How to compare different sets of data at the same time in FBMN？

[Yuan-666-lab]

Hello, I used different collision energies (10-50V) to collect data when I used the classical molecular network for analysis, and then uploaded them simultaneously in the classical molecular network G1 G2 G3 G4 G5, and the result link is (https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=84b1b870c9c54523a4dceff425a5da50). How can I choose the best one? Or how can I upload data at the same time if I want to continue FBMN analysis? Looking forward to receiving a reply. Thank you!

[mwang87]

You can use a metadata file: https://wang-bioinformatics-lab.github.io/GNPS2_Documentation/metadata/

…

On Fri, Feb 21, 2025 at 5:21 PM Yuanyuan ***@***.***> wrote: Hello, I used different collision energies (10-50V) to collect data when I used the classical molecular network for analysis, and then uploaded them simultaneously in the classical molecular network G1 G2 G3 G4 G5, and the result link is ( https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=84b1b870c9c54523a4dceff425a5da50). How can I choose the best one? Or how can I upload data at the same time if I want to continue FBMN analysis? Looking forward to receiving a reply. Thank you! — Reply to this email directly, view it on GitHub <#403>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAXSECWAI3BIE6B7SQCNUL2Q7GLBAVCNFSM6AAAAABXUND3IGVHI2DSMVQWIX3LMV43ASLTON2WKOZSHA3TAMZSGQ4TKNQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> [image: Yuan-666-lab]*Yuan-666-lab* created an issue (CCMS-UCSD/GNPSDocumentation#403) <#403> Hello, I used different collision energies (10-50V) to collect data when I used the classical molecular network for analysis, and then uploaded them simultaneously in the classical molecular network G1 G2 G3 G4 G5, and the result link is ( https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=84b1b870c9c54523a4dceff425a5da50). How can I choose the best one? Or how can I upload data at the same time if I want to continue FBMN analysis? Looking forward to receiving a reply. Thank you! — Reply to this email directly, view it on GitHub <#403>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAXSECWAI3BIE6B7SQCNUL2Q7GLBAVCNFSM6AAAAABXUND3IGVHI2DSMVQWIX3LMV43ASLTON2WKOZSHA3TAMZSGQ4TKNQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Yuan-666-lab]

You can use a metadata file:

https://wang-bioinformatics-lab.github.io/GNPS2_Documentation/metadata/
…

On Fri, Feb 21, 2025 at 5:21 PM Yuanyuan @.***> wrote:
Hello, I used different collision energies (10-50V) to collect data when I
used the classical molecular network for analysis, and then uploaded them
simultaneously in the classical molecular network G1 G2 G3 G4 G5, and the
result link is (
https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=84b1b870c9c54523a4dceff425a5da50).
How can I choose the best one? Or how can I upload data at the same time if
I want to continue FBMN analysis? Looking forward to receiving a reply.
Thank you!

—
Reply to this email directly, view it on GitHub
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[image: Yuan-666-lab]Yuan-666-lab created an issue
(CCMS-UCSD/GNPSDocumentation#403)
<#403>

Hello, I used different collision energies (10-50V) to collect data when I
used the classical molecular network for analysis, and then uploaded them
simultaneously in the classical molecular network G1 G2 G3 G4 G5, and the
result link is (
https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=84b1b870c9c54523a4dceff425a5da50).
How can I choose the best one? Or how can I upload data at the same time if
I want to continue FBMN analysis? Looking forward to receiving a reply.
Thank you!

—
Reply to this email directly, view it on GitHub
<#403>, or
unsubscribe
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ID: @.***>

Thanks for your suggestions. How can I make the best data selection in classic molecular network？

[mwang87]

Classical and FBMN are separate tracks of data analysis. If you want to analyze after feature finding then FBMN is your best bet. Otherwise raw data, you can use in Classical - you can either use default groups or metadata to compare after MS/MS clustering. to visualize the comparisons you can use the in browser visualization in GNPS2 or export to cytoscape as they'll have the clustering and the group counts there ready to visualize

[Yuan-666-lab]

Well, my main workflow is to use the classical network to select the best data first, and then FBMN analysis, but I do not know how to make the best choice of the data I get. Can you help me see the pie chart（https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=84b1b870c9c54523a4dceff425a5da50）composed of different colors and guide me? I'm not sure what constitutes the proportion of these pie charts. Thank you very much. ---- Replied Message ---- | From | Ming ***@***.***> | | Date | 2/22/2025 09:37 | | To | ***@***.***> | | Cc | ***@***.***>, ***@***.***> | | Subject | Re: [CCMS-UCSD/GNPSDocumentation] How to compare different sets of data at the same time in FBMN？ (Issue #403) | Classical and FBMN are separate tracks of data analysis. If you want to analyze after feature finding then FBMN is your best bet. Otherwise raw data, you can use in Classical - you can either use default groups or metadata to compare after MS/MS clustering. to visualize the comparisons you can use the in browser visualization in GNPS2 or export to cytoscape as they'll have the clustering and the group counts there ready to visualize — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***> mwang87 left a comment (CCMS-UCSD/GNPSDocumentation#403) Classical and FBMN are separate tracks of data analysis. If you want to analyze after feature finding then FBMN is your best bet. Otherwise raw data, you can use in Classical - you can either use default groups or metadata to compare after MS/MS clustering. to visualize the comparisons you can use the in browser visualization in GNPS2 or export to cytoscape as they'll have the clustering and the group counts there ready to visualize — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[mwang87]

Use the export to cytoscape button

[Yuan-666-lab]

Thank you for your quick answer, but what I want to know is which module should I choose the best data? ---- Replied Message ---- | From | Ming ***@***.***> | | Date | 2/22/2025 09:52 | | To | ***@***.***> | | Cc | ***@***.***>, ***@***.***> | | Subject | Re: [CCMS-UCSD/GNPSDocumentation] How to compare different sets of data at the same time in FBMN？ (Issue #403) | Use the export to cytoscape button — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***> mwang87 left a comment (CCMS-UCSD/GNPSDocumentation#403) Use the export to cytoscape button — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>