Benchmark datasets for 3D MALDI- and DESI-Imaging Mass Spectrometry (MTBLS176)

DOI: 10.1186/s13742-015-0059-4
创建时间: 2025-01-23 19:02:48

Three-dimensional imaging mass spectrometry (3D imaging MS) is a technique of analytical chemistry for 3D molecular analysis of a tissue specimen, entire organ, or microbial colonies on an agar plate. 3D imaging MS has unique advantages over existing 3D imaging techniques, offers novel perspectives for understanding the spatial organization of biological processes, and has growing potential to be introduced into routine use in both biology and medicine. Due to the sheer quantity of data generated, visualization, analysis, and interpretation of 3D imaging MS data remain a significant challenge. Bioinformatics research in this field is hampered by the lack of publicly available benchmark datasets needed for evaluation and comparison of algorithms. Findings We acquired high-quality 3D imaging MS datasets from different biological systems at several labs, supplied them with overview images and scripts demonstrating how to read them, and deposited them into MetaboLights, an open repository for metabolomics data. 3D imaging MS data was collected from five samples using two types of 3D imaging MS. 3D Matrix-Assisted Laser Desorption/Ionization (MALDI) imaging MS data was collected from murine pancreas, murine kidney, human oral squamous cell carcinoma, and interacting microbial colonies cultured in Petri dishes. 3D Desorption Electrospray Ionization (DESI) imaging MS data was collected from a human colorectal adenocarcinoma. Conclusions With the aim to stimulate computational research in the field of computational 3D imaging MS, we provided selected high-quality 3D imaging MS datasets which can be used by algorithm developers as benchmark datasets.

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blank, colon, transudate

Cite as:
Janina Oetjen, Kirill Veselkov, Jeramie Watrous, James S McKenzie, Michael Becker, Lena Hauberg-Lotte, Jan Hendrik Kobarg, Nicole Strittmatter, Anna K Mróz, Franziska Hoffmann, Dennis Trede, Andrew Palmer, Stefan Schiffler, Klaus Steinhorst, Michaela Aichler, Robert Goldin, Orlando Guntinas-Lichius, Ferdinand von Eggeling, Herbert Thiele, Kathrin Maedler, Axel Walch, Peter Maass, Pieter C Dorrestein, Zoltan Takats, Theodore Alexandrov, Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry, GigaScience, Volume 4, Issue 1, December 2015, s13742–015–0059–4, https://doi.org/10.1186/s13742-015-0059-4

Benchmark datasets for 3D MALDI- and DESI-Imaging Mass Spectrometry (MTBLS176)

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