CCMS-UCSD
[FBMN] Import libraries for search
Hi GNPS team:
I‘d like to add some mgf format reference spectra to the Advanced Library Search Option module. But somehow I can not open the help link: To import libraries for search click here. And I tried to add these reference spectra in the same format as GNPS 'mgf files:
BEGIN IONS
PEPMASS=856.848022460938
CHARGE=1
MSLEVEL=2
SOURCE_INSTRUMENT=SCIEX 5600
FILENAME=N/A
SEQ=*..*
IONMODE=Positive
ORGANISM=LipidBlast
NAME=Cer-NS d57:3
PI=LipidBlast
DATACOLLECTOR=MONA_LipidBlast
SMILES=O=C(NC(CO)C(O)C=CCCC=CCCCCCC)CCCCCCCCCCCCCCCCCCCC=CCCCCCCCCCCCCCCCCCCCC
INCHI=InChI=1S/C57H109NO3/c1-3-5-7-9-11-13-15-16-17-18-19-20-21-22-23-24-25-26-27-28-29-30-31-32-33-34-35-36-37-38-39-40-41-42-43-45-47-49-51-53-57(61)58-55(54-59)56(60)52-50-48-46-44-14-12-10-8-6-4-2/h14,28-29,44,50,52,55-56,59-60H,3-13,15-27,30-43,45-49,51,53-54H2,1-2H3,(H,58,61)/b29-28-,44-14+,52-50+
INCHIAUX=GUYMRLZZCACOQO-JNPMOVPISA-N
PUBMED=N/A
LIBRARYQUALITY=1
SPECTRUMID=LipidBlast
SCANS=1
208.206 20.02002
220.206 100.0
238.2166 20.02002
618.6547 10.01001
820.8269 10.01001
838.8375 10.01001
856.848 5.005005
END IONS
However, it can not work. After adding the additional database, the library search result did not match any of the additional spectra I added. What's worse, the number of features in "all library hit" and "Unique Library Compounds" is reduced.
Before adding the additional database: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=43f7bb14f62847f9bad283b8c54c6d58
After adding the additional database: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=544a0d2b380c4ecba4c9e068ba30c338
Could you tell me the right way to import additional libraries for search? Sometimes some commercial databases (e.g. NIST) may not be suitable for public uploading. But I need to add these additional databases to improve my annotation result.
Thank you!
Zinuo Huang
Hi @zinuo-H, in GNPS, libraries have to be added to the system. Its meant to eventually make the spectral libraries public so it can help the entire community. You can see how to add spectra here:
https://ccms-ucsd.github.io/GNPSDocumentation/batchupload/
Best,
Ming
Thanks for replying to me! I would love to contribute to the GNPS community, but some commercial databases (e.g. NIST) are not suitable for public uploading. The NIST EI library is very important for GCMS annotation, I really hope that my GNPS annotation results can be combined with this database.