The Future of a Myriad of Accelerated Biodiscoveries Lies in AI‐Powered Mass Spectrometry and Multiomics Integration

Bilbao, Aivett

doi:10.1002/jms.5157

The Future of a Myriad of Accelerated Biodiscoveries Lies in AI‐Powered Mass Spectrometry and Multiomics Integration

Journal Article · Sat Jul 05 00:00:00 EDT 2025 · Journal of Mass Spectrometry

DOI:https://doi.org/10.1002/jms.5157· OSTI ID:2574265

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Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL); USDOE Agile BioFoundry, Emeryville, CA (United States)

The intersection of modern artificial intelligence (AI) and mass spectrometry (MS) is set to transform the MS‐based “omics” research fields, particularly proteomics, metabolomics, lipidomics, and glycomics, enabling advancements across a wide range of domains, from health to environment and industrial biotechnology. Beginning with an overview of key challenges inherent in MS software pipelines, this personal perspective explores how AI‐driven solutions can address them to enhance data processing, integration and interpretation. It proposes a paradigm shift in molecular identification and quantitation algorithms, leveraging AI to enable holistic interpretation of MS‐based multiomics data. While centered on MS‐based omics, this holistic AI‐driven paradigm is also critical for connecting dynamic biochemical changes to genomics and transcriptomics contexts, reinforcing the integrative value of MS in multiomics research. Ultimately, this AI‐driven approach could enhance efficiency, accuracy, and molecular breadth of coverage, deepening our systems‐level understanding of biological processes and accelerating a myriad of biodiscoveries.

View Accepted Manuscript (DOE)

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE), Office of Sustainable Transportation. Bioenergy Technologies Office (BETO)

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 2574265

Report Number(s):: PNNL-SA--206770

Journal Information:: Journal of Mass Spectrometry, Journal Name: Journal of Mass Spectrometry Journal Issue: 8 Vol. 60; ISSN 1076-5174; ISSN 1096-9888

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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