Problem exporting data processed in MS-DIAL to GNPS #497
Replies: 4 comments 7 replies
-
|
GNPS is not suitable for MS-DIAL 5 data, and you can try GNPS2 (https://gnps2.org). However, I can find some features with RT, M/z as zero imputed into the table and the network. I believe the input of @mwang87 will be valuable. Here is example GNPS FBMN for MSDIAL 5 data https://gnps2.org/status?task=645ec447ff344b7a82f12083537167f7 |
Beta Was this translation helpful? Give feedback.
-
|
GNPS2 should handle new formats for MSDIAL5 - there were updates that GNPS1 cannot handle. I think in general with MSDIAL5 we shoudl be renumbering the scans - so sequential scan numbers in the original file are not strictly necessary. |
Beta Was this translation helpful? Give feedback.
-
|
Great! Can you send the job url?
…On Fri, Aug 22, 2025 at 8:55 AM aliciacardoso-cmd ***@***.***> wrote:
I use MSDIAL5 to generate the molecular network in GNPS2. But I believe it
is not compatible in the same way. There is an error when exporting the ion
table from MSDIAL5. In version 4 of msdial, I can generate my workflow
normally. However, the new version does not have the “GNPS table” option
that it had previously. Something in the generated file, which in my case
replaces the table called “MS/MS included,” leads to an error where several
m/z and RT values appear as zero. I request that you look into this problem
or help us with a tutorial on how to correctly export the aligned data. I
loved version 5 and the possibility of using more than one database, but
unfortunately I always go back to version 4 because msdial5 does not allow
me to proceed to the molecular network. Please help us!
Screenshot.2025-08-22.125723.png (view on web)
<https://github.com/user-attachments/assets/f27c10eb-8bce-495a-9dd9-cf62079403ad> Screenshot.2025-08-22.125022.png
(view on web)
<https://github.com/user-attachments/assets/6173e0b6-6532-46a6-88af-2d0a64576c52>
—
Reply to this email directly, view it on GitHub
<#497 (reply in thread)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AAAXSEDS7TNWCLFBPPJ4DWL3O44QRAVCNFSM6AAAAACESLC4XWVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTIMJZGEZTINI>
.
You are receiving this because you were mentioned.Message ID:
<systemsomicslab/MsdialWorkbench/repo-discussions/497/comments/14191345@
github.com>
|
Beta Was this translation helpful? Give feedback.
-
|
I am using this app to convert mgf files from MS-DIAL to GNPS and Sirius. Try it, I found it very useful: |
Beta Was this translation helpful? Give feedback.



Uh oh!
There was an error while loading. Please reload this page.
-
Hello, I am using version 5.5.24 of ms-dial to process the data and generate the mgf file and the txt file of the feature detection and GNPs has given an error when inserting the data generated by ms-dial and cannot generate a network. . There is a new way to export data directly in these new versions. In versions 4, there was the possibility to select to generate the GNPS table and now this possibility no longer exists. I don't know if this function has been replaced.
Thank you in advance!
Beta Was this translation helpful? Give feedback.
All reactions