Metabolomics (MRG)

MRG 2021 Study
 - Compound Identification - 

Consistent and accurate compound identification is a major challenge for LC/MS based metabolomics. The presence of multiple isomeric compounds, matrix effects, low and varying analyte concentration, and in source fragmentation and adduct formation are major contributing factors to this challenge. A combination of accurate mass MS1, MS2 fragmentation, and retention time (RT) of external standards is frequently used to provide a high confidence, though unconfirmed, compound identification. However, given this information (MS1, MS2, RT) it is unclear how much compound identification success will vary from lab to lab. The aim of this study is to quantify inter-personal and inter-lab variability of compound identification.

The target population of this study are PIs, trainees, and professional staff of metabolomics laboratories. More than one participant from each lab can participate so we can assess not only inter- but also intra-lab variability of compound identification accuracy.

The study participants will be provided with two datasets. They have the option to return results for only one dataset or both datasets.

Dataset 1: text file with MS1, MS2, and RT information of 10 common metabolites in either MSP or MGF format and a compound list of RTs generated from external standards.

Dataset 2: mzXML file generated from MS1 and ddMS2 raw files.

Participants are asked to detect and ID as many compounds as they can as well as a confidence metric in the ID, molecular weight, chemical formula and other compound classifiers. In addition, participants are asked to provide information on instrumentation, types of application, etc. utilizing the on-line ‘SurveyMonkey’.

Please check back. A link to the study data files will be posted here in November.

Mission

The aims of the Metabolomics Research Group are a) to educate research scientists and resource facilities in the analytical approaches and management of data resulting from comprehensive metabolite studies and b) to promote the science and standardization of metabolomic analyses for a variety of applications. Group efforts will also include conducting surveys and organizing sessions at the annual ABRF meeting to explore the current state of the art in the field and the organization of research studies.  

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Metabolomics is the comprehensive profiling of metabolites and other small molecules. The large structural diversity of these compounds makes both comprehensive profiling and identification challenging. The major platforms are NMR and mass spectrometry, particularly LC/MS and GC/MS. There is currently a great variety of approaches, including untargeted profiling, targeted approaches, and fluxomics. Both semi-quantitative and quantitative approaches can be used. Challenges include identification of metabolites and how they change in relation to a biological perturbation (e.g. drug, diet, disease) and determining the biological significance of these changes. The Metabolomics Research Group consists of members from academic core and research laboratories, industrial analytical laboratories and providers of metabolomic services, analytical standards and instrumentation.

Current Membership

Chris W. Turck (Chair) - Max Planck Institute of Psychiatry 
Amrita K. Cheema -  Georgetown University
Daniel Cuthbertson - Agilent Technologies
Maryam Goudarzi - Cleveland Clinic Lerner Research Institute
Tytus Mak - NIST
Magnus Palmblad (EB Liaison) - Leiden University Medical Center
Reza Salek - International Agency for Research on Cancer
Ryan Sheldon - Van Andel Institute
Baljit Kaur Ubhi - SCIEX

Studies

 1.  The Metabolomics Research Group has conducted another survey study to collect data on the current use of metabolomics technologies in core and research laboratories. Questions are designed to elicit responses concerning the current level of interest in the field of metabolomics. For those already offering/practicing metabolomics technologies we wanted to find out what instrumentation is used, types of application, etc.

A similar survey was conducted by the Metabolomics Research Group 10 years ago. Of particular interest was how the practice of metabolomics in core and research laboratories has changed over a decade. What technologies are used and what are the bottlenecks in the field?

- MRG2020 Survey Study Results 

 2.  The Metabolomics Research Group has organized and finished its second study with a focus on strategies for the analysis of metabolomics data collected with high resolution mass spectrometry. Results of the study were presented at the ABRF 2017 conference in San Diego, CA. A manuscript summarizing the study has been accepted for publication in a Metabolites Special Issue.

MRG2016 Study Results
MRG2016 Study Announcement

3.  The Metabolomics Research Group's second study focused on strategies for the analysis of metabolomics data collected with high resolution mass spectrometry. For study details and materials please consult the Instructions and Bioshare Data    
      repository.

4.  The Metabolomics Research Group has organized and finished its first Research Study. Results of the study were presented at the ABRF 2014 conference in Albuquerque, NM. A manuscript summarizing the MRG study results has been accepted for publication in JBT.

    - MRG2013 Study Announcement 
    - MRG2013 Amrita Cheema Presentation 
    - MRG2013 Study Results (18K)

5.  The MRG has conducted a survey to collect data on the current use of metabolomics technologies in core facilities. Questions were designed to elicit responses concerning the current level of interest in the field of metabolomics, and for those already offering a metabolomics service to find out what instrumentation is used, types of application, etc. The results of the survey were presented at the ABRF2010 meeting during the MRG session.

    - MRG2010 Survey 

Activities

1) MRG member Amrita Cheema's presentation at ABRF 2021

     - ABRF Metabolomics Research Group Survey Study  

2) MRG member Amrita Cheema's presentation at ABRF 2017

     - ABRF Metabolomics Research Group Data Analysis Study

 3) MRG member Amrita Cheema's presentations at ABRF2016

    - Metabolomics: Challenges and Opportunities

    - MRG Session 2016

4) The NIH ‘Common Funds Metabolomics Program’ held its first annual meeting in Ann Arbor, Michigan September 27-29, 2013 at Michigan Regional Comprehensive Metabolomics Research Core (MRC2). The program currently supports a variety of initiatives for increasing national capacity in metabolomics including three ‘Regional Comprehensive Metabolomics Research Cores’ (RCMRC), a ‘Data Repository and Coordination Center’ (DRCC), technology development, education and training grants and several administrative supplements. More information on initiatives can be obtained at http://commonfund.nih.gov/Metabolomics

    - Metabolomics Annual Program Meeting 

5) MRG member Amrita Cheema's presentation at ABRF2013
          - Applications of Metabolomics to Bio-medical research

6) MRG members Bill Wikoff, Vladimir Tolstikov and John Asara presented details on ongoing MRG Study, metabolomics core laboratories and research projects at ABRF2011.
          - Bill Wikoff Presentation 
          - Vladimir Tolstikov Presentation 

7) William Wikoff of the MRG organized a Satellite Workshop entitled 'An Introduction to Metabolomics' at ABRF2011. The workshop was intended for the scientist who wants an introduction to metabolomics, with an emphasis on practical, mass spectrometry-based approaches. The entire process of metabolomics, from study design to data processing and analysis was presented. Topics included: types of detectors and their relative merits for specific metabolomics applications(including standard and specialized instruments), methods for sample extraction peak integration, data alignment, software, and data analysis with an emphasis on selecting straightforward approaches appropriate for a given problem. Approaches to biomarker discovery and metabolomics in drug discovery were discussed and a review of selected case studies from the literaturewereincluded.
         ABRF2011 Satellite Workshop

8) The newly formed 'Metabolomics Research Group' held its first session at ABRF2010. Presentation topics included survey results and metabolomics core facilities.
         Chris Turck Presentation 
         Tom O'Connell Presentation (3,731K)
         Pavel Aronov Presentation (628K)
         Vladimir Tolstikov Presentation (2,608K)

9) Bill Wikoff (MRG chair) organized the ‘Metabolomics Scientific Session’ at ABRF2010. Three prominent scientists in the field spoke about technologies and applications.
         Bill Wikoff Presentation 
         Oliver Fiehn Presentation 
         David Wishart Presentation 
         Chris Beecher Presentation

Protocols

1) A positivenegative ion–switching, targeted mass spectrometry– based metabolomics platform for bodily fluids, cells, and fresh and fixed tissue
    - Targeted metabolomics platform 
2) Validated high quality automated metabolome analysis of Arabidopsis Thaliana leaf disks
    - Arabidopsis Thaliana metabolome analysis 
3) Small molecule metabolite extraction strategy for improving LC/MS detection
    - Small molecule metabolite extraction (1,587K)

Membership History

Member NameOrganizationDetails
Dr. Pavel Aronov Stanford University  Member: 03/09 - 03/12
Dr. John M Asara Beth Israel Deaconess Medical Center  Member: 03/10 - 03/15
Stephen Brown    Member:  - 3/15
Dr. Christopher Colangelo Primary Ion  EB Liaison: 03/15 - 03/18
Dr. Nathan Dodder NIST  Member: 03/09 - 03/10
Dr. Brenda Kesler Thermo Fisher Scientific  Member: 03/09 - 02/11
Dr Thomas Neubert New York Univ Sch of Med  Member: 03/14 - 03/15
Liaison: 03/13 - 03/14
Dr Thomas M. O'Connell University of North Carolina  Member: 03/09 - 11/10
Dr. Andrew Patterson Penn State University Member: 04/14 - 03/17
Dr. Brett S Phinney Proteomics Core UC Davis Genome Center  EB Liaison: 02/11 - 03/12
Prof. Vladimir Shulaev University of North Texas  Member: 03/10 - 03/13
Jack Simpson   EB Liaison: 04/12 - 03/13
Dr. Vladimir V. Tolstikov UC Davis Genome Center  Member: 03/09 - 05/12
Chris W Turck Max Planck Institute of Psychiatry  Ad hoc: 02/11 - 05/12
EB Liaison: 03/10 - 02/11
Dr. William R. Wikoff University of California, Davis  Chair: 03/10 - 05/12
Member: 03/09 - 03/10
Member: 05/12 - 03/13

Publications

  1. Amrita K. Cheema, John M. Asara, Yiwen Wang, Thomas A. Neubert, Vladimir Tolstikov, Chris W. Turck

     

  2. Christoph W. Turck, Tytus D. Mak, Maryam Goudarzi, Reza M. Salek, Amrita K. Cheema

 

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