Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry.
BACKGROUND
Three-dimensional (3D) imaging mass spectrometry (MS) is an analytical chemistry technique for the 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. Owing to the sheer quantity of data generated, the 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 to evaluate and compare algorithms.


RESULTS
High-quality 3D imaging MS datasets from different biological systems at several labs were acquired, supplied with overview images and scripts demonstrating how to read them, and deposited into MetaboLights, an open repository for metabolomics data. 3D imaging MS data were collected from five samples using two types of 3D imaging MS. 3D matrix-assisted laser desorption/ionization imaging (MALDI) MS data were 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 were collected from a human colorectal adenocarcinoma.


CONCLUSIONS
With the aim to stimulate computational research in the field of computational 3D imaging MS, selected high-quality 3D imaging MS datasets are provided that could be used by algorithm developers as benchmark datasets.
MALDI Imaging Lab, University of Bremen, Bremen, Germany.
Janina
J
Oetjen
Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK.
Kirill
K
Veselkov
Department of Medicine, Biomedical Research Facility II, University of California, San Diego, USA.
Jeramie
J
Watrous
Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK.
James S
JS
McKenzie
Bruker Daltonik GmbH, Bremen, Germany.
Michael
M
Becker
Steinbeis Center SCiLS Research, Bremen, Germany.
Lena
L
Hauberg-Lotte
Steinbeis Center SCiLS Research, Bremen, Germany.
Jan Hendrik
JH
Kobarg
Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK.
Nicole
N
Strittmatter
Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK.
Anna K
AK
Mróz
Institute of Physical Chemistry, Friedrich-Schiller-University Jena, Jena, Germany ; Department of Otorhinolaryngology, Jena University Hospital, Jena, Germany.
Franziska
F
Hoffmann
Steinbeis Center SCiLS Research, Bremen, Germany ; SCiLS GmbH, Bremen, Germany.
Dennis
D
Trede
European Molecular Biology Laboratory, Heidelberg, Germany.
Andrew
A
Palmer
SCiLS GmbH, Bremen, Germany.
Stefan
S
Schiffler
SCiLS GmbH, Bremen, Germany.
Klaus
K
Steinhorst
Research Unit Analytical Pathology, Institute of Pathology, Helmholtz Center Munich, Munich, Germany.
Michaela
M
Aichler
Department of Medicine, Faculty of Medicine, Imperial College London, London, UK.
Robert
R
Goldin
Department of Otorhinolaryngology, Jena University Hospital, Jena, Germany.
Orlando
O
Guntinas-Lichius
Institute of Physical Chemistry, Friedrich-Schiller-University Jena, Jena, Germany ; Department of Otorhinolaryngology, Jena University Hospital, Jena, Germany ; Leibnitz Institute of Photonic Technology (IPHT), Jena, Germany ; Jena Center for Soft Matter (JCSM), Friedrich-Schiller-University Jena, Jena, Germany.
Ferdinand
F
von Eggeling
Steinbeis Center SCiLS Research, Bremen, Germany.
Herbert
H
Thiele
MALDI Imaging Lab, University of Bremen, Bremen, Germany ; Islet Research Lab, Center for Biomolecular Interactions, University of Bremen, Bremen, Germany.
Kathrin
K
Maedler
Research Unit Analytical Pathology, Institute of Pathology, Helmholtz Center Munich, Munich, Germany.
Axel
A
Walch
Center for Industrial Mathematics, University of Bremen, Bremen, Germany.
Peter
P
Maass
Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, USA.
Pieter C
PC
Dorrestein
Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK.
Zoltan
Z
Takats
Steinbeis Center SCiLS Research, Bremen, Germany ; SCiLS GmbH, Bremen, Germany ; European Molecular Biology Laboratory, Heidelberg, Germany ; Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, USA.
Theodore
T
Alexandrov
D000818:Animals; D019985:Benchmarking; D016208:Databases, Factual; D006801:Humans; D021621:Imaging, Three-Dimensional; D055432:Metabolomics; D051379:Mice; D015203:Reproducibility of Results; D021241:Spectrometry, Mass, Electrospray Ionization; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
3D imaging mass spectrometry; Benchmark datasets; DESI; MALDI; Three-dimensional; imzML