MetaboNews Masthead

MetaboNews
Issue 12 - August 2012

CONTENTS:


Online version of this newsletter:
http://www.metabonews.ca/Aug2012/MetaboNews_Aug2012.htm

Welcome to the twelfth issue of MetaboNews, a monthly newsletter for the worldwide metabolomics community. In this month's issue, we feature a Software Spotlight article on IDEOM, an Excel interface for the analysis of LC-MS metabolomics data. As of the May 2012 issue, we added a new section called MetaboInterviews that features interviews with metabolomics experts from around the world. This issue includes an interview with Dr. Ute Roessner of Metabolomics Australia. This newsletter is being produced by The Metabolomics Innovation Centre (TMIC, http://www.metabolomicscentre.ca/), and is intended to keep metabolomics researchers and other professionals informed about new technologies, software, databases, events, job postings, conferences, training opportunities, interviews, publications, awards, and other newsworthy items concerning metabolomics. We hope to provide enough useful content to keep you interested and informed and appreciate your feedback on how we can make this newsletter better (metabolomics.innovation@gmail.com).

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Current and back issues of this newsletter can be viewed from the newsletter archive (http://www.metabonews.ca/archive.html).

Software/Stat Spotlight

1) Software Spotlight

 IDEOM Image

IDEOM for data analysis from LC-MS focused metabolomics

Feature article contributed by Darren Creek, NHMRC Training Fellow, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne

LC-MS based metabolomics with high resolution time-of-flight (TOF) or Fourier transform (FT) mass spectrometry offers great promise for untargeted metabolomics. High mass resolution allows detection of many unique peaks in each sample, and accurate mass often allows putative identification of metabolites. However, widespread adoption of this technology has been limited by difficulties associated with extracting meaningful biological information from these datasets.

Numerous software solutions are available for detection and alignment of peaks from multiple samples, to provide a dataset suitable for statistical analysis. Unfortunately, each detected peak in LC-MS data does not correspond to a unique metabolite. Most metabolites give rise to multiple peaks, and many peaks derive from other sources of noise, resulting in a high number of 'false positive' metabolite identifications. Many of these noise peaks can be attributed to common phenomena observed in LC-MS analyses, and a systematic approach to noise reduction can markedly improve interpretation of LC-MS metabolomics data. The most common sources of noise include (1) ESI-MS artefacts (including adducts, fragments, isotopes, complexes, and charge states), and (2) HPLC or peak-picking artefacts (including split peaks, peak shoulders, baseline noise, and ghost peaks), which can both be significantly reduced by filtering algorithms based on mass, retention time, peak shape, and intensity data. The other major source of noise is background contamination, which can be largely filtered from the data by comparison with blank solvent samples, and based on peak intensity (height/area) and reproducibility (relative standard deviation).

Even with filtered high resolution data, it is often difficult to identify peaks, as each exact mass may correspond to multiple chemical formulas, and often many isomers of a specific formula. In addition to accurate mass, LC-MS data is rich in additional information to assist with identification, including isotope profile, isotope abundances, retention time, in-source fragments, ESI adducts, and data-dependent accurate mass re-calibration. Additional confidence can also be gained by knowledge of the organism of study, and by observation of biochemical relationships between detected metabolites. When combined with noise filtering, consideration of this additional biochemical and analytical information to putatively identify metabolites improves the biological interpretation of metabolomics data, and reduces the number of authentic standards required for follow-up analysis in cases where absolute confirmation of an identity is essential.

These approaches to noise reduction and metabolite identification have all been incorporated into the IDEOM software for routine analysis of high resolution LC-MS data. IDEOM (http://mzmatch.sourceforge.net/ideom.php) is a freely available macro-enabled Excel template, which allows user-friendly data analysis from peak-picking and alignment (by calls to XCMS and mzMatch.R), to noise filtering, identification (targeted and/or untargeted), statistics, and visualisation. All parameters are easily adjustable from the graphical user interface to facilitate optimisation of the filtering and identification settings, which are platform-, and often study-, dependent. The standard processing steps are automated to simplify analysis and give rapid results. It should be emphasised that all identifications are considered putative, and the Excel interface allows manual curation assisted by functions that provide analytical, biochemical, and statistical metadata for each putative metabolite. Advanced features include normalisation, stable-isotope tracing, targeted analyses and functions to export curated data for further interpretation by web applications including MetaboAnalyst, iPath2.0, Pathos, and MetExplore. IDEOM is freely available for download and requires Microsoft Excel (Excel 2007 or 2010 for Windows) and R for full functionality.

IDEOM's Major Features

Documentation


Publication
Workshop

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

2) MetaboInterviews
MetaboInterviews, a new section as of May 2012, 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 Dr. Ute Roessner of Metabolomics Australia.


Ute Roessner
Head of School of Botany node of the Australian Centre for Plant Functional Genomics and Metabolomics Australia, The University of Melbourne (Australia)
Ute Roessner 
Biography
Dr. Roessner obtained her PhD in Plant Biochemistry at the Max-Planck-Institute for Molecular Plant Physiology in Germany, where she developed novel GC-MS based methods to analyse metabolites in plants. With the combination of small molecule analytics and sophisticated bioinformatics and statistics, the field of metabolomics was born and is today an important tool in biological sciences, systems biology, and biomarker discovery. In 2003, she moved to Australia where she established a GC-MS and LC-MS based metabolomics platform as part of the Australian Centre for Plant Functional Genomics (www.acpfg.com.au). Since 2011, she has led the ACPFG node at the School of Botany, The University of Melbourne, Australia. Also, since 2007, Dr. Roessner has been involved in the setup of Metabolomics Australia (MA, www.metabolomics.com.au), an Australian Federal Government investment (National Collaborative Research Infrastructure Strategy 5.1 Evolving Biomolecular Platforms) through Bioplatforms Australia Ltd. (www.bioplatforms.com.au) and now leads the MA node at the School of Botany, The University of Melbourne, Australia.


Metabolomics Interview (MN, MetaboNews; UR, Ute Roessner)

MN: How did you get involved in metabolomics?

UR: I was fortunate to become a PhD student under the supervision of Dr. Richard Trethewey at the Max-Planck-Institute for Molecular Plant Physiology in Golm, Germany. Richard was one of the pioneering teams who thought of using GC-MS to analyse hundreds of metabolites in plant tissues. My PhD thesis was to establish and validate GC-MS methodologies for metabolite profiling in potato and to test multivariate statistical analysis methods for data mining and visualisation. Metabolomics as a new research tool was born combining comprehensive and advanced analytical chemistry techniques based on mass spectrometry and NMR with sophisticated computational and statistical methods.

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

UR: Being part of a metabolomics service centre, the most exciting aspect is that I am involved in so many different biological research areas allowing me to get insight into many different questions, approaches, and applications. The learning never ends which is challenging on one side but also quite rewarding. Many clients and collaborators come to us with specific research questions and we offer them new ways of looking at their problems using metabolomics.
 
MN: What key metabolomics initiatives are you pursuing at your research centre or institute? What is happening in your country in terms of metabolomics?

UR: I am now involved in two metabolomics-based initiatives, one is to use the technology in a large research program through the Australian Centre for Plant Functional Genomics, where we investigate abiotic stress responses and tolerances in cereals such as wheat and barley and aim to identify new targets for breeding strategies to develop novel crops with better yield sustainability in harsh environmental conditions. Next to the research, we offer metabolomics technologies, both analytically and computationally, to the research community through a federal government funded national metabolomics research infrastructure facility, Metabolomics Australia. This facility is one example of an exciting funding opportunity for metabolomics in Australia through which the government funds large infrastructure facilities, enabling research to be accessed by academia and industry.

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

UR: I believe Metabolomics will become a routine analytical tool for any biochemical analysis of biological systems just as Genomics has evolved as the first point of investigation to answer basic biological questions. Metabolomics will also be applied more and more for identification of early diagnostic markers for disease and health and in the future will be the major tool for monitoring disease treatments in personalised medicine applications or for improving health through personalised nutrition.

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

UR: That it is comprehensive. Biochemical analyses have been done for many decades, however, metabolomics technologies offer to analyse more than just a handful of metabolites. Although we still only know a low percentage of what we are able to measure with respect to chemical nature; we will soon increase the number of identifications in any given analytical experiment, definitely enriching the information obtained from metabolomics experiments.
 
MN: What do you see as the greatest barriers for metabolomics? What improvements, technological or otherwise, need to take place for metabolomics to really take off?

UR: As mentioned above, we only can identify a low percentage of compounds in metabolite profiles, which is a major bottleneck when it comes to biological interpretation or validation of potential biomarkers. To really unlock the potential of metabolomics in biology, nutrition, and medicine, large improvements in compound identification need to be made. These improvements would require better libraries which are shared on public forums. The usefulness of these libraries will improve once many laboratories use standardised methodologies across the globe.

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

UR: In our region, metabolomics has become an important budget item on grant applications, where researchers request appropriate funding for experimentations, either in their own lab or through access to metabolomics service providers. The systems biology or integrated biology approach will become routine for any project aiming to increase our understanding of biological systems, health and complex diseases in humans, animals, and plants. Funding agencies now better understand that metabolomics is an essential tool for true systems biology and therefore funding will become more readily available to apply the technology.

 MN: What role can metabolomics standards play?

UR: Standards are playing a huge role. As mentioned above, in order to develop comprehensive metabolomics libraries, researchers will need to settle on common and standardised methodologies, which can be described in detail through standards. This will also allow better comparisons of metabolomics results between laboratories, so well established standards and policies on minimal requirements to describe any metabolomics experiment will lead to huge improvements of possible interpretations within a biological context.

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

I would like to emphasise how important it is for everyone starting to use, or already using, metabolomics to make sure to be aware of all the pitfalls and analytical mystics of dealing with extremely complex chemical mixtures. It is very easy to measure lots of noise and background which can interfere and skew resulting data and lead to misinterpretations. Any metabolomics experiment should be repeated a second time from the beginning, not just for the sake of reanalysing the samples. If the identified significant features/markers arise a second time, more conventional and rigorous validation methods need to be employed before a result can be considered true.


Biomarker Beacon

3) Biomarker Beacon

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

Metabolomics is an emerging field that is complementary to other omics sciences and that is gaining increasing interest across all disciplines. Because of metabolomics' unique advantages, it is now being applied in functional genomics, integrative and systems biology, pharmacogenomics, and biomarker discovery for drug development and therapy monitoring. More than 95% of today's biomarkers are small molecules or metabolites (MW <1500 Da), which can be used for disease testing, drug testing, toxic exposure testing, and food consumption tracking. While standard clinical assays are limited in the number and type of compounds that can be detected, metabolomics measures many more compounds. Since a single compound is not always the best biomarker (diagnostic, prognostic, or predictive), healthcare practitioners can use metabolomics information about multiple compounds to make better medical decisions. Global metabolic profiling is now being used to determine clinical biomarkers in assessing the pathophysiological health status of patients.

In the following two recent studies, metabolomics approaches were used to develop biomarker tools for the identification of biomarkers associated with coronary artery disease and acute myocardial ischemia, respectively.
  1. Shah SH, Sun JL, Stevens RD, Bain JR, Muehlbauer MJ, Pieper KS, Haynes C, Hauser ER, Kraus WE, Granger CB, Newgard CB, Califf RM, Newby LK. Baseline metabolomic profiles predict cardiovascular events in patients at risk for coronary artery disease. Am Heart J. 2012 May;163(5):844-850.e1. [PMID: 22607863]

    To date, a good model for cardiovascular risk prediction has not been developed. This group of investigators sought to determine if small-molecule metabolites could serve as useful predictors of cardiovascular risk. In this paper, the research team performed mass spectrometry profiling of 69 metabolites and lipid assessments using plasma samples from patients undergoing cardiac catheterization. Out of 13 metabolite factors evaluated, this group was able to identify five associated with mortality: factor 1 (medium-chain acylcarnitines), factor 2 (short-chain dicarboxylacylcarnitines), factor 3 (long-chain dicarboxylacylcarnitines), factor 6 (branched-chain amino acids), and factor 12 (fatty acids). These sets of metabolites may offer improved cardiovascular risk assessment and point to new mechanisms of disease.


  1. Bodi V, Sanchis J, Morales JM, Marrachelli VG, Nunez J, Forteza MJ, Chaustre F, Gomez C, Mainar L, Minana G, Rumiz E, Husser O, Noguera I, Diaz A, Moratal D, Carratala A, Bosch X, Llacer A, Chorro FJ, Viña JR, Monleon D. Metabolomic profile of human myocardial ischemia by nuclear magnetic resonance spectroscopy of peripheral blood serum: a translational study based on transient coronary occlusion models. J Am Coll Cardiol. 2012 May 1;59(18):1629-41. [PMID: 22538333]

    Early detection of myocardial ischemia (MIS) remains a challenge for clinical cardiologists. In this study, the researchers used high-resolution nuclear magnetic resonance spectroscopy to profile 32 blood serum metabolites from swine (n=9) and 20 patients undergoing angioplasty balloon-induced transient coronary occlusion. These results were compared with blood serum from 10 control patients. The investigators noted several changes in the blood profiles of swine and patients immediately following MIS. While the researchers found increased levels of circulating glucose, lactate, glutamine, glycine, glycerol, phenylalanine, tyrosine, and phosphoethanolamine, they discovered decreased levels of choline-containing compounds and triacylglycerols. Also, the creatinine levels increased two hours after ischemia. This group used multivariate analyses to develop a biosignature for the accurate detection of patients with MIS. This work could lead to the development of an early-stage diagnostic for MIS in patients.
Metabolomics Current Contents

4) Metabolomics Current Contents

Recently published papers in metabolomics:


MetaboNews

5) MetaboNews
24 Jul 2012
Molecular Profiles Point The Way To A Better Pint Of Beer

You don’t have to look too hard to find beer on the Colorado State University campus in Fort Collins. But not all of it is at keggers. In the microbiology building, it’s a legitimate study subject.

What started as a creative teaching tool has now blossomed into cutting-edge research that may change the brewing industry.

Visit CSU’s Proteomics and Metabolomics Core Facility on a typical day, and you’re likely to see scientists running samples of bodily fluids on state-of-the-art machines.

The usual suspects are serum, urine, and tissue extracts, says Jessica Prenni, the Core Facility’s director. Oh, and feces, too.

Prenni and her colleagues study a relatively new field of science called metabolomics that focuses on the many products of metabolism in a given organism. The tool of their trade is a mass spectrometer, a kind of molecular scale that weighs the tiny products, or metabolites. From the weight, the scientists can piece things together like an atomic jigsaw puzzle, and figure out what the metabolites are.

By comparing urine from healthy people to that of sick patients, for example, Prenni can identify molecules that could be used to diagnose diseases. But minute differences in urine aren’t all that exciting to students. And Prenni and her coworkers were big connoisseurs of another far tastier and more interesting liquid to most budding scientists.

Why not see if their machine could also pick up minute differences between beers?

Audio: http://cpa.ds.npr.org/kunc/audio/2012/07/JM_beerfinal_web.mp3


 
23 Jul 2012
Compatibility study for metabolomics: Combined sample preparation for LC/MS and NMR

The two principal methods for studying the metabolome involve the complementary techniques of NMR and mass spectrometry. Between them, they reveal a far broader range of metabolites than either technique alone but this advantage is not one that scientists generally take advantage of. Most metabolomics studies involve one or the other.

There are three key reasons for this apparent deficiency. Firstly, lab personnel are usually trained in only one of the technologies, so extra resources are required. However, the main restraint is the difference in the sample preparation protocols and the amount of sample that is required for successful analysis.

NMR is often carried out directly on biofluids without any preliminary extraction. However, its inherent lack of sensitivity compared with mass spectrometry often results in overlapping signals for complex mixtures of metabolites, hindering the identification and measurement of individual components. This situation can be improved by a preliminary extraction procedure.

For LC/MS, which is gaining in popularity compared with GC/MS, far smaller sample volumes are adequate (typically 20 µL compared with 500 µL for NMR) but extraction of the sample is a prerequisite in order to remove proteins and other interfering components.

The third factor which makes it difficult to integrate the two technologies is the use of deuterated solvents in NMR spectroscopy. They are employed to simplify the proton regions of the spectra, since any hydrogen atoms that are replaced by deuterium are shifted to a different region of the spectrum. However, the use of deuterated solvents in mass spectrometry will cause problems. The substitution of labile hydrogen atoms with deuterium can prevent the correct structural assignment.

It seems that an opportunity is being missed when NMR and LC/MS are used independently for metabolomics studies, so a team of scientists in Spain has attempted to simplify the procedures by systematically examining extraction protocols for both techniques to try and find common ground. Their aim was to find conditions for preparing one extract which can be used directly for NMR and LC/MS without solvent exchange or any other manipulations.


 
12 Jul 2012
Researchers to Use Novel Metabolomics Technology to Discover Which Cigarette Smokers are at Highest Risk for COPD

Researchers at Weill Cornell Medical College were awarded a $6.5 million grant from the National Heart, Lung, and Blood Institute for a five-year investigation into metabolic changes occurring within airway epithelial cells in the lungs of chronic obstructive pulmonary disease (COPD) patients caused by cigarette smoking. In addition, researchers aim to identify which cigarette smokers are at highest risk of developing COPD as well as novel biomarkers to assist in the development of new therapeutic treatments for the disease.

One-fifth of the adult population in the United States smokes cigarettes, and each puff can burden the human lungs with a hundred trillion oxidants and more than 4000 chemical compounds. Cigarette smoking is a major cause of disease, including COPD, the fourth leading cause of death of Americans. There is currently no cure, no effective treatments beyond oxygen therapy and no biomarkers to diagnose the disease early.

"Twenty percent of smokers get COPD, so it is vital that we identify who is at the highest risk and why," says Dr. Ronald G. Crystal, co-principal investigator for the study and chairman of genetic medicine at Weill Cornell Medical College. "Gaining a better understanding of COPD's underlying biology and the metabolic changes forced by cigarette smoke to airway epithelial cells will help us effectively deal with this major health problem. We can use this information to develop new ways to protect the lungs."

Smoking-induced COPD patients can experience shortness of breath and loss of lung function due to the severe narrowing of their lung airways. COPD is associated with the progression of "ciliopathy," the cellular dysfunction within the airway epithelial cells that leads to the shortening of cilia cells, mucus accumulation and the impairment of infection defenses. The majority of epithelial cells are made up of cilia, important cells in lung health that play the crucial role of moving mucus and any inhaled pathogens, such as bacteria, up and out of the lungs to prevent infection.

"Ciliopathy occurs long before there are any clinical signs of smoking-induced COPD. However, the underlying genesis of smoking-induced airway ciliopathy is unknown," says Dr. Steven S. Gross, co-principal investigator of the study and professor of pharmacology and director of the Mass Spectrometry Facility at Weill Cornell. "The goal of our study is to fill this knowledge gap and identify what exactly drives ciliopathy in smokers with COPD."

The researchers hypothesize that ciliopathy is linked to the oxidant stress placed on airway epithelium cells by cigarette smoke and that smoking-induced COPD is associated with altered metabolism in lung tissue and serum. Researchers believe the profiling of metabolites in the biofluids of COPD patients will provide fundamental insight into the underlying molecular mechanisms of ciliopathy development and the pathogenesis of COPD.


Source: Weill Cornell Medical College

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


Metabolomics Events

6) Metabolomics Events
28-31 Aug 2012

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

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

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

Presymposium (ECNIS & NUGO): 'Micronutrients and gene polymorphisms, and Nutrition and epigenetics'  28 August 2012, Helsinki, Finland
A presymposium (ECNIS & NUGO): 'Micronutrients and gene polymorphisms, and Nutrition and epigenetics' will be organised on Tuesday afternoon 28 August, from 12.30-17.00 hrs. Participation in this symposium is free of charge but registration is Mandatory.  For more information and registration [visit Pre-symposium]

For further information, please visit http://www.nugo.org/nugoweek/42113/5/0/30.
3-7 Sep 2012

4th Australasian Metabolomics Symposium and Workshop
Venue: Kuala Lumpur, Malaysia

Moving Forward to Integrate Systemic Biology into Post-Genomics Era

Metabolomics is a new emerging field of "omics" research which has attracted attention and focus of academia, industry and government sectors. As for year 2011, there are more than 700 papers being published on this subject. Metabolomics is a comprehensive characterization of the small molecule metabolites in biological systems which provide an overview of the metabolic status and global biochemical events associated with a cellular or biological system. It is an interesting tool which allows researchers to understand the changes in networks and pathways and provide insights into physiological and pathological states. Systems Biology and the ability to integrate genomics, transcriptomics, proteomics, and metabolomics data is evolving at a rapid pace. Metabolomics has the potential and has promised to enable detection of disease states and their progression, monitor response to therapy, stratify patients based on biochemical profiles, and identify targets for drug design. Together with internationally recognized metabolomics experts, we would like to invite you to participate in the Australasian Symposium and Workshop in Metabolomics organised by the Malaysian Metabolomics Society and Pharmacogenomics Centre (PROMISE), UiTM. The event would be held in Shah Alam, Malaysia.

For the symposium, a series of plenary lectures will be held by prominent speakers who have been working on metabolomics. There will be also sessions for oral presentation by selected participants. This workshop will be a combination of lectures and practical sessions focusing on LC-MS data acquisition, data extraction and statistical analysis of large datasets. At the end of the course participants should be familiar with sample preparation, LC-MS data acquisition, LC-MS data interpretation, statistical analysis of metabolomics data sets and challenges associated with all of the above.

For further information, please visit http://metabolomics.my/



18-20 Sep 2012

Metabolomics in Drug Discovery & Development
Venue: Boston, USA

The world’s first and only pharmaceutical focused metabolomics meeting

The last decade of exciting academic research in metabolomics is now being applied by drug developers to determine and validate tox and safety biomarkers. Investment from drug developers is huge as the pharmaceutical industry is now using metabolomics to find novel targets, enhance experimental design, and ensure clinical success. However, statistical challenges and inherent variability in data sets must be overcome to realize the full potential of this exciting technology.

Metabolomics in Drug Discovery and Development is the only meeting where you can hear cutting edge case studies from drug developers who are already reaping the benefits of metabolomics.

The 19 expert speakers include…
  • Rick Beger, Director at the Centre of Excellence for Metabolomics, FDA
  • Bjoern Riefke, Head of Metabolic Profiling & Clinical Pathology, Bayer Healthcare
  • Thomas Ruddy, Director of Analytical Chemistry, Merck
  • David Wishart, Professor, University of Alberta
  • Jeff Trimmer, Executive Director, Pfizer
  • Reza Salek, Scientific Investigator, European Bioinformatics Institute
  • Thomas Hankemeier, Director, Netherlands Metabolomics Facility
  • Shashi Ramaiah, Drug Safety Biomarker & Precision Medicine Lead, Pfizer
Visit the event website to see the full speaker line up and exactly what will be covered.

Quote ‘METABO’ when registering for 10% off standard prices.

There is a special rate of $599 for those representing not-for-profit organizations

www.metabolomics-drugdevelopment.com

Conference brochure
20-21 Sep 2012

Metabolomics Data Analysis Workshop: Analysis of LC-MS focused metabolomics data with IDEOM and mzMatch
Venue: Bioinformatics Research Centre, Joseph Black Building, University of Glasgow, Glasgow, UK

We kindly invite you to attend a workshop "Analysis of LC-MS focused metabolomics data with IDEOM and mzMatch".
  • IDEOM workshop: Thursday 20th September 2012 (£ TBA)
  • mzMatch workshop: Friday 21st September 2012 (£ TBA)
Times: 10am to 5pm
Catering: Lunch and Tea/Coffee provided
Computers: Bring own laptop or book a desktop

Registration
Places are limited and booking is mandatory.

Outline

  • Introduction to LC-MS focused metabolomics
  • Practical tutorials to get familiar with the software
  • Explanation of tips and tricks for non-experts in the field
  • Demonstration of advanced features
  • Discussions for future development of data processing software

More details are available via http://mzmatch.sourceforge.net/workshop.php
25-27 Sep 2012

Metabomeeting 2012
Venue: Manchester Conference Centre, Manchester, UK

The Metabolic Profiling Forum is pleased to announce that Metabomeeting 2012 will be held at the Manchester Conference Centre, Manchester, UK from September 25-27th 2012.

The conference centre is located within the University of Manchester campus, close to major transport links and one of the most cosmopolitan centres in the UK. The meeting is the seventh of the Metabomeeting conferences and continues the series of highly successful events held across Europe since 2005. The program will focus on the increasingly diverse range of applications as well as the latest developments to enhance the practise of metabolomics.

Confirmed speakers for the meeting include:
  • Professor Robert Hall, Plant Research International, The Netherlands, who will present the plenary lecture.
  • Professor Rainer Breitling, University of Glasgow, UK.
  • Professor Hannelore Daniel, Technical University of Munich, Germany.
  • Dr Jules Griffin, University of Cambridge, UK
  • Dr George Harrigan, Monsanto, USA
  • Dr Jerome Jansen, Raboud University, Nijmegen, The Netherlands.
  • Dr Nick Lockyer, University of Manchester, UK.
  • Professor George Nychas, Agricultural University of Athens, Greece.
  • Professor Ian Wilson, AstraZeneca, UK.
  • Dr Asaph Aharoni, Weizmann Institute of Science, Israel
Submission of abstracts for poster presentation has now opened. All abstracts for poster presentation must be submitted before August 10th 2012.

More details are available via http://thempf.org/mpf_cms/index.php/conferencesworkshops/forthcoming-mpf-events/78-metabomeeting-2012.
1-3 Oct 2012

2nd International Workshop on Metabolomics & Proteomics
Venue: CIC bioGUNE, Bilbao, Spain

Metabolomics and Proteomics constitute two key technologies that have paramount importance in the Systems Biology era. Each of the techniques allows tackling the huge complexity that a living systems displays at metabolome and proteome level.
 
Proteomics was born after the sequences of genomes were released and by the hand of the great advances performed in mass spectrometry and bioinformatics. This way, with the genomics sequences available, hundreds of proteins can be identified in the same experiment and latest developments also allow systematic quantification of the gene products. These developments allow studying variations suffered by the proteins within a cell in a perturbed condition (e.g. disease, drug treatment etc.). Proteins constitute the major catalytic entities in cell and knowing the details of dynamics, modifications and interactions of proteins will help getting insights about basic molecular mechanisms that rule the fate of the cell. Moreover, since most of drugs are targeted against proteins, it is clear the interest in getting as much information as possible that will eventually render new insights into clinics.

Metabolomics can be defined as the quantitative and qualitative analysis of all metabolites (molecules with a molecular weight of less than 1.500 Da) in a given organism. This results in the construction of a metabolome or metabolic fingerprint, analogous to the genome or the proteome. Since the set of all metabolites is directly linked to the actual state of a cell, tissue or an organism and thus to the phenotype, the metabolome is optimally suited for the determination of biomarkers that are typical for certain genotypes or pathologies, and to identify key cellular pathways involved in the development and progression of diseases.
 
CIC bioGUNE has prepared a very interesting scientific program in which leading academics speakers will tell us about the state-of-the-art in metabolomics and proteomics including technological aspects related to the different platforms (RMN, GC-MS, LC-MS and protein arrays). The workshop will also cover recent breakthroughs in each of the disciplines as single-cell and high-throughput metabolomic approaches, protein characterization and large scale protein quantification, along with the applications that these technologies have found in environmental and disease biomarker discovery areas. Importantly, the scientific program will be completed with poster sessions and presentations from equipment manufacturers.  In summary, the participants will have the opportunity to learn, meet and interact with experts in different metabolomic and proteomic related areas obtaining a deep and broad vision on these  powerful technologies
  • Workshop Invitation: [PDF]
  • Workshop Agenda: [PDF]
For further information, please visit http://metabolomicsandproteomicsworkshop2012.cicbiogune.es/
16-17 Oct 2012

Metabolic Profiling & Lipidomics
Venue: Madrid, Spain (Part of Systems Biology Europe)

Welcome to the Metabolic Profiling & Lipidomics track of the Systems Biology Europe conference and exhibition.

This conference aims to discuss the latest developments in the rapidly evolving area of metabolic profiling with particular emphasis on the break out field of Lipidomics. Recent HPLC-MS advances now allow for individual molecular species of lipids to be isolated and identified. This meeting will detail the cutting edge research taking place as a result of these developments with emphasis on understanding not only lipid metabolism but also ascertaining the role of lipids in conditions such as atherosclerosis, inflammatory disease, arthritis, cancer, diabetes and Alzheimer's disease, with a view to improving treatment. As a whole focus will be drawn to the key technological developments being made in both the separation and detection analytical fields used in profiling as well as the area’s other key applications including toxicity assessment, functional genomics and nutrigenomics.

Other conference tracks at this event include Cancer Proteomics, Exosomes/Markers in Biological Fluids, and Informatics. Registered delegates will have access to all four meetings ensuring a very cost-effective trip.

In addition the event will also host two cutting edge business courses which can be viewed here.

For further information, please visit http://selectbiosciences.com/conferences/index.aspx?conf=MPL2012
7-9 Nov 2012

29th LC/MS Montreux Symposium
Venue: Montreux, Switzerland

Short Courses: November 5-6, 2012
The Montreux LC/MS 2012 conference: Special highlights on Metabolomics and Clinical Chemistry

The field of LC/MS is continuously growing as is reflected by the participation of over 30 nationalities and by scientific contributions from a variety of research and development domains such as pharmaceutical, biotechnological, food, environmental and research on novel instrumentation and new LC/MS fields such as nanotechnology and microfluidics, UPLC, low flow rate spray techniques, proteomics, and systems biology.

In collaboration with the Metabolomics Society, a special joint parallel program for this rapidly emerging field is organized addressing the technology as well as novel systems-based biology approaches in pharma, nutrition, clinical chemistry, plant sciences, and medical biology. A parallel program is organized together with various Clinical Chemistry societies focusing on current and future LC/MS options in clinical diagnosis. Accreditation by related societies for the program as well as the short course has been applied for.
For more information, visit http://www.lcms-montreux.com/.



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

7) 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 4 issues (8 weeks) unless the position is filled prior to that date.

Jobs Offered

Job Title Employer Location Date Posted Source
Postdoctoral researchers: "Biostatistician for functional genomics data integration" The Biosystems Data Analysis group Amsterdam, Netherlands
 9-Aug-2012 Naturejobs.com
Postdoc on metabolomics Andalusian Centre for Developmental Biology (CABD-CSIC)
 Sevilla, Spain
 7-Aug-2012 Naturejobs.com
Post-doctoral Scientist Leibniz Institute of Plant Biochemistry Halle (Saale), Germany
 7-Aug-2012 Naturejobs.com
Research Scientist (Plant Metabolomics) Hudson Shribman Scientific Recruitment Ltd East Anglia, United Kingdom
 27-Jul-2012 Naturejobs.com
Computer Scientist University of Manchester Manchester, United Kingdom
 16-Jul-2012 Naturejobs.com
Postdoctoral Fellowship at UCSF - Metabolomics of Cancer Models Department of Radiology and Biomedical Imaging at the University of California, San Francisco (UCSF) San Francisco, USA
 19-June-2012 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 (metabolomics.innovation@gmail.com). Upon review, a limited number of job submissions will be selected for publication in the Jobs Wanted section.
  • Position Sought: Seeking a position in drug research and development and biomarker discovery. [Candidate's CV]


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