Metabolomics Research Group

Metabolomics Research Group 2022 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 are provided with two datasets. They have the option to return results for only one dataset or both datasets.

The study material can be downloaded as a single Zip file: https://osf.io/xbgc5/download. It consists of an Excel spreadsheet including instructions and a survey (MRG_CompoundID study.xlsx) and two mzML data files (MS1.mzML and ddMS2.mzML). The Excel file is used for returning results by email.

IMPORTANT: All results are submitted anonymously, identified only by an 8-digit identification number that you select.

Please return your results to mrgabrf2022@gmail.com no later than December 31, 2022.

If you have any questions please contact Ryan Sheldon or Chris Turck.

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.

Questions or interest in joining an ABRF research group?

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

Ryan Sheldon (Chair) - Van Andel Institute
Amrita K. Cheema - Georgetown University
Caroline Chidley - University of Massachusetts Chan Medical School
Daniel Cuthbertson - Agilent Technologies
Maryam Goudarzi - Sciex
Tytus Mak - NIST
Magnus Palmblad - Leiden University Medical Center
Reza Salek - International Agency for Research on Cancer
Chris W. Turck - Max Planck Institute of Psychiatry
Sue Weintraub (Executive Board Liaison) - University of Texas Health Science Center at San Antonio

Studies

1. The Metabolomics Research Group...

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...

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...

4. The Metabolomics Research Group has organized...

5. The MRG has conducted a survey....

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

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

3) MRG member Amrita Cheema's presentations at ABRF2016

4) The NIH ‘Common Funds Metabolomics Program’ held its first annual...

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

6) MRG members Bill Wikoff, Vladimir Tolstikov and John Asara presented....

7) William Wikoff of the MRG organized a Satellite Workshop....

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....

9) Bill Wikoff (MRG chair) organized the ‘Metabolomics Scientific Session’....

Protocols

1) A positivenegative ion–switching, targeted mass spectrometry– based metabolomics platform for bodily fluids, cells, and fresh and fixed tissue

2) Validated high quality automated metabolome analysis of Arabidopsis Thaliana leaf disks

3) Small molecule metabolite extraction strategy for improving LC/MS detection

Membership History

Member Name	Organization	Details
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	Primary Ion
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
Baljit Kaur Ubhi	Sciex	Member through 12/21
Dr. William R. Wikoff	University of California, Davis	Chair: 03/10 - 05/12 Member: 03/09 - 03/10 Member: 05/12 - 03/13

Publications

The ABRF Metabolomics Research Group 2013 Study: Investigation of Spiked Compound Differences in a Human Plasma Matrix
Amrita K. Cheema, John M. Asara, Yiwen Wang, Thomas A. Neubert, Vladimir Tolstikov, Chris W. Turck
The ABRF Metabolomics Research Group 2016 Exploratory Study: Investigation of Data Analysis Methods for Untargeted Metabolomics
Christoph W. Turck, Tytus D. Mak, Maryam Goudarzi, Reza M. Salek, Amrita K. Cheema

Metabolomics (MRG)