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2023-03-20

This is Maëlle's DBGI daily open-notebook.

Today is 2023.03.20

TODO

CODE

NOTES

GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser

Petras, D., Phelan, V.V., Acharya, D. et al. GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. Nat Methods 19, 134–136 (2022). https://doi.org/10.1038/s41592-021-01339-5

GNPS

=> Developped to provide open and transparent solutions to use, share, inspect and reproduce mass spectrometry data analysis.

  • Enable remote and synchronous collaborative research in a common analysis environment for MS data analysis (same idea as Google Docs for example)
    • Includes leader-follower synchronization (real-time updates from one lead user) and fully collaborative synchronization (real-time updates from multiple users)
    • Followers can disconnect the synchronization to continue the analysis from where the leader left off
  • Makes spectrometry data adherent to FAIR (findable, accessible, interoperable and reusable)
  • Final state of the analysis is saved together with every discrete action, enabling inspection of the evolution of data analysis

Data:

  • All public data from compatible repositories can be selected using the GNPS dataset explorer
  • Files not deposited in public MS repositories can be uploaded through a drag-and drop option for file transfer

Visualization:

  • enables inspection of
    • total ion chromatograms,
    • retention time versus m/z heat map,
    • extracted ion chromatograms,
    • tandem mass spectra for inspection/visualization of individual compounds
    • and quantitative comparison of the peak abundances of two groups as boxplots
  • all with publication-quality figures

Sharability:

  • shareable URL and QR code(for final visualization)
    • empowers users to share the exact same visualization with colleagues, thus reducing miscommunication and improving data transparency

To sum up:

Help improve MS data acccessibility and interoperability, lower barriers of entry for MS data analysis in the research environment and the classroom, encourage data transparency and sharing, and strengten the reproducibility of MS data analysis.

TODO NEXT

Important for redaction