TY  - JOUR
AU  - Hoffmann, Nils
AU  - Mayer, Gerhard
AU  - Has, Canan
AU  - Kopczynski, Dominik
AU  - Al Machot, Fadi
AU  - Schwudke, Dominik
AU  - Ahrends, Robert
AU  - Marcus, Katrin
AU  - Eisenacher, Martin
AU  - Turewicz, Michael
TI  - A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics
JO  - Metabolites
VL  - 12
IS  - 7
SN  - 2218-1989
CY  - Basel
PB  - MDPI
M1  - FZJ-2022-04058
SP  - 584 -
PY  - 2022
AB  - Mass spectrometry is a widely used technology to identify and quantify biomolecules such as lipids, metabolites and proteins necessary for biomedical research. In this study, we catalogued freely available software tools, libraries, databases, repositories and resources that support lipidomics data analysis and determined the scope of currently used analytical technologies. Because of the tremendous importance of data interoperability, we assessed the support of standardized data formats in mass spectrometric (MS)-based lipidomics workflows. We included tools in our comparison that support targeted as well as untargeted analysis using direct infusion/shotgun (DI-MS), liquid chromatography−mass spectrometry, ion mobility or MS imaging approaches on MS1 and potentially higher MS levels. As a result, we determined that the Human Proteome Organization-Proteomics Standards Initiative standard data formats, mzML and mzTab-M, are already supported by a substantial number of recent software tools. We further discuss how mzTab-M can serve as a bridge between data acquisition and lipid bioinformatics tools for interpretation, capturing their output and transmitting rich annotated data for downstream processing. However, we identified several challenges of currently available tools and standards. Potential areas for improvement were: adaptation of common nomenclature and standardized reporting to enable high throughput lipidomics and improve its data handling. Finally, we suggest specific areas where tools and repositories need to improve to become FAIRer.
LB  - PUB:(DE-HGF)16
C6  - 35888710
UR  - <Go to ISI:>//WOS:000831792900001
DO  - DOI:10.3390/metabo12070584
UR  - https://juser.fz-juelich.de/record/910686
ER  -