GC-MS Library Search Query (NIST .lib)

[Luis Manuel Quiros guerrero]

Hello everyone, 

Lately I have been working with the GC-MS data in GNPS  and is fascinating. But for the identification (Library Search) I would like to include the database from NIST, I have it but in format .lib (vendor...). 

Does anyone have tried to convert the format .lib to .mgf ? if so, could you guide me. I have not found yet a good solution to do it. 

Luis

[Ricardo M Borges]

I was about to ask here the same thing.

[stefano papazian]

Yes, I have the same question.

Also in the tutorial video of the GC workflow it is mentioned the possibility to convert the library NIST to mgf format and load it to the database search in GNPS.
Min 7:50 https://youtu.be/yrru-5nrsdk

It would be wonderful to know how

Stefano

[Mabel Gonzalez]

Hi Stefano,

In this link you can find some general information of how to create your own library: https://ccms-ucsd.github.io/GNPSDocumentation/batchupload/

This is general for GNPS libraries for both LC and GC data.

The steps that you need to follow are:

• Export excel file as a tab separated text file and upload to GNPS (recommended export from Windows office 2013 or newer. Verify that line endings are UNIX and not Windows line endings)

• Launch Batch Validator Workflow with all spectrum files and annotation table found here. NOTE: Creating spectral libraries from MGF files is discouragedas it is not a well defined format. If you do insist, you must make sure each MGF start from scan 1 (e.g. SCANS=1 in the file) and are incremented sequentially without any missing scan numbers.

• Users will then need to contact Morgan (ccms...@cs.ucsd.edu) and send her the completed job from above.

• A private spectral library will then be created by Morgan.

• After the contributor may review the library to be made into a public library and will be made public after approval.

Let us know how is the process following these steps and if do you have more questions. 

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Best regards,

Mabel Cristina González Montoya, M.Sc.
Ph.D. Student
Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Chemistry Department, Universidad de los Andes
 
Visiting Scholar 
Dorrestein Laboratory
University of California - San Diego
Skaggs School of Pharmacy & Pharmaceutical Sciences
9500 Gilman Drive
La Jolla, CA 92093-0751

[zipora Tietel]

Hi Stefano,

I have the same question about converting our NIST14 .lib to .mgf, in order to use it in GNPS for annotations, as mentioned on the link .

I was wondering whether you were able to convert your library, and if so if you have any specific recommendations on how to do it. 

Thanks,

Zipora