Loading...
Please wait, while we are loading the content...
Similar Documents
A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics
| Content Provider | MDPI |
|---|---|
| Author | Hoffmann, Nils Mayer, Gerhard Has, Canan Kopczynski, Dominik Machot, Fadi Al Schwudke, Dominik Ahrends, Robert Marcus, Katrin Eisenacher, Martin Turewicz, Michael |
| Copyright Year | 2022 |
| Description | 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 $MS^{1}$ 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. |
| Starting Page | 584 |
| e-ISSN | 22181989 |
| DOI | 10.3390/metabo12070584 |
| Journal | Metabolites |
| Issue Number | 7 |
| Volume Number | 12 |
| Language | English |
| Publisher | MDPI |
| Publisher Date | 2022-06-23 |
| Access Restriction | Open |
| Subject Keyword | Metabolites Biochemical Research Lipidomics Bioinformatics Data Format Database Mass Spectrometry Standardization Fair |
| Content Type | Text |
| Resource Type | Article |
