Issue 13 - September 2012
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1) Database Spotlight
Professor of Chemistry and Molecular Biology and Director of the Scripps Center for Metabolomics at The Scripps Research Institute in La Jolla, California
Gary Siuzdak is Professor of Chemistry and Molecular Biology and Director of the Scripps Center for Metabolomics at The Scripps Research Institute in La Jolla, California (http://masspec.scripps.edu/). He is also Faculty Guest at Lawrence Berkeley National Laboratory and served as Vice President of the American Society for Mass Spectrometry. His research interests include developing novel mass spectrometry-based approaches in metabolomics and nanostructure-based imaging. He has written two books, "Mass Spectrometry for Biotechnology" and the "The Expanding Role of Mass Spectrometry in Biotechnology". He is also in the process of writing a third book on Metabolism and Mass Spectrometry with Gary J. Patti (Assistant Professor at Washington University in St. Louis).
3) Biomarker Beacon
4) Metabolomics Current Contents
|10 Aug 2012
EasyLCMS: An asynchronous web application for the automated quantification of LC-MS data
Downstream applications in metabolomics, as well as mathematical modelling, require data in a quantitative format, which may also necessitate the automated and simultaneous quantification of numerous metabolites. Although numerous applications have been previously developed for metabolomics data handling, automated calibration and calculation of the concentrations in terms of mumol have not been carried out.
Moreover, most of the metabolomics applications are designed for GC-MS, and would not be suitable for LC-MS, since in LC, the deviation in the retention time is not linear, which is not taken into account in these applications. Moreover, only a few are web-based applications, which could improve stand-alone software in terms of compatibility, sharing capabilities and hardware requirements, even though a strong bandwidth is required. Furthermore, none of these incorporate asynchronous communication to allow real-time interaction with pre-processed results.
Findings: Here, we present EasyLCMS (http://www.easylcms.es/), a new application for automated quantification which was validated using more than 1000 concentration comparisons in real samples with manual operation. The results showed that only 1% of the quantifications presented a relative error higher than 15%.
Using clustering analysis, the metabolites with the highest relative error distributions were identified and studied to solve recurrent mistakes.
Conclusions: EasyLCMS is a new web application designed to quantify numerous metabolites, simultaneously integrating LC distortions and asynchronous web technology to present a visual interface with dynamic interaction which allows checking and correction of LC-MS raw data pre-processing results. Moreover, quantified data obtained with EasyLCMS are fully compatible with numerous downstream applications, as well as for mathematical modelling in the systems biology field.
Paper: Fructuoso S, Sevilla Camins A, Bernal C, Lozano AB, Iborra JL, Canovas M. EasyLCMS: An asynchronous web application for the automated quantification of LC-MS data. BMC Res Notes. 2012 Aug 11;5(1):428. [Epub ahead of print] [PMID: 22884039]
Source: 7thSpace Interactive
|2 Aug 2012
Waters and Nonlinear Dynamics to Co-Develop Next Generation Research Solutions for Large-Scale, Complex Data Sets
Firms to Combine Complementary Expertise in Analytical Science and Informatics to Advance Proteomics and Metabolomics Research
Waters Corporation (wat:NYSE) and Nonlinear Dynamics Ltd. have entered into an agreement to co-develop a new analytical solution that derives information from complex data sets generated by large-scale proteomics and metabolomics experiments.
Waters and Nonlinear Dynamics collaborated on the development of the Waters Omics Research Platform with TransOmics™ Informatics first introduced in May during the ASMS Conference on Mass Spectrometry and Allied Topics in Vancouver combining both Waters® SYNAPT® G2-S HDMS and TransOmics Informatics developed by Nonlinear Dynamics' under an exclusive worldwide OEM agreement.
With the launch of Waters Omics Research Platform, Waters introduced two new solutions powered by Waters TransOmics Informatics:
Used in small molecule research, protein characterization, metabolite identification and bio-pharmaceutical applications, the Synapt HDMS system is still the only mass spectrometer to employ high efficiency ion-mobility based measurements and separations to enable the analysis of sample ions differentiated by size, shape and charge as well as mass. The added dimension of shape-selective separation increases the analytical specificity and sample definition so that scientists can extract more information from their samples, including the detection of components previously unseen by conventional mass spectrometers.
"The complexity of biological samples is so great that the sensitivity and specificity of analytical techniques required for biological discovery presents scientists with significant challenges when it comes to managing experimental data," said James Langridge, Ph.D., Director of Pharmaceutical & Life Sciences Discovery, Waters Division. "We believe that through our partnership with Nonlinear Dynamics we can address this situation and advance the pace of discovery."
"I'm delighted to see this exciting partnership bring together the latest MS technology with world-renowned data analysis software," said Will Dracup, Executive Chairman, Nonlinear Dynamics. "Researchers today are faced with large, complex data sets and they need to be able to visualize this and extract reliable results. The software Nonlinear has developed specifically addresses these issues, unlocking the potential of the valuable, content-rich, omics data that Waters' ion mobility technology generates."
A common goal of any omics studies - whether proteomics or metabolomics - is to gain a clear understanding of the interplay between molecules at the protein and metabolite level leading to a better understanding of the underlying biology of an organism or a specific disease state. The Waters Omics Research Platform Solution facilitates research across multiple discovery areas for researchers in the pharmaceutical and life sciences, food, and clinical research areas.
Waters intends to commence shipments of its UPLC®/SYNAPT G2-S HDMS-based instrument solutions with TransOmics Informatics announced at ASMS during the fourth quarter of 2012.
|1 Aug 2012
Metabolon Strengthens Metabolomics Leadership With Acquisition of Lipomics Technologies
Gains proprietary lipids technology platform and further opportunities for diagnostics, personalized medicine and commercial services
Metabolon, Inc. announces the completion of its acquisition of Lipomics Technologies, Inc. This transaction combines Metabolon’s world-leading metabolomics technology platform for commercial services and diagnostics with Lipomics’ world-leading TrueMass® Profiling lipids technology platform.
Lipomics’ laboratory facilities will remain at its headquarters in Sacramento, California while Metabolon’s headquarters and laboratories will remain in Research Triangle Park. Steven M. Watkins, Ph.D., Lipomics’ founder, will join Metabolon’s executive team as chief technology officer. Financial terms of the transaction were not disclosed.
Michael Milburn, Ph.D., chief scientific officer of Metabolon, stated, “Metabolon has pioneered metabolomics technology and is the largest provider of solutions globally to the pharmaceutical, healthcare, consumer products, nutrition and agricultural industries, as well as to hundreds of academic institutions. Lipomics is the leader in technology to analyze lipids, including metabolites of fatty acids, acylcarnitines, sterols, amino acids, bile acids and eicosanoids. Together we have an unprecedented suite of technologies and capabilities to benefit our expanding customer base. The combined technologies will deliver new and improved diagnostic products and personalized medicine solutions for unmet needs, particularly in metabolic disease and cancer.”
“For the past 10 years Lipomics has taken pride in providing the best technology and science for understanding the role of lipids in human disease, principally in metabolic diseases associated with obesity and the lipid remodeling aspects of cancer,” said Dr. Watkins. “The prospect of combining our approach with Metabolon’s global platform is extremely exciting. Integrating the technologies will provide a deep and coherent understanding of biological systems and allow us to produce unparalleled services and products for years to come.”
John Ryals, Ph.D., chief executive officer of Metabolon, expressed his support of the acquisition saying, “By combining Metabolon and Lipomics, we have created the undisputed technology leader in the emerging field of metabolomics. We have product offerings that span from global metabolomics to complex lipid analysis to targeted analysis of many different classes of molecules. By combining our two companies, we have more than 140 employees and 450 clients, have completed 2,000 commercial projects and have 200 scientific papers either published or under review. We are not aware of another company or institution with this record of scientific and commercial achievement in the field of metabolomics.
“We are the leader in the commercialization of metabolomics with a profitable commercial life sciences service business and have launched the world’s first metabolomics-based diagnostic test for type 2 diabetes risk based on biomarkers that measure insulin resistance. We expect that in 2013 we will be marketing additional diagnostic products aimed at diseases related to obesity and cancer, and are committed to maintaining our position as the world’s leader in metabolomics.”
Source: Metabolon Press Release
|3-7 Sep 2012||
4th Australasian Metabolomics Symposium and
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 &
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…
Quote ‘METABO’ when registering for 10% off standard prices.
There is a special rate of $599 for those representing not-for-profit organizations
|20-21 Sep 2012||
Metabolomics Data Analysis Workshop: Analysis
of LC-MS focused metabolomics data with IDEOM and
Catering: Lunch and Tea/Coffee provided
Computers: Bring own laptop or book a desktop
Places are limited and booking is mandatory.
More details are available via http://mzmatch.sourceforge.net/workshop.php
|25-27 Sep 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:
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 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
|16-17 Oct 2012||
Metabolic Profiling & Lipidomics
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
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.
|27 Jan-1 Feb 2013||
Gordon Research Conference on Plant Lipids:
Structure, Metabolism & Function
Applications for this meeting must be submitted by December 30, 2012. Please apply early, as some meetings become oversubscribed (full) before this deadline. If the meeting is oversubscribed, it will be stated here. Note: Applications for oversubscribed meetings will only be considered by the Conference Chair if more seats become available due to cancellations.
Related Meeting Information
The Plant Lipids: Structure, Metabolism & Function Gordon Research Conference will be held in conjunction with the Plant Lipids: Structure, Metabolism & Function Gordon Research Seminar. Those interested in attending both meetings must submit an application for the GRS in addition to an application for the GRC. Please refer to the Plant Lipids: Structure, Metabolism & Function GRS web page for more information.
For more information, visit http://www.grc.org/programs.aspx?year=2013&program=plantlipid.
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 (firstname.lastname@example.org).
Job postings will be carried for a maximum of 4
issues (8 weeks) unless the position is filled prior to that
|Job Title||Employer||Location||Date Posted||Source|
research fellow: Food metabolomics
||European Commission, Joint Research Centre, Institute for Reference Materials and Measurements||Geel, Belgium||30-Aug-2012||Naturejobs.com|
|Associate Professor||Georgia Health Sciences University||Augusta, GA, United States
|Biochemistry and Molecular Biology Faculty Position||University of California, Los Angeles (UCLA)||Los Angeles, CA, United States
|Clinical Laboratory Director||Metabolon||Durham, NC, USA||15-Aug-2012||Metabolomics
|Senior Bioanalytical Chemist||Metabolon||Durham, NC, USA||15-Aug-2012||Metabolomics Society|
||Stemina Biomarker Discovery
||Madison, WI, USA
|Postdoctoral researchers: "Biostatistician for functional genomics data integration"||The Biosystems Data Analysis group||Amsterdam, Netherlands
|Research Scientist (Plant Metabolomics)||Hudson Shribman Scientific Recruitment Ltd||East Anglia, United Kingdom
|Computer Scientist||University of Manchester||Manchester, United Kingdom
Ian J. Forsythe, M.Sc.MetaboNews
Department of Computing Science
University of Alberta
221 Athabasca Hall
Edmonton, AB, T6G 2E8, Canada
This newsletter is produced by The Metabolomics Innovation Centre (TMIC, http://www.metabolomicscentre.ca/) for the benefit of the worldwide metabolomics community.
A single source destination for fee-for-service metabolic profiling including comprehensive metabolite identification, quantification, and analysis