Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry
File(s)
Author(s)
Type
Journal Article
Abstract
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.
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.
Date Issued
2015-05-04
Date Acceptance
2015-04-09
Citation
GigaScience, 2015, 4
ISSN
2047-217X
Publisher
BioMed Central
Journal / Book Title
GigaScience
Volume
4
Copyright Statement
© 2015 Oetjen et al.; licensee BioMed Central.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
License URL
Sponsor
Commission of the European Communities
National Physical Laboratory
Grant Number
305259
410740
Subjects
Science & Technology
Multidisciplinary Sciences
Science & Technology - Other Topics
Benchmark datasets
3D imaging mass spectrometry
Three-dimensional
MALDI
DESI
imzML
METABOLIC EXCHANGE
SEGMENTATION
DESORPTION
SECTIONS
Publication Status
Published
Article Number
20