Accessible and reproducible mass spectrometry imaging data analysis in Galaxy
Background: Mass 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...
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| Main Authors: | , , |
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| Format: | Article (Journal) |
| Language: | English |
| Published: |
09 December 2019
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| In: |
GigaScience
Year: 2019, Volume: 8, Pages: 1-12 |
| ISSN: | 2047-217X |
| DOI: | 10.1093/gigascience/giz143 |
| Online Access: | Verlag, Volltext: https://doi.org/10.1093/gigascience/giz143 Verlag: https://academic.oup.com/gigascience/article/8/12/giz143/5670614 
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| Author Notes: | Melanie Christine Föll, Lennart Moritz, Thomas Wollmann, Maren Nicole Stillger, Niklas Vockert, Martin Werner, Peter Bronsert, Karl Rohr, Björn Andreas Grüning and Oliver Schilling |
| Summary: | Background: Mass 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. Findings: We 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. Conclusion: The 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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| Item Description: | Gesehen am 18.02.2020 |
| Physical Description: | Online Resource |
| ISSN: | 2047-217X |
| DOI: | 10.1093/gigascience/giz143 |