msiFlow: automated workflows for reproducible and scalable multimodal mass spectrometry imaging and microscopy data analysis
Multimodal imaging by matrix-assisted laser desorption ionisation mass spectrometry imaging (MALDI MSI) and microscopy holds potential for understanding pathological mechanisms by mapping molecular signatures from the tissue microenvironment to specific cell populations. However, existing software solutions for MALDI MSI data analysis are incomplete, require programming skills and contain laborious manual steps, hindering broadly applicable, reproducible, and high-throughput analysis to generate impactful biological discoveries. Here, we present msiFlow, an accessible open-source, platform-independent and vendor-neutral software for end-to-end, high-throughput, transparent and reproducible analysis of multimodal imaging data. msiFlow integrates all necessary steps from raw data import to analytical visualisation along with state-of-the-art and self-developed algorithms into automated workflows. Using msiFlow, we unravel the molecular heterogeneity of leukocytes in infected tissues by spatial regulation of ether-linked phospholipids containing arachidonic acid. We anticipate that msiFlow will facilitate the broad applicability of MSI in multimodal imaging to uncover context-dependent cellular regulations in disease states.
Authors
- Lars C. Moeller (ORCID: https://orcid.org/0000-0002-9330-9036)
- Jens Soltwisch (ORCID: https://orcid.org/0000-0002-0258-1561)
- Mathis Richter (ORCID: https://orcid.org/0000-0002-3110-6137)
- Sascha D. Krauß (ORCID: https://orcid.org/0000-0001-6271-9940)
- Raf Van de Plas (ORCID: https://orcid.org/0000-0002-2232-7130)
- Prasad Phapale (ORCID: https://orcid.org/0000-0002-9487-597X)
- Stephanie Thiebes (ORCID: https://orcid.org/0000-0001-5320-3889)
- Devon Siemes (ORCID: https://orcid.org/0000-0003-1869-1930)
- Jens Kleesiek (ORCID: https://orcid.org/0000-0001-8686-0682)
- Oliver Soehnlein (ORCID: https://orcid.org/0000-0002-7854-0694)
- Matthias Gunzer (ORCID: https://orcid.org/0000-0002-5534-6055)
- Klaus Dreisewerd (ORCID: https://orcid.org/0000-0002-7619-808X)
- Philippa Spangenberg (ORCID: https://orcid.org/0000-0002-5593-5546)
- Sebastian Bessler (ORCID: https://orcid.org/0000-0002-0377-1164)
- Olga Shevchuk (ORCID: https://orcid.org/0000-0003-1150-7344)
- Lukasz G. Migas (ORCID: https://orcid.org/0000-0002-1884-6405)
- Daniel Robert Engel (ORCID: https://orcid.org/0000-0001-7301-353X)
- Siva Swapna Kasarla
- Heike Heuer (ORCID: https://orcid.org/0000-0001-7094-6959)
- Jenny Bottek (ORCID: https://orcid.org/0000-0002-4418-6092)
- Lars Widera
- Dagmar Führer
Institutions
- Vanderbilt University (US)
- University of Münster (DE)
- Institut für Medizinische Informatik, Biometrie und Epidemiologie (DE)
- Essen University Hospital (DE)
- Leibniz Institute for Analytical Sciences - ISAS (DE)
- Delft University of Technology (NL)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-01-27
- DOI
- https://doi.org/10.1038/s41467-024-55306-7
- Citations
- 17
- Primary Topic
- Metabolomics and Mass Spectrometry Studies
- Type
- article
- Field-Weighted Citation Impact
- 13.70
Funders
- Deutsche Forschungsgemeinschaft
- Fondation Leducq
- Novo Nordisk
- Westfälische Wilhelms-Universität Münster
- Universität Duisburg-Essen