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Mass Spec Molecular Simulation

Full Campaign Name:

Integrating High-Resolution Mass Spectrometry and Molecular Simulation

Hundreds of metal shavings in a pile

Understanding metal-binding processes is essential for advancements in critical mineral recovery and biotechnology, as these processes help us understand biologically driven mineral extraction. 

Through this Computing, Analytics, and Modeling Community Science Campaign, EMSL will partner with invited research community members to use EMSL’s cutting-edge molecular simulation methods to uncover innovative solutions for metal-binding processes important for compound identification and biodesign. By combining experimental data with molecular simulations and artificial intelligence (AI) frameworks, the campaign will deliver predictive insights advancing priorities like critical minerals and materials (CMMs) and biotechnology research through automated and scalable workflows. 

Successful approaches will be made available to the research community as EMSL resources. 

By participating in this campaign, you will 

  • Help solve a big science problem 
  • Drive important outcomes 
  • Advance your own research

Participation

How researchers have been invited to participate 
  • A panel of researchers was invited to participate in the initial community science meeting based on their domain expertise, experience, and overlapping interests with the campaign topic. After this meeting to identify high-priority campaign objectives, a call for proposals was opened and shared with the community science meeting attendees.
Required participant background 
  • Possess high-resolution mass spectrometry (MS) data related to the metal complexes of proteins and metabolites that are important in CMMs and biotechnology. 
  • Have subject matter expertise in current methodologies, molecular simulation techniques, and AI frameworks related to the enhanced understanding of MS results and/or compound identification by means of MS. 
How will you contribute? 
  • Identify and Prioritize Knowledge Gaps and needs
    • Provide input on potential applications related to critical mineral management, biotechnology development, or other relevant fields. Contribute to shaping ideas around innovations and future advancements in this area. 
  • Supply Data
    • Contribute use cases and high-resolution MS data related to the metal complexes of proteins and metabolites that are important in CMMs and biotechnology. 
  • Feedback Through Community Science Meetings
    • Offer insights into current methodologies, molecular simulation techniques, and AI frameworks related to the enhanced understanding of MS results and/or compound identification by means of MS. Refine the proposed goals for integrating MS with molecular simulations and AI workflows.
  • Expert Input
    • Provide context, formulate scientific hypotheses, and explore potential classes of molecules and metal complexes important to CMMs and biotechnology and enabling strategies for elucidating metal binding.

About the Campaign

EMSL’s MS equipment and expertise, including a recently upgraded 21 Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer now coupled with a high-resolution Exploris 480 Orbitrap mass spectrometer, enables unique MS experiments. These experiments will yield rich datasets that shed new light on critical metal-binding metabolites and proteins from microbial systems. The new capability enables the precise characterization of complex mixtures and macromolecules, vital for resolving metal interactions and accurately determining molecular compositions. 

The objective of this campaign is to apply EMSL’s leading expertise in molecular simulation (molecular dynamics, ab initio calculations, and multiscale modeling) to uncover novel insights into reaction mechanisms, fragmentation pathways, and resource utilization strategies. Given the scale and complexity of the data, workflows that leverage AI and machine learning (ML) for predictive capabilities will be used to accelerate scientific discovery in the application domains. To maximize the potential of MS data (e.g., FTICR + Orbitrap) integration and molecular simulations, automated workflows are critical for delivering the flexibility needed to support comprehensive analysis. 

This campaign supports the recent presidential memorandum on fiscal year 2027 national research and development priorities and the Genesis Mission demonstrating how AI accelerates scientific discovery within Earth sciences. In addition, this campaign aligns with the Department of Energy’s science priorities in CMM research.

Campaign Timeline

OCTOBER 2025 – CAMPAIGN TOPICS AND DESCRIPTIONS DRAFTED 

  • Identify community science campaign topics aimed at solving a significant scientific challenge or filling current gaps in knowledge. 

NOVEMBER 2025 – POTENTIAL CAMPAIGN PARTICIPANTS IDENTIFIED 

  • Strategically identify researchers with ideal domain expertise and experience to invite participation in the upcoming community science meeting. 

DECEMBER 2025 – COMMUNITY SCIENCE MEETING 

  • Host a community science meeting to identify methodologies, systems of interest, and user community needs. 

DECEMBER 2025 – CALL FOR PROPOSALS 

  • Invite community science meeting attendees to submit proposals for projects contributing to overall campaign goals. 

JANUARY 2026 – CAMPAIGN PROPOSAL DEADLINE 

  • Deadline for invited campaign participants to submit proposals for projects contributing to overall campaign goals. 

JANUARY 2026 – INITIATE WORK ON ACCEPTED PROPOSALS 

  • Work begins on accepted proposals for projects contributing to overall campaign goals. 

FEBRUARY–SEPTEMBER 2026 – APPLY MOLECULAR SIMULATION WORKFLOWS 

  • Apply EMSL’s molecular simulation workflows to address key science questions refined by campaign participants. 

SEPTEMBER 2026 – COMPLETE CAMPAIGN 

  • Complete the campaign and deliver workflows and documentation to the community.

Campaign Methods

HIGH-QUALITY DATA 
  • Use participant or EMSL-provided MS data, in addition to leveraging data from other EMSL campaigns, that focus on metal binders found in complex mixtures such as biomass and cell lysates. 
SIMULATIONS FOR EXPLORATION 
  • Ab initio quantum chemistry simulations and classical molecular dynamics simulations, and potentially combined multiscale simulations, will explore metal-binding processes critical to compound identification and biodesign. 
WORKFLOW AND AI AGENT FRAMEWORKS 
  • Workflow frameworks and AI agent frameworks will be used to develop and validate pipelines that integrate modeling and simulation methods with advanced algorithms for high-throughput, semiautomated data analysis.

Solve a Big Challenge

This campaign helps address the scientific challenge of understanding metal-binding processes critical to advancing the Biological and Environmental Research (BER) program’s science priorities, such as CMMs and biotechnology. It integrates EMSL’s cutting-edge MS capabilities, including the 21 Tesla FTICR and Orbitrap MS, with molecular simulations and AI-driven workflows to tackle the complexity of characterizing metal-binding metabolites and proteins. By enabling high-throughput, semiautomated analysis and predictive modeling, the campaign overcomes barriers in data processing and scalability to deliver insights into reaction mechanisms and biochemical interactions. These advancements will unlock new strategies for sustainable resource utilization, accelerating innovation in critical minerals, biodesign, and biotechnology applications that align with BER's mission.

Expected Campaign Outcomes

Integrated MS–simulation workflows 
  • Semiautomated workflows that combine high-resolution MS data with molecular simulation to support compound identification and metal-binding characterization. 
Predictive modeling capabilities 
  • Computational approaches for predicting metal-binding behavior and related molecular interactions relevant to critical minerals and biotechnology applications. 
Curated datasets for AI/ML 
  • High-quality experimental and simulated datasets that can support downstream ML models and future community research. 
Community-accessible methods and documentation 
  • Documented workflows, methods, and lessons learned that can inform future EMSL user proposals and broader community applications.

Advance Your Research

  • Accelerate your science
  • Access cutting-edge technology
  • Gain experience and key knowledge
  • Co-author scientific publications

Why "Community" Science Campaigns?

Each community science campaign is intended to bring together researchers with a wide variety of expertise to tackle a set of strategically identified challenges that are bigger than what an individual principal investigator or small team research effort can accomplish alone.

With the help of the scientific community, EMSL can ensure that the computational simulations and AI-driven workflows developed are targeting the most critical challenges, incorporating the right methodologies, and advancing insights into metal-binding processes and biotechnology priorities.

Contacts

Campaign leader (science domain expert): Mark Maupin | Website bio

EMSL user program contact (logistics): Rick Washburn | Proposal calls