Issue 21 - May 2013
1) Software Spotlight
Figure 1. Overview of the MassCascade plug-in for KNIME.
An example workflow is shown with two result windows. The left
window illustrates total ion chromatograms of three samples. The
third, bottom-most sample, row 33, results from a failed
injection. The right window depicts a PCA plot (PC1/PC2) from
processed quality control samples.
The MassCascade plug-in contains a set of nodes, also known as
2). Each node carries out a particular function for
processing input data. MassCascade is intuitive to use and comes
with a set of pre-defined nodes. Every node can be utilized via
drag and drop and configured using node dialog windows. Various
node types exist for processing, visualisation, and statistical
analysis. Workflows can be built or rearranged fast, LC-MS data
comprehensively explored, and complete sets of workflows
exchanged between collaborators, including all parameters for
reproducibility. The integration into a workflow environment
also makes it easy to maintain an overview of the complex
analysis workflow and explore new methods and approaches for
Click on the thumbnail below to view a larger size image
Figure 2. Screenshot of the KNIME workflow platform with MassCascade-KNIME. The node repository on the left contains all available nodes. Nodes can be moved onto the editor view in the centre via drag and drop, where they can be configured and run. Additional information is provided in the node description at the bottom.
Every step in the analysis is transparent and can be visually
inspected or corrected if required. Parameter settings can be
explored using smaller datasets before re-running the workflow
for larger data sets. KNIME uses a tabular data model that is
used to transport data between nodes. In the case of MassCascade
that is LC-MS data. Because all nodes follow the same data
model, generic KNIME nodes from different projects can be
seamlessly integrated in the same workflow.
Consequently, resulting tables can be analysed with generic KNIME nodes or installed extensions. For example, the statistical computing language R can be used within KNIME to analyse result tables (Figure 3). Alternatively other nodes (implemented tools or methods) can be used. In any case, MassCascade-KNIME provides smooth integration of LC-MS data processing capabilities for the rich workflow platform KNIME.
Figure 3. Screenshots of a data table and plot of m/z
traces. The left window shows a typical table containing scan
data and profile cells. Scan data cells outline the total ion
chromatogram of a sample; profile cells plot a histogram of m/z
traces in the time domain. The right window depicts an
interactive plot to inspect m/z traces (time vs m/z).
Currently the library contains a set of standard algorithms for
LC-MS data processing and is under active development. We
believe that a workflow-driven approach is intuitive, visual,
interactive, and helps with standardization and reproducibility.
To that effect, we promote the use of open-source workflow
applications that allow the combination of various tools into
one to facilitate LC-MS data processing.
More information on MassCascade and the plug-in can be found on the Wiki pages (https://github.com/SBeisken/MassCascadeKnime/wiki) of the project or obtained from the primary author of this article.
|| Professor of
Metabolomics at the University of Birmingham, Director
of the UK’s NERC Environmental Metabolomics Facility,
and President of the International Metabolomics Society
Mark R. Viant is a Professor of Metabolomics at the University of Birmingham, Director of the UK’s NERC Environmental Metabolomics Facility, and President of the International Metabolomics Society. He received his BSc in Chemistry and PhD in Chemical Physics at the University of Southampton, UK, before conducting postdoctoral research in chemistry and then environmental toxicology at the University of California, Berkeley and then UC Davis, respectively. Upon returning to the UK in 2003, as a NERC Advanced Fellow at the University of Birmingham, he built a research group focusing on the development of metabolomics approaches and their application to the environmental sciences. His current interests include (1) the development of optimised analytical approaches for mass spectrometry based metabolomics and high throughput biology; (2) development of optimal computational workflows including database resources for metabolomics; (3) the application of these technologies primarily to investigate the metabolic pathways underlying stress and toxicity in aquatic organisms, with a particular focus on nanoparticle toxicology and the freshwater invertebrate Daphnia as a model organism; and (4) the translation of metabolomics based ‘discovery’ research into mechanistically-based tools for environmental diagnostics.
3) Biomarker Beacon
|23 Apr 2013
Metabolon Expands Biochemical Profiling Capabilities with the New TrueVision™ Metabolomics Offering and Online Client Tools
Metabolon, the pioneering leader in metabolomics-driven biomarker discovery and analysis, today announced expanded capabilities in its extensive biochemical profiling technology. The new TrueVision™ offering combines Metabolon’s powerful biochemical profiling discovery platform with complex lipid profiling. With this expansion, Metabolon can survey biological samples for over 4000 known metabolites contained in its chemical library and provide a more complete picture of lipid metabolism. The acquisition of Lipomics Technologies in 2012, now operating as a division of Metabolon with core competency in lipidomics, has enabled this unprecedented new capability.
“The new TrueVision™ offering is the result of our commitment to meet our clients’ needs to find answers to their critical biological questions, advance their research, and is evidence of our dedication to continuous innovation in the field of metabolomics.”
Michael Milburn, Chief Scientific Officer at Metabolon, commented “The new TrueVision™ offering is the result of our commitment to meet our clients’ needs to find answers to their critical biological questions, advance their research, and is evidence of our dedication to continuous innovation in the field of metabolomics.”
Metabolon’s TrueVision™ platform has extensive application across the life sciences for biomarker discovery and elucidation of the effects of drugs or nutrients on metabolism. In addition, TrueVision™ provides insight into disease biology, in particular metabolic diseases, which are a family of disorders driven in large part by the subtle, long-term dysregulation of lipid metabolism. Metabolism in general and especially lipid metabolism are thought to play an important role in the development of cancer, inflammatory and central nervous system disorders which makes this comprehensive offering ideally suited for research in these therapeutic areas.
The company is also unveiling the newest version of Client Tools, a secure web portal for data delivery, interpretation and visualization of its lipidomics profiles. Client Tools includes Lipomics Surveyor® pathway maps for each analytical panel, allowing customers to view differences in lipid metabolism between treatment groups, organized by metabolic pathways. “This new software tool expands the ability of clients to visualize, present and interpret their focused lipid panel study data”, states Steve Watkins, Chief Technology Officer, Metabolon.
Source: Business Wire
|10 Apr 2013
An efficient post-hoc integration method improving peak alignment of metabolomics data from GCxGC/TOF-MS
Since peak alignment in metabolomics has a huge effect on the subsequent statistical analysis, it is considered a key preprocessing step and many peak alignment methods have been developed. However, existing peak alignment methods do not produce satisfactory results.
Indeed, the lack of accuracy results from the fact that peak alignment is done separately from another preprocessing step such as identification. Therefore, a post-hoc approach, which integrates both identification and alignment results, is in urgent need for the purpose of increasing the accuracy of peak alignment.
Results: The proposed post-hoc method was validated with three datasets such as a mixture of compound standards, metabolite extract from mouse liver, and metabolite extract from wheat.
Compared to the existing methods, the proposed approach improved peak alignment in terms of various performance measures. Also, post-hoc approach was verified to improve peak alignment by manual inspection.
Conclusions: The proposed approach, which combines the information of metabolite identification and alignment, clearly improves the accuracy of peak alignment in terms of several performance measures.
R package and examples using a dataset: http://mrr.sourceforge.net/download.html
Paper: Jeong J, Zhang X, Shi X, Kim S, Shen C. BMC Bioinformatics. 2013 Apr 10;14(1):123. doi: 10.1186/1471-2105-14-123. An efficient post-hoc integration method improving peak alignment of metabolomics data from GCxGC/TOF-MS. [PMID: 23575005]
Source: 7thSpace Interactive
|28 Mar 2013
Thermo Fisher Scientific Forms Technology Alliance Partnership With the University of Birmingham, UK
Collaboration aimed at advancing LC-MS techniques in life science research
Thermo Fisher Scientific Inc., the world leader in serving science, has entered into a Technology Alliance Partner agreement with scientists at the University of Birmingham, UK, establishing a collaboration to accelerate research in high-resolution accurate mass (HRAM) and triple quadrupole liquid chromatography-mass spectrometry (LC-MS) for life science applications.
The alliance will focus on two research areas:
Thermo Fisher’s Technology Alliance Partnership program is an ongoing initiative to drive innovation through the sharing of ideas and expertise between a number of academic research laboratories and the company.
“The University of Birmingham scientists share our drive to make the world healthier, cleaner and safer,” said Iain Mylchreest, vice president, research and development, Thermo Fisher. “We look forward to a very productive collaboration with this innovative, creative group for advancing metabolomic and proteomic research.”
“We are excited to become Thermo Fisher Scientific’s first Technology Alliance Partner within Europe,” said Professor Adam Tickell, the University’s pro vice chancellor for research and knowledge transfer. “We anticipate that innovations from this research will translate directly into improved healthcare and environmental diagnostics. We are particularly excited by Thermo Fisher’s commitment to supporting graduate research.”
The partnership builds upon the University of Birmingham’s Systems Science for Health initiative, which focuses on introducing a variety of life science technologies into clinical research. It follows almost a decade of collaboration between the two organizations.
Source: Thermo Fisher Scientific
6) Metabolomics Events
|13-14 May 2013||
Joint symposium on Metabolomics: Translational
approaches in metabolomics - Spa, Belgium
“Small molecules involved in biochemical processes provide a great deal of information on the status and functioning of a living system under study both from effects causes by changes in gene expression, and also by differences in life style and diet in humans and other mammals. The process of monitoring –and evaluating such changes is termed ‘metabonomics’. A parallel approach has also been under way, mostly in model organisms and in plant systems, and that has led to the term ‘metabolomics’”.
Metabol(n)omics utilizes NMR and MS spectroscopy together with multivariate analysis approaches to characterise perturbations in metabolic pathways occurring during biological processes. This new predictive tool holds great promises for applications in a variety of scientific fields ranging from basic biology through to food sciences.
This two day symposium aims to initiate the discovery of the metabolomics approach for the uninitiated but also to present high level and interest conferences for those involved in basic and industrial researches and interested in understanding altered biochemical processes in various living system. The symposium will mainly focus on Translational approaches in metabolomics.
Two educational sessions are scheduled for the PhD students.
All the sessions are organized in the Sol Cress in Spa on May 13 & 14, 2013.
The symposium is organized under the aegis of the CIRM, the Belgian FNRS and the “école doctorale thématique en sciences pharmaceutiques” in collaboration with the Netherlands Metabolomics Center (NMC).
For more information, visit http://www.metabolomicscentre.nl/news/first-belgian-netherlands-joint-symposium-metabolomics-translational-approaches-metabolomics-sp?goback=%2Egde_2414599_member_224905745.
|22-24 May 2013||
on FoodOmics, a Science for Nutrition, Health
and Wellness in the post-genomic era
Francesco Capozzi and Alessandra Bordoni
In the past 20 years, the scientific community has faced a great development in different fields due to the development of high-throughput, omics technologies. Starting from the four major types of omics measurements (genomics, transcriptomics, proteomics, and metabolomics), a variety of omics subdisciplines (epigenomics, lipidomics, interactomics, metallomics, diseasomics, etc.) has emerged.
Thanks to the omics approach, researchers are now facing the possibility of connecting food components, foods, the diet, the individual, the health, and the diseases, but this broad vision needs not only the application of advanced technologies, but mainly the ability of looking at the problem with a different approach, a “foodomics approach”.
Foodomics is the comprehensive, high-throughput approach for the exploitation of food science in the light of an improvement of human nutrition. Foodomics is a new approach to food and nutrition that studies the food domain as a whole with the nutrition domain to reach the main objective, the optimization of human health and well-being […].
For more information, visit http://www.foodomics.eu/.
|28-29 May 2013||
NSF hands-on workshop and
symposium “Metabolic pathways in
microorganisms for biofuels”
May 29, 2013, 10.00am- 4.00pm
UC Davis Genome Center auditorium, room 1005
451 Health Sciences Drive, Davis, CA 95616
A poster session is planned for the breaks. Poster size: 35’’x 57’’
Hands-on workshop in metabolomics
for up to 20 graduate students and postdocs
May 28, 2013, 9am- 6pm
UC Davis Genome Center, room 1314
Mass spectrometry, compound identification, data processing.
Please register with: Jeannette Martins, email@example.com
Please register posters with: Jeannette Martins, firstname.lastname@example.org
|1-7 June 2013||
GRC on Computational NMR
and Associated Seminar on Metabolomic NMR
The meeting is the eighth GRC on Computational NMR and the first to include a dedicated Seminar for graduate students and postdocs. The focus of the GRS is to discuss new contributions in computational Nuclear Magnetic Resonance to the growing field of metabolomics and will feature a keynote talk by David Wishart, University of Alberta, and discussions led by experts in metabolomic NMR as a complement to oral presentations by graduate students and postdocs.
For more information: http://www.grc.org/programs.aspx?year=2013&program=grs_bionmr
For registration: http://www.grc.org/application.aspx?id=15572
We do hope that you will both consider attending and provide this information to your students and postdocs and encourage them join us in Vermont for what we anticipate will be an enjoyable and stimulating meeting.
|1-4 Jul 2013||
9th Annual International
Meeting of the Metabolomics Society
We expect this to be the 'must attend' meeting in 2013 for researchers from around the world, where the best speakers in the world and rising stars of the future will present their work in a mixture of plenary and parallel sessions. The Metabolomics Society came into being with the development of the Metabolomics as a discipline and as a result provides a focus for the most varied aspects of the subject ranging from microbes to man. As a result of this it brings together a diverse mixture of scientists from many disciplines, which produces very stimulating meetings.
One of the main aims of the conference will be to create a unique platform for young scientists. Come and listen and talk to the top experts in the field. Find out about the latest exciting technologies that can advance your own research, but most of all come and enjoy Scotland's largest and most vibrant city and the beautiful countryside around it.
We look forward to welcoming you to Glasgow in 2013!
Chair, Local Organising Committee
Metabolomics Glasgow 2013
For more information, visit http://www.metabolomics2013.org/.
|2-4 Jul 2013||
3rd European Lipidomic
For more information, visit http://mab.uochb.cas.cz/iochb/ELM2013/.
|8-9 Jul 2013||
Informatics and Statistics
for Metabolomics (2013)
Target Audience: This course is intended for graduate students, post-doctoral fellows, clinical fellows and investigators who are interested in learning about both bioinformatic and cheminformatic tools to analyze and interpret metabolomics data.
Prerequisite: Your own laptop computer. Minimum requirements: 1024x768 screen resolution, 1.5GHz CPU, 1GB RAM, recent versions of Windows, Mac OS X or Linux (Most computers purchased in the past 3-4 years likely meet these requirements). If you do not access to a laptop, you may loan one from the CBW. Please contact email@example.com for more information.
Pre-Readings: You are expected to have completed the following tutorials in R beforehand. The tutorial should be very accessible even if you have never used R before. Please complete the following: R Tutorial
For more information, visit http://bioinformatics.ca/workshops/2013/informatics-and-statistics-metabolomics-2013.
|6 Aug 2013||
Frontiers in Nutritional
Science: The Inaugural Australian Symposium on
About the event
Nutritional Metabolomics is an exciting, emerging frontier field of science.
Metabolomics (measuring metabolites from physiological process) provide information, 'windows into the body', which have the potential to transform how we measure health, how we identify and monitor people most at risk of disease, and the way we monitor food intake.
The event will provide food and health science professionals and researchers, an exciting insight into how this new science can be applied to better understand the ways in which food, diet and the body interact.
To stimulate interest and collaboration in this frontier field of health sciences, we are organising a symposium which aims to explore opportunities for using metabolomics to improve human health by nutritional means.
This one day symposium will bring together international and national experts to provide a comprehensive, up-to-date overview of this fast growing field.
The event will provide food and health science professionals and researchers, an exciting insight into how this new science can be applied to better understand the ways in which food, diet and the body interact.
Topics to be covered include:
Registrations for the event will open soon.
Find out more about CSIRO's work in Animal, Food and Health Sciences and Preventative Health.
Program Download: The Nutritional Metabolomics Symposium program (PDF)
For more information, visit http://www.csiro.au/en/Organisation-Structure/Divisions/Animal-Food-and-Health-Sciences/Nutritional-Metabolomics-Symposium.aspx?goback=%2Egde_4185659_member_229009122.
|13-17 Aug 2013||
Daniel Kelly, Sanford-Burnham Medical Research Institute
Mitchell Lazar, University of Pennsylvania
Susanne Mandrup, University of Southern Denmark
We are pleased to announce the first Cold Spring Harbor meeting on Metabolic Signaling & Disease: From Cell to Organism which will begin on Tuesday evening, August 13 and end at noon on Saturday, August 17, 2013.
Metabolic regulation is at the intersection of many scientific fields, ranging from basic biochemistry and molecular biology to physiology, to the study of disease pathogenesis. Currently, a major challenge for these diverse fields is to define commonalities and differences in metabolic pathways and their regulation, and determine the role of these processes for physiology and disease states. This meeting will fill an important gap by bringing together outstanding researchers focused on diverse pathways, cell types, or diseases with a common theme of understanding how metabolism is regulated in physiology and disease states.
For more information, visit http://meetings.cshl.edu/meetings/2013/metab13.shtml.
|9-11 Sep 2013||
Environmental ‘Omics Synthesis Conference
The aim of this conference is to bring together researchers and organisations from a range of disciplines representing those involved in the development of new approaches in data handling and generation with those harnessing ‘Omics to advance key areas in Environmental Science. It is our hope is that the resulting interaction and exchange of ideas will lead to novel approaches, new collaborations and the establishment of a wider integrated ‘Omics community.
iEOS2013 – Announcement Poster: http://environmentalomics.org.gridhosted.co.uk/wp-content/uploads/2013/03/iEOS2013-Final-Announcement.pdf
For more information, visit http://environmentalomics.org/iEOS2013/.
|1-3 Oct 2013||
The 10th International
Symposium on Milk Genomics and Human Health
The venue for this year's event is the U.C. Davis Conference Center located on the University of California, Davis campus in the United States.
The three day event will bring together international experts in nutrition, genomics, bioinformatics and milk research to discuss and share the latest breakthroughs and their implications.
The Annual Symposium is our flagship event that features scientific research related to milk and human health done throughout the world. The symposium draws from the diversity of its memberships to cover the breath of genomics themes that reflect the interest of the Consortium. The goal of the Consortium is to bring together the research and dairy communities to share, translate, and interpret data that are happening within the fields of the "-omics" science.
For more information, visit http://milkgenomics.org/symposia/the-10th-international-symposium-on-milk-genomics-and-human-health-october-1-3-2013.
|7-11 Oct 2013||
SLC-Tjärnö marinebiological laboratory
Application should include a short motivation (<1 page) and a brief CV. Submit by E-mail to firstname.lastname@example.org
Application deadline 15th of August 2013
Prof. Georg Pohnert, Biorganic Analytics, Friedrich Schiller University, Jena
Prof. Johan Trygg, Department of Chemistry, Umeå University
Dr. Ulf Sommer, NERC Metabolomics Facility, University of Birmingham
Contact and inquiries:
Erik Selander email@example.com
Göran Nylund firstname.lastname@example.org
Course Flyer: http://www.metabonews.ca/May2013/events/Metabolomics%20course%20flyer.pdf
11th Annual Metabolomics
7) Metabolomics Jobs
|Postdoctoral position in malaria mass spectrometry-based metabolomics||Pennsylvania State University||
College, Pennsylvania, USA
|Postdoc Position||Palacky University||Olomouc, Czech Republic||30-Apr-2013||15-Jun-2013||naturejobs.com
|Permanent Metabolomist Position||DEINOVE||
|LC-MS Metabolomics Specialist||Metabolomic Discoveries GmbH||Potsdam, Germany||26-Apr-2013||21-Jun-2013||Metabolomic
|PhD Studentship in Department of Twin Research & Genetic Epidemiology||King's College London||London, United Kingdom||20-Apr-2013||17-Jun-2013||naturejobs.com|
|Full-Time Research Coordinator||University of Alberta||
|Sr Scientist - Metabolomics Technical Marketing-AB 001492||AB SCIEX||
City, California, USA
|Scientist / Specialist Mitochondrial Function||The Nestlé Institute of Health Sciences||Lausanne, Switzerland||25-Mar-2013||24-May-2013||naturejobs.com|
|Omics Data Analyst||The Nestlé Institute of Health Sciences||Lausanne, Switzerland||7-Mar-2013||7-May-2013||naturejobs.com|
|Metabolomics / Lipidomics Analyst||The Nestlé Institute of Health Sciences||Lausanne, Switzerland||7-Mar-2013||7-May-2013||naturejobs.com|
|Sales Representative / Business Developer (m/f)||Metabolomic Discoveries GmbH||Potsdam, Germany||27-Feb-2013||metabolomicdiscoveries.com|
|Internship/Thesis: Development of suitable plugins for the knowledge base||Metabolomic Discoveries GmbH||Potsdam, Germany||27-Feb-2013||metabolomicdiscoveries.com|
Ian J. Forsythe, M.Sc.MetaboNews
University of Alberta
221 Athabasca Hall
Edmonton, AB, T6G 2E8, Canada
A single source destination for fee-for-service metabolic profiling including comprehensive metabolite identification, quantification, and analysis