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Data released on February 16, 2015

Supporting materials for "Benchmark datasets for 3D MALDI- and DESI-Imaging Mass Spectrometry".

Aichler, M; Alexandrov, T; Becker, M; Dorrestein, P; Goldin, R; Guntinas-Lichius, O; Hauberg-Lotte, L; Hoffmann, F; Kobarg, J; Maass, P; Maedler, K; McKenzie, J, S; Mroz, A, K; Oetjen, J; Palmer, A; Schiffler, S; Steinhorst, K; Strittmatter, N; Takats, Z; Thiele, H; Trede, D; Veselkov, K; von Eggeling, F; Walch, A; Watrous, J (2015): Supporting materials for "Benchmark datasets for 3D MALDI- and DESI-Imaging Mass Spectrometry". GigaScience Database. RIS BibTeX Text

Three-dimensional imaging mass spectrometry (3D imaging MS) is a technique of analytical chemistry for three-dimensional molecular analysis of a tissue specimen, entire organ, or microbes on an agar plate. 3D imaging MS has unique advantages over existing 3D imaging techniques and offers novel perspectives for understanding the spatial organization of biological processes with possible applications in both biology and medicine. Due to the sheer quantity of data generated, visualization, analysis, and interpretation of big 3D imaging MS data remain a significant challenge. In this paper, we provide to the community selected high-quality 3D imaging MS datasets from different biological systems acquired at several labs with the aim to stimulate computational research in this field.
3D imaging MS data was collected from five different samples using two different 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.

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Read the peer-reviewed publication(s):

Oetjen, J., Veselkov, K., Watrous, J., McKenzie, J. S., Becker, M., Hauberg-Lotte, L., … Alexandrov, T. (2015). Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry. GigaScience, 4(1). doi:10.1186/s13742-015-0059-4

Accessions (data included in GigaDB):

MetaboLights: MTBLS176



Samples: Table Settings


Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
3DMouseKidney10090Mousehouse mouseMus musculus Geographic location (country and/or sea,region):no...
Strain:not available
3D_Mouse_Pancreas10090Mousehouse mouseMus musculus Geographic location (country and/or sea,region):no...
3D_OSCC9606HumanhumanHomo sapiens Cell type:EV:0200165
Disease status:DOID:0050866
Geographic location (country and/or sea,region):Ge...
3D_Timecourse2 eubacteriaBacteria Description:Metabolic exchange of the interacting microbes Streptomyces coelicolor A3(2) and Bacillus subtilis PY79 was followed in a time-course experiment on the first, fourth, and eighth days after co-inoculation in a Petri dish.
Colorectal_Adenocarcinoma9606HumanhumanHomo sapiens Cell type:BTO:0000604
Disease status:DOID:0050861
Geographic location (country and/or sea,region):no...
Displaying 1-5 of 5 Sample(s).

Files: (FTP site) Table Settings


File Description
Sample ID
Data Type
File Format
Release Date
Download Link
File Attributes

File NameSample IDData TypeFile FormatSizeRelease Date 
3DMouseKidneyMass Spectrometry dataUNKNOWN38.95 GB 
3DMouseKidneyMass Spectrometry datamzML2.19 GB 
3D_Mouse_PancreasMass Spectrometry dataUNKNOWN24.63 GB 
3D_Mouse_PancreasMass Spectrometry datamzML817.94 MB 
3D_OSCCMass Spectrometry dataUNKNOWN23.66 GB 
3D_OSCCMass Spectrometry datamzML1.33 GB 
Colorectal_AdenocarcinomaMixed archivezip242.42 MB 
Colorectal_AdenocarcinomaMass Spectrometry dataHDF51.14 GB 
3D_TimecourseMass Spectrometry dataUNKNOWN2.65 GB 
3D_TimecourseMass Spectrometry datamzML29.04 MB 
Displaying 1-10 of 11 File(s).



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