ArticleGigaScience2019
Accessible and reproducible mass spectrometry imaging data analysis in Galaxy.
Article in GigaScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
20 citing papers in PubMed.
- MALDI Matrix: Origins, Innovations, and Frontiers.Chemical reviews · 2026Review
- From Sample to Mixed Reality: A Translational 3D MALDI Imaging Platform for Advanced 3D Spatial Omics Analysis of 3D Cell Culture Disease Models.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Review
- msiFlow: automated workflows for reproducible and scalable multimodal mass spectrometry imaging and microscopy data analysis.Nature communications · 2025Article
- Frontiers in Mass Spectrometry-Based Spatial Metabolomics: Current Applications and Challenges in the Context of Biomedical Research.Trends in analytical chemistry : TRAC · 2024Article
- Spatial pharmacology using mass spectrometry imaging.Trends in pharmacological sciences · 2024Review
- aXonica: A support package for MRI based Neuroimaging.Biotechnology notes (Amsterdam, Netherlands) · 2024Article
- Cardinal v.3: a versatile open-source software for mass spectrometry imaging analysis.Nature methods · 2023Article
- Transformer-based tool recommendation system in Galaxy.BMC bioinformatics · 2023Article
- Spatial analysis of drug absorption, distribution, metabolism, and toxicology using mass spectrometry imaging.Biochemical pharmacology · 2022Review
- Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: a case study of an urothelial cancer cohort analyzed in the Galaxy framework.Clinical proteomics · 2022Article
- Preparing ductal epithelial organoids for high-spatial-resolution molecular profiling using mass spectrometry imaging.Nature protocols · 2022Review
- M2aia-Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data.GigaScience · 2021Article
- Metabolomics-Guided Elucidation of Plant Abiotic Stress Responses in the 4IR Era: An Overview.Metabolites · 2021Review
- Article
- Contrast optimization of mass spectrometry imaging (MSI) data visualization by threshold intensity quantization (TrIQ).PeerJ. Computer science · 2021Article
- Spatial Metabolomics and Imaging Mass Spectrometry in the Age of Artificial Intelligence.Annual review of biomedical data science · 2020Article
- Deep multiple instance learning classifies subtissue locations in mass spectrometry images from tissue-level annotations.Bioinformatics (Oxford, England) · 2020Article
- Evaluation of Data Analysis Platforms and Compatibility with MALDI-TOF Imaging Mass Spectrometry Data Sets.Journal of the American Society for Mass Spectrometry · 2020Article
- Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMass spectrometry imaging is increasingly used in biological and translational research because it has the ability to determine the spatial distribution of hundreds of analytes in a sample. Being at the interface of proteomics/metabolomics and imaging, the acquired datasets are large and complex and often analyzed with proprietary software or in-house scripts, which hinders reproducibility. Open source software solutions that enable reproducible data analysis often require programming skills and are therefore not accessible to many mass spectrometry imaging (MSI) researchers.
findingsWe have integrated 18 dedicated mass spectrometry imaging tools into the Galaxy framework to allow accessible, reproducible, and transparent data analysis. Our tools are based on Cardinal, MALDIquant, and scikit-image and enable all major MSI analysis steps such as quality control, visualization, preprocessing, statistical analysis, and image co-registration. Furthermore, we created hands-on training material for use cases in proteomics and metabolomics. To demonstrate the utility of our tools, we re-analyzed a publicly available N-linked glycan imaging dataset. By providing the entire analysis history online, we highlight how the Galaxy framework fosters transparent and reproducible research.
conclusionThe Galaxy framework has emerged as a powerful analysis platform for the analysis of MSI data with ease of use and access, together with high levels of reproducibility and transparency.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.