[GNPS] Export to Cytoscape

[정영흔]

Dear community.

I am working on starting feature-based molecular networking.

The peaks and MS2 data are processed by MZmine 3.

1. The first question is, how to discriminate between the test groups and the control group results as a peak intensity using a pie chart as a node in GNPS or using Cytoscape. Each group consists of 3 samples, and it was discriminated by setting a sample parameter at MZmine. Since I am also a beginner at using Cytoscape, maybe I couldn't find a way to solve it. Ultimately, I want to compare the test group and the control group (3 samples each, as an average or sum of the mass intensities).

2. The second question. I am following instructions from GNPS documentation - (Advanced Data Analysis - Feature Based Molecular Networking - FBMN export to Cytoscape) tab. After FBMN by Quick Start in GNPS, files of FBMN results were able to be downloaded. When trying to import the table file into Cytoscape, the instruction says to navigate to the "DB_result" folder and select the .csv file. However, instead of .csv file, there is one .tsv file in the folder. Is this a normal situation that can happen or wonder if I missed something during the process? 

I would really appreciate for any help from you guys. Thank you!

[Young-Heun]

Hello to the cummunity.

I have found the solution by using the metadata table when uploading the files to GNPS for feature based molecular networking.

Hope nobody struggle with this kind of situation..

Thank you!

Young-Huen

2022년 6월 2일 목요일 오후 12시 15분 12초 UTC+9에 Young-Heun님이 작성:

[Wender Gomes]

Dear Young-Heun,

1. If you're working with classical molecular networks, you can discriminate by groups (G1, G2, G3, G4, G5, G6), and then, when you're using cytoscape, choose the pie chart format and use groups to each color (samples). Check the documentation here https://ccms-ucsd.github.io/GNPSDocumentation/networking/

2. to fbmn, use the graphml file to visualize molecular network in cytoscape. I'm not sure what you'd like to see using .csv file, but you can convert from .tsv to .csv using excel. 

Best,

Wender Gomes