in their infancy.


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

PBM: One major hurdle in MS-based metabolomics remains the low sample throughput and high costs notably when using conventional separation techniques [1]. As a result, major infrastructure investment and human resources are required for data acquisition and data pre-processing that are subject to bias. Our research group has recently introduced a multiplexed separation platform to enable higher throughput metabolomic studies referred to as multisegment injection (MSI)-CE-MS [2]. In essence, serial injection of up to ten discrete samples is used to enhance throughput by one order of magnitude while ensuring high data fidelity within a single capillary/MS instrument. This approach has been a game changer as it enables us to “do more with less” while implementing an accelerated data workflow for biomarker discovery in metabolomics with quality assurance [3].

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

PBM: Our research group continues to focus on fundamental research in separation science [5], including the development of models for predicting solute ionization efficiency and electromigration behavior together with chemical derivatization as a way to expand metabolome coverage [4]. We are also involved in several exciting collaborative research projects, including the validation of practical exercise training protocols for improving health outcomes on an individual level [5]. Also, our group is also striving to identify novel metabolic signatures of cystic fibrosis in infants for improved population-based screening in newborn screening programs, as well as assessment of dietary interventions for chronic disease prevention [6].

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

PBM: A growing number of funding agencies in Canada recognize the importance of metabolomics. However, there is still a long way to go to ensure that Canadian researchers remain competitive on an international level. The Metabolomics Innovation Centre (Edmonton/Victoria) is at the forefront of metabolomics research as recognized by their widely popular bioinformatic tools, metabolome databases and quantitative analytical services. There are several other independent research groups at universities involved in biomedical, nutritional and environmental focused metabolomics research as well (Calgary, Hamilton, Toronto, Montreal). However, there is an urgent need for establishing a national metabolomics consortium with regional facility nodes (similar to Metabolomics Australia) to ensure wise infrastructure investments are coupled with cutting-edge training programs in core areas of research of national importance.

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

PBM: Indeed, CE-MS remains somewhat of a fringe analytical platform within the metabolomics community, notably outside of Japan. However, CE technology is experiencing “a renaissance” given recent developments in improving concentration sensitivity, and its expanding use within the biopharmaceutical industry, including intact protein separations, peptide mapping and glycan analysis. With improved vendor support and training, we remain optimistic that MSI-CE-MS will provide researchers major incentives as a viable platform for deciphering the “ionic metabolome”. In comparison to hydrophilic interaction chromatography, benefits of MSI-CE-MS include higher sample throughput, lower operating costs, unique data workflows, minimal sample pretreatment requirements, better quantitative performance and compatibility to volume-restricted, highly saline or mass-limited biospecimens. One major milestone to achieve still is rigorous inter-lab validation studies using standardized operating protocols to facilitate method adaptation by new users [7], as well as its application to diverse biological samples ranging from lyophilized fecal extracts, placenta tissue to pilocarpine-stimulated sweat.

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

PBM: As other researchers have demonstrated, metabolomics offers an exciting opportunity to characterize the molecular phenotype of organism underlying the complex interplay of genes, environment, and gut microflora relevant to human health. In many ways, metabolomics transcends conventional molecular biology since metabolites are not only related to endogenous cellular processes (e.g., central energy metabolism), but also represent extrinsic bioactive components from the diet, as well as “lifelong” chemical exposures in the environment. In essence, metabolomics offers a holistic approach to better understand the confounding factors that impact human health while being applicable to a remarkable diversity of fields of interest.


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

PBM: In addition to limitations related to sensitivity, sample throughput and data comparability, other major barriers still exist for metabolomics, notably unknown metabolite identification, automated data pre-preprocessing, and mechanistic insights into the significance of perturbations in dynamic metabolic pathways. Similar to the early promise of other “-omics” sciences, careful experimental design and statistical interpretations using validated protocols are needed to reduce false discoveries. This is critical for successful translation of metabolomics research that ultimately has measurable benefits to society.

MN: What improvements, technological or otherwise, need to take place for metabolomics to really take off?

PBM: Better outreach and education is needed to promote metabolomics to the wider research community, including government and industry in order to overcome fundamental challenges in the field. For instance, a North American Chapter of the Metabolomics Society has recently been formed to better coordinate activities, and engage members to identify core areas of regional concern. One initiative that the chapter has introduced is a series of free webinars posted on YouTube related to the “Grand Challenges in Metabolomics” that incorporates live polling information and questions/answers from the community [8]. Congratulations to Lloyd Sumner and Dan Bearden for spearheading this exciting initiative!

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

PBM: Overall, funding opportunities for metabolomics have expanded rapidly over the past several years as reflected by the NIH Common Fund. Although Canada still lacks a national program for metabolomics, funding opportunities do exist, yet are fragmented among different agencies (CFI, Genome Canada, CIHR, NSERC) with separate investments made to infrastructure, personnel training and research programs. However, recent multidisciplinary initiatives related to microbiome, nutrition, epidemiology and exposure biology have increased awareness of the pivotal role metabolomics plays in cutting-edge discovery-based scientific research, such as the recent CIHR-funded developmental origins of health and disease (DOHaD) competition.

MN: What role can metabolomics standards play?

PBM: As the field has matured, community-based metabolomics standards have been critical to ensure that high quality scientific research is published that minimizes bias and is amenable to replication. Minimum reporting requirements are now demanded by most reputable journals, including detailed descriptions of experimental design, sample pretreatment, metabolite identification, data pre-processing, and statistical analyses. New venues to share metabolomics experiments and reference spectra within curated databases (e.g., MetaboLights) will also enable improved transparency and cooperation among fellow researchers.

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

PBM: Although metabolomics has grown rapidly over the past five years, major technical, instrumental and bioinformatics challenges remain when compared to more established “–omics” fields. Although access to high resolution MS infrastructure has been a welcome addition, fundamental research programs in separation science, gas-phase ion chemistry and solute ionization together with rigorous training in analytical method development and quality assurance are critical aspects to successful long-term metabolomics initiatives.

References:
  1. N.L. Kuehnbaum and P. Britz-McKibbin “New Advances in Separation Science for Metabolomics: Resolving Chemical Diversity in a Post-genomic Era” Chem. Rev. 2013, 113: 2437-2468.
  2. N.L. Kuehnbaum, A. Kormendi and P. Britz-McKibbin “Multi-segment Injection Capillary Electrophoresis-Mass Spectrometry: A High-throughput Platform for Metabolomics with High Data Fidelity” Anal. Chem. 2013, 85: 10664-10669.
  3. N.L. Kuehnbaum,* A. Kormendi*, A. DiBattista,* K.P. Lam,* J.B. Gillen,* M.J. Gibala and P. Britz-McKibbin “Multiplexed Separations for Biomarker Discovery in Metabolomics: Elucidating Adaptive Responses to Exercise Training” Electrophoresis 2015, 36, 2226-2236.
  4. L. A. D’Agostino, K. P. Lam, R. Lee and P. Britz-McKibbin “Comprehensive Plasma Thiol Redox Status Determination for Metabolomics” J. Proteome Res. 2011 10, 592-603.
  5. N.L. Kuehnbaum, J.B. Gillen, M.J. Gibala and P. Britz-McKibbin “Personalized Metabolomics for Predicting Glucose Tolerance Changes in Sedentary Women After High-Intensity Interval Training” Scientific Reports 2014, 4: 6166.
  6. F. Badoud, K. P. Lam, M Perreault, M.A. Zulyniak, P. Britz-McKibbin and D. Mutch, “Metabolomics Reveals Metabolically Healthy and Unhealthy Obese Individuals Differ in their Response to a Caloric Challenge” PLoS One 2015, 10: e0134613.
  7. C. Wenz, C. Barbas, Á. López-Gonzálvez, A. Garcia, F. Benavente, V. Sanz-Nebot, T. Blanc, G. Freckleton, P. Britz-McKibbin, M. Shanmuganathan,* F. de l’Escaille, J. Far, R. Haselberg, S. Huang, C. Huhn, M. Pattky, D. Michels, S. Mou, F. Yang, C. Neusuess, N. Tromsdorf, E.E.K. Baidoo, S. Suhr Park  “Inter-laboratory Study to Evaluate the Robustness of Capillary Electrophoresis-Mass Spectrometry for Peptide Mapping” J. Sep. Science 2015, 38: 3262-3270.
  8. P. Britz-McKibbin “Improving Metabolomics Cost, Throughout and Data Comparability” In: Metabolomics Grand Challenges Webinar Series. Published: December 9, 2015
    https://www.youtube.com/watch?v=JIuAD8FV_Jk

 
Please note: We are open to suggestions for our MetaboInterviews section. Please send suggestions for future interview candidates to Ian Forsythe at [email protected].

Metabolomics Current Contents

Metabolomics Current Contents


Recently published papers in metabolomics:

MetaboNews

MetaboNews

22 Mar 2016

New GigaScience series on "Metabolomics: approaches, applications, and integration"

Guest edited by Ute Roessner and Ruth Welti, this cutting-edge series aims to shed light on new advances, applications, and challenges, and to improve data sharing and reproducibility in research utilizing metabolomics.

See the series page at http://www.biomedcentral.com/collections/metabolomics

This rolling/ongoing series has launched with the first two papers. The Viant group at the University of Birmingham has published a Technical Note presenting the first end-to-end metabolomics data analysis workflow that is implemented in the popular Galaxy platform. Galaxy-M (following the naming convention of the proteomics Galaxy-P pipeline) showcases the sharing and reproducibility goals of the series, with all the test data in MetaboLights and GigaDB, and the scripts, Galaxy files and a virtual machine all archived in GigaDB. Also launching the series is a Review article, written by Yozo Okazaki and Kazuki Saito, highlighting integrated metabolomic and phytochemical genomic studies to improve breeding strategies and quality of rice.

Okazaki Y, Saito K. Integrated metabolomics and phytochemical genomics approaches for studies on rice. Gigascience. 2016, 5:11. doi:10.1186/s13742-016-0116-7.

Davidson RL, Weber RJ, Liu H, Sharma-Oates A, Viant MR. Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data. Gigascience. 2016, 5:10. doi: 10.1186/s13742-016-0115-8.

For further questions about the series, please contact GigaScience at [email protected]; they look forward to receiving your integrative metabolomics submissions.

Metabolomics

                  Events

Metabolomics Events

3-7 Apr 2016

Microscale Separations and Bioanalysis: MSB 2016
Venue: Queen’s Landing, Niagara-on-the-Lake, ON, Canada

We invite you to join us for the 32nd International Symposium on Microscale Separations and Bioanalysis (MSB 2016), which is the premier forum for the discussion of cutting-edge research on the frontiers of separation science relevant to human health and the environment. If you are currently incorporating microscale separations like capillary electrophoresis, nano-LC, multidimensional separations, ion mobility spectrometry, microfluidics and lab-on-a-chip devices into your research, then this is a meeting you will not want to miss!

To ensure a stimulating yet intimate environment for discussions, MSB 2016 will be limited to 275 delegates. We invite you to browse our conference website (www.msb2016.org) to learn more about our exciting scientific program.

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 ([email protected]).

17-19 Apr 2016

4th Workshop on Holistic Analytical Methods for Systems Biology Studies
Venue: Aristotle University, Thessaloniki, Greece

This is the fourth in a series of successful meetings that started in Thessaloniki in 2008 and then moved to Athens and Patras.

We expect again high level presentations and an open, friendly atmosphere. We plan tutorial sessions on protocols, tips and tricks, live demonstration of software, and training session for small number of young participants with hands on PC.

The first day is devoted to fundamentals/methods/protocols, the second day to health/life sciences and the last day to food/plant/nutrition.

Topics:
  • Analytical Technologies for Metabolite Profiling: LC-MS, GC-MS, NMR
  • Informatics, Chemometrics, Validation
  • Biomarker Discovery: Disease, Drug Efficacy, Embryo Growth, Ageing, Physical Exercise
  • Food authenticity/geographical origin, Nutrition
  • Investigation of gut microbiota host-guest symbiosis
Information: [email protected]
Looking forward to seeing you in the historic port city of Thessaloniki.

For more information, visit http://bioanalysis.web.auth.gr/metabolomics.

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 ([email protected]) as soon as possible for keeping your seat!

How to enroll in the CSC-2016? Please, send an e-mail to Jose Amigo ([email protected]) 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 ([email protected]).

28 Apr 2016

Omics eSeminar Series: Introducing Agilent’s Newest Metabolomics Solution!
Note: Registration is required to join this event. If you have not registered, please do so now.

Agilent is the leader in providing innovative metabolomics solutions. This webinar will introduce Agilent’s newest addition to our comprehensive portfolio. Come join our celebration as we introduce our newest contribution to the world of metabolomics research!

For more information and to register for this event, visit the event website. For a list of recorded past Omics eSeminar Series events, visit http://www.agilent.com/en-us/training-events/eseminars/emerging-omics.

3-4 May 2016

2016 SECIM Metabolomics Symposium
Venue: Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida, USA

The 3rd Annual SECIM Metabolomics Symposium will be held Tuesday, May 3 through Wednesday, May 4, at our partner institution, Sanford Burnham Prebys Medical Discovery Institute in Orlando, Florida.

The two-day symposium will review the basics of metabolomics, while showcasing the application of metabolomics in a variety of fields. Registration is FREE! The event is appropriate for graduate students, technicians, postdocs and faculty new to the field.

RSVP Deadline: Friday, April 22

Please feel free to distribute the 2016 SECIM Metabolomics Symposium flyer to any interested persons.

For more information and to register for this event, visit http://secim.ufl.edu/education/events/.

9-12 May 2016

Metabolomics Summer Workshop
Venue: Kellogg Eye Center (Kellogg Auditorium), located at 1000 Wall Street, Ann Arbor, MI, USA

The Michigan Regional Comprehensive Metabolomics Resource Core (MRC)2 is presenting a four-day Metabolomics Summer Workshop, May 9-12, 2016.

Registration: https://umichumhs.ut1.qualtrics.com/SE/?SID=SV_bPEVDn7I5wSEcwl
 
This workshop is intended for investigators seeking a solid foundation to expand their research using metabolomics.
Sessions include:
  • Study design
  • Sample collection
  • Analytical methods
  • Data processing, statistical analysis, and metabolite identification
  • Exploratory analysis with bioinformatics tools
  • Case study applications
  • Hands-on data analysis training, including statistical analysis and data visualization
After attending the workshop, you will be able to:
  1. Understand the principles of the analytical methodologies and data analysis techniques used in metabolomics.
  2. Use this knowledge to incorporate metabolomics into your research.
  3. Understand the reasoning behind data processing and statistical analysis.
  4. Gain a working familiarity with bioinformatics tools for exploratory analysis.
Costs per participant are $350 for internal U-M investigators and $750 for external investigators. Lunches are included.

If you have any questions about the workshop, please contact Terri Ridenour.
 
For more information, visit the MRC2 website.

26-27 May 2016

Informatics and Statistics for Metabolomics (2016)
Venue: Downtown Toronto, Canada

CBW will be hosting a Metabolomics workshop May 26-27 in downtown Toronto.

The workshop will cover many topics ranging from understanding metabolomics technologies, data collection and analysis, using pathway databases, performing pathway analysis, conducting univariate and multivariate statistics, working with metabolomic databases and exploring chemical databases. Participants will be given various data sets and short assignments to assist with the learning process.

For more information and to register, visit http://bioinformatics.ca/workshops/2016/informatics-and-statistics-metabolomics-2016.

30 May-2 Jun 2016

10th conference of the Francophone Metabolomics and Fluxomics Society (RFMF)
Venue: Montpellier, France

RFMF is pleased to announce the 10th conference of the Francophone Metabolomics and Fluxomics Society (RFMF), to be held in Montpellier between the 30th of May and the 2nd of June 2016. Every year since 2005, this conference gathers scientists who are interested in metabolomics and fluxomics, and more generally in the study of metabolism. This year, the main scientific themes are:
  • Ecotoxicology, environmental metabolomics and microbiology
  • Health: clinical applications, therapeutic monitoring, biomarker determination
  • Agricultural resources and food science
This conference is also a good opportunity to hear about recent developments in analytical methods/hardware and bioinformatics tools in metabolomics and fluxomics. The meeting will include:
  • Plenary lectures by renowned international invited speakers:
    • Prof. Arthur Edison (University of Georgia, USA)
    • Prof. Elizabeth Hill (University of Sussex, UK)
    • Dr. Kris Moreel (University of Gent, Belgium)
    • Dr. Patrick Kiefer (ETH Zurich, Switzerland)
  • Oral presentations
  • Flash communications associated with poster sessions
  • Thematic workshops and round-tables
The registration and submission interfaces will open on February 1st 2016. The deadline for abstracts to be considered for oral presentations is April 1st 2016. More information can be obtained on the website of the RFMF conference: http://10-js-rfmf.sciencesconf.org/

27-30 Jun 2016

Metabolomics 2016
Venue: Convention Centre, Dublin, Ireland

The 12th Annual International Conference of the Metabolomics Society will be held in Dublin from June 27-30, 2016. The conference venue is the Convention Centre Dublin, located conveniently in the city centre with easy access to the airport. In the historic, compact city centre there is lots to do and see, and visitors will love the rich selection of galleries, museums, restaurants, pubs and shops, not to mention the traditionally warm welcome from Dubliners.

The conference programme will cover all aspects of metabolomics under five broad themes: Metabolomics in Nutrition and Food Research, Metabolomics in Health and Disease, Advancing the Field, Environmental, Plant and Model Organisms.

For further details, visit http://metabolomics2016.org.

17-21 Jul 2016

4th Annual Workshop on Metabolomics
Venue: University of Alabama, Birmingham, Alabama, USA

The 4th Annual UAB Metabolomics Workshop, sponsored by the NIH Common Fund Metabolomics Program, will be held Sunday, July 17 to Thursday, July 21, 2016. Registration is now open (http://www.uab.edu/proteomics/metabolomics/workshop/workshop_july_2016.php) and will close on April 29, 2016. There will be slots for up to 40 registrants. An R25 grant from the NIGMS provides funding support for graduate students and postdoctoral fellows. Slots are also available for Faculty at all levels who wish to receive training in this rapidly growing complement to biomedical research.

Women, members of under-represented minority groups, and individuals with disabilities are strongly encouraged to apply.

The metabolome, in distinction to the other –Omics, provides a better assessment of the exposure to the chemicals of life – it is truly intergenomic providing information on “metabolites” coming from ourselves or the model we’re using, the unique, non-human/mammalian compounds we consume as part of our food, compounds generated by the microorganisms that are part of “us”, and other compounds that are in the environments we live in. If ever precision medicine is able to deliver what is claimed it will, it has to include the metabolome context in which genes and proteins are operating.

The themes in this fourth year of the workshop are:
  1. Design of a metabolomics experiment
  2. Sample stability and extraction methods
  3. Analytical systems (nuclear magnetic resonance and gas- and liquid chromatography-mass spectrometry)
    • Targeted metabolomics
    • Untargeted metabolomics
    • Quantitative metabolomics
  4. Pre-processing of analytical data (Mzmine 2 and XCMSonline and Chenomx)
  5. Statistical analysis of the data (MetaboAnalyst, Simca, SAS)
  6. Metabolite databases (METLIN, HMDB, LIPIDMAPS, PubChem, ChemSpider)
  7. Identification of metabolites (MetaboSearch, MSMS analysis)
  8. Metabolite pathway analysis (Mummichog, KEGG, GeneGo, Ingenuity)
  9. Advanced elective sessions allow attendees to fine tune their training experience
    • Imaging mass spectrometry
    • isotope ratio analysis
    • Ion mobility
    • Using metabolomics software at the command line and based programs
For further details, visit http://www.uab.edu/proteomics/metabolomics/workshop/workshop_july_2016.php.

12-23 Sep 2016

2016 International Summer Sessions in Metabolomics
Venue: Campus UC Davis, CA, USA

The course will include:
  • Study design, including pitfall analysis and hidden biases in studies from microbial, plant, mouse and human cohort research
  • Sample preparation and quality control
  • In-laboratory detailed discussions standard operating procedures for GC-MS and LC-MS data acquisitions
  • Targeted metabolomics, including monitoring charts and use of isotope labeled internal standards
  • Exercises on flux analysis in cancer cells by isotope tracer analysis
  • Exercises on identification of unknowns by cheminformatics software workflows (incl. CFM-ID, MassFrontier, and various databases and small software routines)
  • Untargeted data processing and exercises on MZmine and MS-DIAL software
  • Data normalizations and transformations with and without internal standards and Quality Controls
  • Multivariate and univariate statistics (incl. Devium, MetaboAnalyst and other software)
  • Pathway mapping (incl. MetaboAnalyst and MetaMapR)
For further details, visit http://metabolomics.ucdavis.edu/courses-and-seminars/courses.


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 ([email protected]).
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 ([email protected]). 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
Research Postdoctoral Scientist
Beaumont Health System Michigan, USA 31-Mar-2016
Beaumont Health System
Professor of Chemistry
University of Loughborough Loughborough, UK 22-Mar-2016 13-Apr-2016
Metabolomics Society
Senior Lecturer/Reader in Chemistry (2 posts available)
University of Loughborough Loughborough, UK 22-Mar-2016 13-Apr-2016 Metabolomics Society
Postdoctoral Position in Tumor Metabolism
Michigan State University  East Lansing, MI USA 16-Mar-2016 Until filled Metabolomics Society
Post-doctoral research associate in breathomics
University of Loughborough
Loughborough, UK 7-Mar-2016 5-Apr-2016
Metabolomics Society
Assistant or Associate Professor
University of Nebraska-Lincoln
Lincoln, NE, USA 4-Mar-2016 Until filled Metabolomics Society
Postdoctoral scholar
Oregon State University Corvallis, OR, USA 26-Feb-2016 Until filled Metabolomics Society
Postdoctoral Fellowship in Metabolomics
Lund University Malmö, Sweden
23-Feb-2016
Lund University
Cornell University Assist./Assoc. Professor in Plant Metabolomics
Cornell University Ithaca, NY, USA 1-Feb-2016 Until filled Metabolomics Society


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 ([email protected]). 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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