Molecular Networking and Spectral Library Search

A molecular network was created with the Feature-Based Molecular Networking (FBMN) workflow (Nothias L-F, Petras D, Schmid R et al. Nature Methods 17, 905–908 (2020)) on GNPS (https://gnps.ucsd.edu, Wang M et al. Nat. Biotech. 2016). The mass spectrometry data were first processed with MZMINE2 (cite accordingly, see below in the Citations section) and the results were exported to GNPS for FBMN analysis. The data was filtered by removing all MS/MS fragment ions within +/- 17 Da of the precursor m/z. MS/MS spectra were window filtered by choosing only the top 6 fragment ions in the +/- 50 Da window throughout the spectrum. The precursor ion mass tolerance was set to 0.01 Da and the MS/MS fragment ion tolerance to 0.01 Da. A molecular network was then created where edges were filtered to have a cosine score above 0.6 and more than 3 matched peaks. Further, edges between two nodes were kept in the network if and only if each of the nodes appeared in each others respective top 10 most similar nodes. Finally, the maximum size of a molecular family was set to 100, and the lowest scoring edges were removed from molecular families until the molecular family size was below this threshold. The analogue search mode was used by searching against MS/MS spectra with a maximum difference of 150.0 in the precursor ion value. The library spectra were filtered in the same manner as the input data. All matches kept between network spectra and library spectra were required to have a score above 0.7 and at least 6 matched peaks. Additional edges were provided by the user. The molecular networks were visualized using Cytoscape software (Shannon, P. et al. Genome Res. 13, 2498-2504 (2003)).

Data Deposition and Job Accessibility

The mass spectrometry data were deposited on public repository (provide the deposition accession number), such as MassIVE or MetaboLights. The molecular networking job can be publicly accessed at https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=fafdbfc058184c2b8c87968a7c56d7aa (we recommend sharing this link in your manuscript).

Citations

For Feature-Based Molecular Networking: Nothias LF et al. Feature-based Molecular Networking in the GNPS Analysis Environment. bioRxiv 812404 (2019). https://doi.org/10.1101/812404.

For the GNPS web-platform: Wang M et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nature Biotechnology 34.8 (2016): 828-837. https://doi.org/10.1038/nbt.3597.

For MZmine2: Pluskal T et al. MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics 11, 395 (2010), https://doi.org/10.1186/1471-2105-11-395. Katajamaa M. et al, MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics 22, 634-636 (2006), https://doi.org/10.1093/bioinformatics/btk039.

Additional Citations

If you used the molecular network web-based visualiser: Ono, K., Demchak, B. and Ideker, T. Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. F1000Res. 3, 143 (2014), https://dx.doi.org/10.12688/f1000research.4510.2.

Disclaimer

This description is generated to facilitate the report and the reproducibility of the analysis. It also provides the citation of the tools used. Note that if copy/pasted as is in your manuscript, it might be flagged as plagiarism by the editor. For that reason, we recommend cautiouness and using it as a guideline.