We (me and @ramanujamr) are finding links in our NPLinker output between GCFs that are comprised only of MIBiG BGCs and metabolite ions from our strain cultures. The scores for these links span the full range, with some of the scores being among the highest in our results. My understanding is that this shouldn't be possible. MIBiG BGCs are introduced in the BiG-SCAPE networking step as a sort of 'standard' and do not have corresponding mass spec files or features, so if a GCF is comprised solely of MIBiG BGCs, then it should not be possible for any correlation to exist between that GCF and a metabolite ion.
I am attaching a screenshot from a table that I derived from the NPLinker output data. You can see that Link index 3186 gives a link between GCF 18 (completely comprised of the five MIBiG BGCs shown) and spectrum ID 2649. The metcalf score for this link is rather high at 635 vs our highest metcalf scores at 795. The same spectrum ID has links to other GCFs but a shared link like that isn't intended to link those GCFs to one another, correct?
Do you all have any idea how this might be happening? Thanks in advance!
We (me and @ramanujamr) are finding links in our NPLinker output between GCFs that are comprised only of MIBiG BGCs and metabolite ions from our strain cultures. The scores for these links span the full range, with some of the scores being among the highest in our results. My understanding is that this shouldn't be possible. MIBiG BGCs are introduced in the BiG-SCAPE networking step as a sort of 'standard' and do not have corresponding mass spec files or features, so if a GCF is comprised solely of MIBiG BGCs, then it should not be possible for any correlation to exist between that GCF and a metabolite ion.
I am attaching a screenshot from a table that I derived from the NPLinker output data. You can see that Link index 3186 gives a link between GCF 18 (completely comprised of the five MIBiG BGCs shown) and spectrum ID 2649. The metcalf score for this link is rather high at 635 vs our highest metcalf scores at 795. The same spectrum ID has links to other GCFs but a shared link like that isn't intended to link those GCFs to one another, correct?
Do you all have any idea how this might be happening? Thanks in advance!