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Pakkir Shah AK, Walter A, Ottosson F, Russo F, Navarro-Diaz M, Boldt J, Kalinski JCJ, Kontou EE, Elofson J, Polyzois A, González-Marín C, Farrell S, Aggerbeck MR, Pruksatrakul T, Chan N, Wang Y, Pöchhacker M, Brungs C, Cámara B, Caraballo-Rodríguez AM, Cumsille A, de Oliveira F, Dührkop K, El Abiead Y, Geibel C, Graves LG, Hansen M, Heuckeroth S, Knoblauch S, Kostenko A, Kuijpers MCM, Mildau K, Papadopoulos Lambidis S, Portal Gomes PW, Schramm T, Steuer-Lodd K, Stincone P, Tayyab S, Vitale GA, Wagner BC, Xing S, Yazzie MT, Zuffa S, de Kruijff M, Beemelmanns C, Link H, Mayer C, van der Hooft JJJ, Damiani T, Pluskal T, Dorrestein P, Stanstrup J, Schmid R, Wang M, Aron A, Ernst M, Petras D. Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data. Nat Protoc 2024:10.1038/s41596-024-01046-3. [PMID: 39304763 DOI: 10.1038/s41596-024-01046-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 07/02/2024] [Indexed: 09/22/2024]
Abstract
Feature-based molecular networking (FBMN) is a popular analysis approach for liquid chromatography-tandem mass spectrometry-based non-targeted metabolomics data. While processing liquid chromatography-tandem mass spectrometry data through FBMN is fairly streamlined, downstream data handling and statistical interrogation are often a key bottleneck. Especially users new to statistical analysis struggle to effectively handle and analyze complex data matrices. Here we provide a comprehensive guide for the statistical analysis of FBMN results, focusing on the downstream analysis of the FBMN output table. We explain the data structure and principles of data cleanup and normalization, as well as uni- and multivariate statistical analysis of FBMN results. We provide explanations and code in two scripting languages (R and Python) as well as the QIIME2 framework for all protocol steps, from data clean-up to statistical analysis. All code is shared in the form of Jupyter Notebooks ( https://github.com/Functional-Metabolomics-Lab/FBMN-STATS ). Additionally, the protocol is accompanied by a web application with a graphical user interface ( https://fbmn-statsguide.gnps2.org/ ) to lower the barrier of entry for new users and for educational purposes. Finally, we also show users how to integrate their statistical results into the molecular network using the Cytoscape visualization tool. Throughout the protocol, we use a previously published environmental metabolomics dataset for demonstration purposes. Together, the protocol, code and web application provide a complete guide and toolbox for FBMN data integration, cleanup and advanced statistical analysis, enabling new users to uncover molecular insights from their non-targeted metabolomics data. Our protocol is tailored for the seamless analysis of FBMN results from Global Natural Products Social Molecular Networking and can be easily adapted to other mass spectrometry feature detection, annotation and networking tools.
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Affiliation(s)
- Abzer K Pakkir Shah
- Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany
| | - Axel Walter
- Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Filip Ottosson
- Section for Clinical Mass Spectrometry, Danish Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen S, Denmark
| | - Francesco Russo
- Section for Clinical Mass Spectrometry, Danish Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen S, Denmark
| | - Marcelo Navarro-Diaz
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany
| | - Judith Boldt
- Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- German Center for Infection Research, Partner Site Braunschweig-Hannover, Braunschweig, Germany
| | - Jarmo-Charles J Kalinski
- Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Eftychia Eva Kontou
- Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA
- The Novo Nordisk Foundation for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - James Elofson
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA
| | - Alexandros Polyzois
- Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Carolina González-Marín
- Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA
- Universidad EAFIT, Medellín, Antioquia, Colombia
| | - Shane Farrell
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
- School of Marine Sciences, Darling Marine Center, University of Maine, Walpole, ME, USA
| | - Marie R Aggerbeck
- Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Thapanee Pruksatrakul
- Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Thailand Science Park, Pathum Thani, Thailand
| | - Nathan Chan
- Department of Computer Science, University of California Riverside, Riverside, CA, USA
| | - Yunshu Wang
- Department of Computer Science, University of California Riverside, Riverside, CA, USA
| | - Magdalena Pöchhacker
- Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA
- Department of Food Chemistry and Toxicology, University of Vienna, Vienna, Austria
| | - Corinna Brungs
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Beatriz Cámara
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | | | - Andres Cumsille
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Fernanda de Oliveira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, São Paulo, Brazil
| | - Kai Dührkop
- Department of Bioinformatics, University of Jena, Jena, Germany
| | - Yasin El Abiead
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Christian Geibel
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany
| | - Lana G Graves
- Department of Environmental Systems Analysis, University of Tübingen, Tübingen, Germany
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Martin Hansen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Steffen Heuckeroth
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Simon Knoblauch
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany
| | - Anastasiia Kostenko
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA
| | - Mirte C M Kuijpers
- Department of Ecology, Behavior and Evolution, University of California San Diego, San Diego, CA, USA
| | - Kevin Mildau
- Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
- Bioinformatics Group, Wageningen University and Research, Wageningen, the Netherlands
| | | | - Paulo Wender Portal Gomes
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Tilman Schramm
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany
- Department of Biochemistry, University of California Riverside, Riverside, CA, USA
| | - Karoline Steuer-Lodd
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany
- Department of Biochemistry, University of California Riverside, Riverside, CA, USA
| | - Paolo Stincone
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany
| | - Sibgha Tayyab
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany
| | - Giovanni Andrea Vitale
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany
| | - Berenike C Wagner
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany
| | - Shipei Xing
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Marquis T Yazzie
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA
| | - Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Martinus de Kruijff
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarbrücken, Germany
| | - Christine Beemelmanns
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarbrücken, Germany
- Saarland University, Saarbrücken, Germany
| | - Hannes Link
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany
| | - Christoph Mayer
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany
| | - Justin J J van der Hooft
- Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA
- Bioinformatics Group, Wageningen University and Research, Wageningen, the Netherlands
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Tito Damiani
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Pluskal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Pieter Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Jan Stanstrup
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, Denmark
| | - Robin Schmid
- Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Mingxun Wang
- Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA
- Department of Computer Science, University of California Riverside, Riverside, CA, USA
| | - Allegra Aron
- Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA
| | - Madeleine Ernst
- Section for Clinical Mass Spectrometry, Danish Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen S, Denmark.
| | - Daniel Petras
- Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA.
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany.
- Department of Biochemistry, University of California Riverside, Riverside, CA, USA.
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