Question about RT information in GNPS

[Jingsheng Wang]

hello everyone, i am just a green hand in using gnps, and i feel confused about the RT information in a visualized subnetwork. There is a figure (generally few hundreds to a thousand) together with a σ value for one node in RT information. I dont know how they mean, and how they generate. Besides, when i see the result in "view all library hits" of a gnps workflow, I found for a specific cluster, the RT query value is just from one of the spectrum RT values, I don't know why it choose that spectrum, not the others. I am looking forward to your professional help. 

[Pieter Dorrestein]

I assume that since you are discussing RT that you are doing FBMN. There the RT is based on the feature-finding tool you are using (openMS, XCMS, MZMine 3.0, MS-Dial are all awesome) and each of them have their own strategies to report the RTs.

P

On Sat, Sep 23, 2023 at 10:53 PM Jingsheng Wang <sjtu...@126.com> wrote:

hello everyone, i am just a green hand in using gnps, and i feel confused about the RT information in a visualized subnetwork. There is a figure (generally few hundreds to a thousand) together with a σ value for one node in RT information. I dont know how they mean, and how they generate. Besides, when i see the result in "view all library hits" of a gnps workflow, I found for a specific cluster, the RT query value is just from one of the spectrum RT values, I don't know why it choose that spectrum, not the others. I am looking forward to your professional help. 

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[Jingsheng Wang]

Thanks for your reply. I just run a classical workflow and use only msconvert to transform three ddms2 thermo raw file into mzml. And I attached a figure where everyone can see the concent i feel confused about.