microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data in Nature Microbiology
Using MASST or fastMASST to search all public datasets on GNPS/MassIVE, adding extensive metadata onto an ontology for microbes.
- Navigate to the jobs.py file add entries to the files list as
("input file", "output_directory/file_prefix) - Run jobs.py
- Some entries might fail - adding the same input output file combination multiple times to run iteratively with the option:
skip_existing=True
# single USI or GNPS library ID
microbe_masst.py
# batch jobs
microbe_masst_batch.py