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systemsomicslab / MsdialWorkbench

Universal workbench incorporating msdial, msfinder, and mrmprobs
https://systemsomicslab.github.io/compms/msdial/main.html
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Molecular network export option - Scoring #430

Closed Roninaro closed 1 month ago

Roninaro commented 1 month ago

Hello everyone, which scoring algorithm (modified cosine score eg) is used when I use the molecular network export feature to export the nodes and edges table to load it into cytoscape? We had recently a discussion about scoring algorithms for FMNB and now are curious which one is used for MS-Dial. Thank you for your help, Roninaro

kozo2 commented 1 month ago

Hi Roninaro, we use "Bonanza spectral clustering algorithm" [Falkner, J. A., Falkner, J. W., Yocum, A. K. & Andrews, P. C. J. Proteome Res. 7, 4614–4622 (2008)].

Roninaro commented 1 month ago

Hi Roninaro, we use "Bonanza spectral clustering algorithm" [Falkner, J. A., Falkner, J. W., Yocum, A. K. & Andrews, P. C. J. Proteome Res. 7, 4614–4622 (2008)].

Thank you for the quick reply :)

judezhang1997 commented 2 weeks ago

Hi, the data of Agilent Qtof were imported into msdial 5, and every compounds with 3 kinds of CEs, have 3 spectrums. So, how can i deal with the data into the molecular network，and let the melecular network more accuarate?