Tailored Mass Spectral Data Exploration Using the SpecXplore Interactive Dashboard
- Author(s)
- Kevin Mildau, Henry Ehlers, Ian Oesterle, Manuel Pristner, Benedikt Warth, Maria Doppler, Christoph Bueschl, Jürgen Zanghellini, Justin J.J. van der Hooft
- Abstract
Untargeted metabolomics promises comprehensive characterization of small molecules in biological samples. However, the field is hampered by low annotation rates and abstract spectral data. Despite recent advances in computational metabolomics, manual annotations and manual confirmation of in-silico annotations remain important in the field. Here, exploratory data analysis methods for mass spectral data provide overviews, prioritization, and structural hypothesis starting points to researchers facing large quantities of spectral data. In this research, we propose a fluid means of dealing with mass spectral data using specXplore, an interactive Python dashboard providing interactive and complementary visualizations facilitating mass spectral similarity matrix exploration. Specifically, specXplore provides a two-dimensional t-distributed stochastic neighbor embedding embedding as a jumping board for local connectivity exploration using complementary interactive visualizations in the form of partial network drawings, similarity heatmaps, and fragmentation overview maps. SpecXplore makes use of state-of-the-art ms2deepscore pairwise spectral similarities as a quantitative backbone while allowing fast changes of threshold and connectivity limitation settings, providing flexibility in adjusting settings to suit the localized node environment being explored. We believe that specXplore can become an integral part of mass spectral data exploration efforts and assist users in the generation of structural hypotheses for compounds of interest.
- Organisation(s)
- Department of Analytical Chemistry, Department of Biophysical Chemistry, Department of Food Chemistry and Toxicology
- External organisation(s)
- acib – Austrian Centre of Industrial Biotechnology, Vienna Doctoral School in Chemistry (DoSChem), Technische Universität Wien, Universität für Bodenkultur Wien, Wageningen University and Research Centre, University of Johannesburg (UJ)
- Journal
- Analytical Chemistry
- Volume
- 96
- Pages
- 5798-5806
- No. of pages
- 9
- ISSN
- 0003-2700
- DOI
- https://doi.org/10.1021/acs.analchem.3c04444
- Publication date
- 04-2024
- Peer reviewed
- Yes
- Austrian Fields of Science 2012
- 104027 Computational chemistry, 106057 Metabolomics
- ASJC Scopus subject areas
- Analytical Chemistry
- Portal url
- https://ucris.univie.ac.at/portal/en/publications/tailored-mass-spectral-data-exploration-using-the-specxplore-interactive-dashboard(6d8eec79-acd0-408e-b5d4-4c36de22f2c5).html