PuSH - Publikationsserver des Helmholtz Zentrums München

Export: TXT Text RIS Endnote (RIS) BIB BibTeX
Oetjen, J.* ; Veselkov, K.* ; Watrous, J.* ; McKenzie, J.S.* ; Becker, M.* ; Hauberg-Lotte, L.* ; Kobarg, J.H.* ; Strittmatter, N.* ; Mróz, A.K.* ; Hoffmann, F.* ; Trede, D.* ; Palmer, A.* ; Schiffler, S.* ; Steinhorst, K.* ; Aichler, M. ; Goldin, R.* ; Guntinas-Lichius, O.* ; von Eggeling, F.* ; Thiele, H.* ; Maedler, K.* ; Walch, A.K. ; Maass, P.* ; Dorrestein, P.C.* ; Takats, Z.* ; Alexandrov, T.*

Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry.

GigaScience 4:20 (2015)
Verlagsversion DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
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.
Impact Factor
Scopus SNIP
Web of Science
Times Cited
Scopus
Cited By
Altmetric
0.000
2.532
40
42
Tags
Anmerkungen
Besondere Publikation
Auf Hompepage verbergern

Zusatzinfos bearbeiten
Eigene Tags bearbeiten
Privat
Eigene Anmerkung bearbeiten
Privat
Auf Publikationslisten für
Homepage nicht anzeigen
Als besondere Publikation
markieren
Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Schlagwörter 3d Imaging Mass Spectrometry ; Benchmark Datasets ; Desi ; Maldi ; Three-dimensional ; Imzml
Sprache englisch
Veröffentlichungsjahr 2015
HGF-Berichtsjahr 2015
e-ISSN 2047-217X
Zeitschrift GigaScience
Quellenangaben Band: 4, Heft: , Seiten: , Artikelnummer: 20 Supplement: ,
Verlagsort London
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Pathology (PATH)
Research Unit Analytical Pathology (AAP)
POF Topic(s) 30504 - Mechanisms of Genetic and Environmental Influences on Health and Disease
30205 - Bioengineering and Digital Health
Forschungsfeld(er) Enabling and Novel Technologies
PSP-Element(e) G-500300-001
G-500390-001
PubMed ID 25941567
DOI 10.1186/s13742-015-0059-4
WOS ID WOS:000365664400001
Scopus ID 84991528853
Erfassungsdatum 2015-05-07
[➜Korrektur melden]