AutonoMS: Automated Ion Mobility Metabolomic Fingerprinting.

Daniel Brunnsåker, Gabriel K Reder, Ross D King, John A McLean, John P Wikswo, Otto I Savolainen, Erik Y Bjurström, Filip Kronström, Praphapan Lasin, Ievgeniia Tiukova, James N Dodds, Jody C May

Journal: Journal of the American Society for Mass Spectrometry 2024;35(3):542-550

PMID: 38310603

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Abstract

Automation is dramatically changing the nature of laboratory life science. Robotic lab hardware that can perform manual operations with greater speed, endurance, and reproducibility opens an avenue for faster scientific discovery with less time spent on laborious repetitive tasks. A major bottleneck remains in integrating cutting-edge laboratory equipment into automated workflows, notably specialized analytical equipment, which is designed for human usage. Here we present AutonoMS, a platform for automatically running, processing, and analyzing high-throughput mass spectrometry experiments. AutonoMS is currently written around an ion mobility mass spectrometry (IM-MS) platform and can be adapted to additional analytical instruments and data processing flows. AutonoMS enables automated software agent-controlled end-to-end measurement and analysis runs from experimental specification files that can be produced by human users or upstream software processes. We demonstrate the use and abilities of AutonoMS in a high-throughput flow-injection ion mobility configuration with 5 s sample analysis time, processing robotically prepared chemical standards and cultured yeast samples in targeted and untargeted metabolomics applications. The platform exhibited consistency, reliability, and ease of use while eliminating the need for human intervention in the process of sample injection, data processing, and analysis. The platform paves the way toward a more fully automated mass spectrometry analysis and ultimately closed-loop laboratory workflows involving automated experimentation and analysis coupled to AI-driven experimentation utilizing cutting-edge analytical instrumentation. AutonoMS documentation is available at https://autonoms.readthedocs.io.

Address: Department of Computer Science and Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden.; Department of Applied Physics, SciLifeLab, KTH Royal Institute of Technology, Solna 171 21, Sweden.; Department of Life Sciences, Chalmers University of Technology, Gothenburg 412 96, Sweden.; Department of Computer Science and Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden.; Department of Life Sciences, Chalmers University of Technology, Gothenburg 412 96, Sweden.; Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio 702 11, Finland.; Chemistry Department, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.; Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.; Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States.; Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee 37235, United States.; Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States.; Department of Physics and Astronomy, Vanderbilt University, Nashville, Tennessee 37235, United States.; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37240, United States.; Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.; Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States.; Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee 37235, United States.; Department of Computer Science and Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden.; Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, U.K.; The Alan Turing Institute, London NW1 2DB, U.K.

DOI: 10.1021/jasms.3c00396

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MeSH Terms: Humans, Reproducibility of Results, Mass Spectrometry, Software, Automation, Metabolomics