TY - JOUR
T1 - Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry
AU - Oetjen, Janina
AU - Veselkov, Kirill
AU - Watrous, Jeramie
AU - McKenzie, James S.
AU - Becker, Michael
AU - Hauberg-Lotte, Lena
AU - Kobarg, Jan Hendrik
AU - Strittmatter, Nicole
AU - Mróz, Anna K.
AU - Hoffmann, Franziska
AU - Trede, Dennis
AU - Palmer, Andrew
AU - Schiffler, Stefan
AU - Steinhorst, Klaus
AU - Aichler, Michaela
AU - Goldin, Robert
AU - Guntinas-Lichius, Orlando
AU - Eggeling, Ferdinand von
AU - Thiele, Herbert
AU - Maedler, Kathrin
AU - Walch, Axel
AU - Maass, Peter
AU - Dorrestein, Pieter C.
AU - Takats, Zoltan
AU - Alexandrov, Theodore
N1 - Publisher Copyright:
© 2015 Oetjen et al.
PY - 2015
Y1 - 2015
N2 - 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. Findings: 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.
AB - 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. Findings: 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.
KW - 3D imaging mass spectrometry
KW - Benchmark datasets
KW - DESI
KW - ImzML
KW - MALDI
KW - Three-dimensional
UR - http://www.scopus.com/inward/record.url?scp=84991528853&partnerID=8YFLogxK
U2 - 10.1186/s13742-015-0059-4
DO - 10.1186/s13742-015-0059-4
M3 - Article
C2 - 25941567
AN - SCOPUS:84991528853
SN - 2047-217X
VL - 4
JO - GigaScience
JF - GigaScience
IS - 1
M1 - 20
ER -