Compound annotation issues in GNPS molecular networking database comparison.

[Yashuai Kong]

Hi everyone,

I'm currently encountering a perplexing issue while running the GNPS Classical Molecular Networking and FBMN workflows. Several years ago, when I ran a Classical Molecular Networking workflow (using an .mgf mass spectrometry data file), it matched and annotated over 350 compounds. However, now when I rerun the same .mgf data file with identical parameters, it only matches around 50 compounds. I have attempted this multiple times, but the results consistently show very few annotated compounds.

Workflow from several years ago:
https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=f8d4f97d74364d9cb8ca579c5b7ab042

Current workflow:
https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=7b3f08fb47da4bc8aaa9e8d5c943785c

[Mingxun Wang]

I would really recommend GNPS2 from now on. 

Ming

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