MANA 2023 Workshop Recaps

MANA 2023 offered 13 workshops spanning data management, advanced analysis techniques, and interdisciplinary approaches, showcasing practical applications, tool development, and fostering collaboration within metabolomics. Check out the recaps from a few of the workshops below. For more details about the workshop click here!

Lipidomics Minimal Reporting Checklist for Metabolomics co-lead by Kim Ekroos, Tom Metz, Gerhard Liebisch, Ruth Welti

The Lipidomics Minimal Reporting Checklist workshop began with Gerhard Liebisch presenting the Lipidomics Standard Initiative’s “Lipidomics Minimal Reporting Checklist”, which is designed to collect standardized details about a lipidomics experiment from the biological experiment to lipid extraction to mass spectral analysis to data processing. The parameters are saved in a database, can be printed as a report, and can be published online with a DOI that can be referenced in a manuscript. Tom Metz then talked about the potential for adapting the checklist to other types of metabolomic experiments, and Ruth Welti discussed changes that would make the checklist friendly for plant, as well as animal, lipid research. Kim Ekroos led a discussion about potential checklist changes to cover experimental or data processing processes that are hard to describe with the current checklist choices. The potential for journals to require the checklist was also discussed. The workshop provided a great opportunity to inform the lipidomics community with the goals of improving the checklist and expanding its user group.

The Art of Industry Collaboration: Empowering Early Career Scientists in Establishing Corporate Member Relationships co-led by Arpana Vaniya, Nicole Prince

The workshop included the following panel speakers: Randy Arnold from SCIEX, Ryan Groves from the Calgary Metabolomics Research Facility, Katherine Sanders from MilliporeSigma, Iggy Kass from Waters Corporation, John Hayes from LECO, Dan Cuthbertson from Agilent Technologies, Erica Forsberg from Bruker, and Susan Bird from Thermo Fisher Scientific. Some key takeaways from the workshop include:

• Building Bridges Between ECMs and Industry Partners: Our panelists provided feedback on how to build connections with industry partners. It's never too early to build relationships with corporate members, and working with them is the best way to get access to cutting-edge technology.

• Proactive Collaboration: Our panelists shared insights about involving industry partners during the design phase of a project and getting advice early in the process. They can help you get the tools you need to succeed!

• Defining Collaboration with Industry Partners: The role of industry collaborators can be shaped to fit your specific needs. Our panels talked about how they assist ECMs in starting new labs through unique funding opportunities and access to programs to use instruments at reduced costs.

Overall, the workshop underscored the importance of fostering relationships, sharing ideas, and defining collaboration while recognizing the potential of early career scientists in driving future collaborations and innovation within the industry. We asked our panel speakers about their main insights from the event, and here's what a few had to say:

• "I was very encouraged to see that so many young researchers expressed an interest in pursuing a career in industry. Having gone through the experience of moving from academia to industry in my own career, I appreciate how challenging that transition can be. I thought the issues and questions raised during the workshop were insightful and informative." - Randy Arnold, SCIEX (The statement is not an official position or declaration on behalf of SCIEX)

• "It never hurts to ask: Relationships and collaborations evolve over time. Share ideas as early as possible. While all proposals can't possibly move forward, surely collaborative ideas that are not put forth will not gain momentum.  Take advantage of your vendor partners as often the simple good thought grows into a greater idea via networks of collaborators that you may not normally encounter. Your vendor partners gain from your expertise in new and emerging science and markets - and have an incentive to work with you." - Iggy Kass, Waters

  "I really loved the workshop and am so grateful for being included. I learned that the nuance of the word “collaboration” is something to continually strive to better define as a clearer understanding of the concept will create a safer space for networking. I also really loved hearing [about] my competitive colleagues' paths to their current positions. I think hearing these stories are invaluable regardless of your career stage." - Susan Bird, Thermo Fisher Scientific

• "ECM members offer perhaps the best opportunity for vendors to get a window into the future of metabolomics. Today’s up-and-coming members are already well-versed in existing metabolomics workflows, yet are also motivated to carve their own path with novel insights and technologies: the potential for exciting collaborations is tremendous!" - John Hayes, LECO

Colorful word cloud for the question “What comes to mind when you think of industry/academic research collaborations?”

Multi-omics Analysis and Interpretation co-lead by Isin Tuna Sakallioglu, Stephanie Bishop

• Summary: The workshop facilitators provided an overview of statistical approaches, non-coding software, and R-based software that can be used to integrate several kinds of omics data, including metabolomics, proteomics, transcriptomics, and genomics.

• Outcomes: The audience was able to participate in live demos and tutorials of these software tools and engage in discussions regarding multi-omics integration. We also encourage the MANA community to check out our GitHub page and contribute any resources they may have on this topic: https://github.com/sgosline/metabolomics-integration

• Key Takeaway: Multi-omics approaches are becoming more and more common, but there are still several challenges to address including cost of analysis, data interpretation , and ensuring good practices in data collection and annotation. With improved access to open-source tools with in-depth tutorials, more researchers will be able to use multi-omics approaches in their routine studies.

Thank you to Pawan Sandhu and Sara Gosline who also helped to facilitate the workshop.

The View of the Microbiome Through the Lens of Metabolomics: Data Analysis and Integration Strategies co-lead by Renny Lan, Rob Quinn, Maryam Goudarzi, Chris Zhu

Dr. Ipsita Mohanty and Dr. Simone Zuffa from UC San Diego participated in “The View of the Microbiome through the Lens of Metabolomics: Data Analysis and Integration Strategies” workshop. The postdoctoral researchers from the Dorrestein lab gave a live demo of two tools developed in the past years: GNPS Dashboard and microbeMASST. The GNPS Dashboard allows users to quickly open and explore open format mzML and mzXML files and share them with collaborators. During the live demo Dr. Ipsita Mohanty showed how to easily visualize and extract the MS/MS spectrum of a novel conjugated bile acid from an mzML file, which was then used by Dr. Simone Zuffa to illustrate the functionality of microbeMASST. This novel tool allows searching for known and unknown MS/MS spectra against a reference database of more than 100 millions MS/MS spectra acquired from monocultures of microorganisms. Participants at the workshop were really interested in this novel tool, engaging in several questions and confirming that they will use this tool in their projects. Additionally some of the participants asked for the possibility to contribute to the open data reference of the microbeMASST database. Participant learnt how to use novel open source tools and understand the importance of public data and how this can be leveraged in novel way to shine a light on the unexplored chemical space of untargeted metabolomics.

Opportunities and Challenges in Developing a Web-accessible, Community-sourced Database of Reproducible Metabolomics Methods in Compliance with FAIR Principles: An ABRF Initiative co-led by Ryan Sheldon, Maryam Goudarzi

We discussed at length challenges in metabolomics methods reproducibility and how current metabolomics data repositories are ineffective because they are data-centric rather than method-centric. The general consensus that these are problems but are hard to address. The ABRF Metabolomics Research Group is undertaking steps towards solving these problems, and [we'd] like to get interested folks from MANA involved. [We] also used mentimeter to get a feel for the types of metabolites and samples the people are working with and the results are fun, see below:

Colorful word cloud for the question “What comes to mind when you think of industry/academic research collaborations?”

SQUAD Metabolomics, the New Standard in Discovery Metabolomics Analyses co-led by Susan Bird, Eric Tague, Bashar Amer, and Rahul Deshpande

• Outcome: Customers felt more informed and empowered to utilize intelligent acquisition strategies on their own MS systems.

MANA Members attending SQUAD Metabolomics Workshop at MANA 2023.

The NP-MRD: An NMR Database for Metabolomics and Natural Product Discovery co-lead by David Wishart, Lloyd Sumner, Roger Linington, John Cort

A workshop on the Natural Products Magnetic Resonance Database (NP-MRD, https://np-mrd.org) was given on the first evening of MANA2023 by John Cort and Jess Bade of Pacific Northwest National Laboratory, and David Wishart and Vasuk Gautam from the University of Alberta. NP-MRD team member and MANA 2023 chair Lloyd Sumner was present as well. Around 35 people attended the 2-hour workshop. The NP-MRD is a database and repository for nuclear magnetic resonance (NMR) data for natural products and specialized metabolites, as well as their primary metabolite precursors. The workshop surveyed the content and features of the NP-MRD, including types of NMR data available, structure and chemical shift search tools, the raw data deposition user interface, and chemical shift predictions made with both machine learning and quantum chemical methods. Interactive demonstrations of these features helped attendees develop a better understanding of NP-MRD and how it could benefit their research. Presentation materials for the workshop are available at https://np-mrd.org/presentations.

MANA Interest Groups: What They Are and How to Get Involved co-led by Ewy Mathé, Arpana Vaniya

In the MANA Interest Groups workshop, participants were introduced to MANA's seven interest groups. The session facilitated a deep dive into each interest group's core mission, ongoing endeavors, and active initiatives, allowing attendees to grasp the unique contributions of each group within the metabolomics landscape. With leaders from these groups in attendance, attendees gained firsthand insights into their current ongoing and strategic goals. The workshop not only showcased the diverse array of activities these groups undertake but also provided attendees with actionable guidance on how to actively engage and contribute, nurturing a collaborative ethos among members and encouraging broader involvement in advancing metabolomics research. If you'd like more information about MANA's Interest Groups check out our website here.