[GC] Change the MOLECULAR-LIBRARYSEARCH-GC "[ Networking Parameters and Written Description ]" text

[aaksenov1]

To something like this (changes highlighted in italic):

Library Search/Molecular Networking GC workflow

A molecular network was created with the Library Search/Molecular Networking GC workflow at GNPS (https://gnps.ucsd.edu, Wang M et al. Nat. Biotech. 2016; Aksenov A et al. Nat. Biotech. 2020). The data was filtered by removing __all fragment ions within +/- 17 Da of the precursor m/z. EI 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 20000 Da and the __fragment ion tolerance to 0.5 Da. A molecular network was then created where edges were filtered to have a cosine score above 0.7 and more than 6 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 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 0.5 and at least 6 matched peaks. The molecular networks were visualized using Cytoscape software (Shannon, P. et al. Genome Res. 13, 2498-2504 (2003)).

Citations

For the GC-MS deconvolution and library search: Aksenov, A.A. et al. Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data. Nat Biotechnol 39, 169–173 (2021). https://doi.org/10.1038/s41587-020-0700-3 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.

Disclaimer

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