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GNPS_GC_libraries #789

Open lydia1201 opened 2 years ago

lydia1201 commented 2 years ago

Besides downloading the mgf file, I was wondering if there is a way to get access to the GNPS_GC_libraries and perform queries to see whether certain volatile compounds are in the library or not, I was also wondering how to add new annotations to the GNPS GC-MS libraries. Thank you very much

mwang87 commented 2 years ago

We are in the process of revamping our GNPS GC library visualizations to make browsing easier. For adding GC libraries, you can follow this guide here:

https://ccms-ucsd.github.io/GNPSDocumentation/batchupload/

Hope this helps and hopefully our new interface is out soon after ASMS.

lydia1201 commented 2 years ago

Thank you very much for your reply. They are very helpful. But besides the GNPS library search method, I was also wondering if there are any in silicon annotation tools (like NAP) available for GC-MS networks? The modified MolNetEnhancer on Github for GC-MS molecular networking is not working for me, I was wondering if there is any user-friendly tool we can use to classify the libraries hits we got? Thank you very much

mwang87 commented 2 years ago

I believe ClassyFire and NP Classifer should be integrated directly into GNPS. Those would be the tools I would recommend.

lydia1201 commented 2 years ago

We are in the process of revamping our GNPS GC library visualizations to make browsing easier. For adding GC libraries, you can follow this guide here:

https://ccms-ucsd.github.io/GNPSDocumentation/batchupload/

Hope this helps and hopefully our new interface is out soon after ASMS.

Hi Ming, When I was trying to add annotations to the GNP-GC-MS libraries, I found that the input libraries don't have the GNPS-GC-libraries, I was wondering whether the spectrum will be add to the GC-MS libraries or not? image Thank you

mwang87 commented 2 years ago

This will be a totally new library, but if you're running the batch validation workflow:

https://gnps.ucsd.edu/ProteoSAFe/index.jsp?params=%7B%22workflow%22:%22ADD-BATCH-ANNOTATED-VALIDATOR%22%7D

You shouldn't need to select a target library anyway.

Best,

Ming

On Mon, Nov 1, 2021 at 6:29 AM lydia1201 @.***> wrote:

We are in the process of revamping our GNPS GC library visualizations to make browsing easier. For adding GC libraries, you can follow this guide here:

https://ccms-ucsd.github.io/GNPSDocumentation/batchupload/

Hope this helps and hopefully our new interface is out soon after ASMS.

Hi Ming, When I was trying to add annotations to the GNP-GC-MS libraries, I found that the input libraries don't have the GNPS-GC-libraries, I was wondering whether the spectrum will be add to the GC-MS libraries or not? [image: image] https://user-images.githubusercontent.com/71855567/139679346-84a5f252-e55b-48f6-9a74-6175e567a84f.png Thank you

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