Question regarding the "Advanced Extras" in the FBMN workflow in GNPS2

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Omer Sabti

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Dec 30, 2025, 9:09:08 AM (16 hours ago) Dec 30
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Hi everyone, 

I am running the FBMN workflow on GNPS2 using processed data from MZmine 3.

I have generated an edge file in MZmine (containing MS2Deepscore and IIMN connections), and I noticed the "Supplementary Pairs/Edges" option under the Advanced Extras section of the FBMN workflow.

My question is: How does GNPS2 handle this external edge file?

  1. Additive: Does it append these external edges to the standard Modified Cosine edges that GNPS2 calculates? (i.e., will the final network contain both?)

  2. Replacement: Does providing this file override the internal networking calculation, resulting in a network containing only the edges from my uploaded CSV?

Thank you for your help!

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