MSNovelist: De novo structure generation from mass spectra

Michael A. Stravs (1), Kai Dührkop (2), Sebastian Böcker (2), Nicola Zamboni (1)

1 Institute of Molecular Systems Biology, ETH Zürich, CH-8092 Zürich, Switzerland

2 Institut für Informatik, Friedrich-Schiller-Universität Jena, D-07743 Jena, Germany

Build docker

docker build . -t msnovelist

General:

docker run -v $DATAFOLDER:/msnovelist-data msnovelist predict.sh SPECTRA SIRIUS_SETTINGS
DATAFOLDER is a folder that contains at least the spectra to be processed.
If SPECTRA is a file within DATAFOLDER, it is first processed with SIRIUS. This works with *.mgf and *.ms (SIRIUS format) files.
SIRIUS_SETTINGS is optional; by default, the settings are formula -p qtof structure -d ALL_BUT_INSILICO.
A RUNID (based on the timestamp when running the script) identifies the processing results.
The SIRIUS results are stored in DATAFOLDER/sirius-RUNID and used as input for MSNovelist.
If SPECTRA is a folder, it is assumed to be a pre-processed SIRIUS 4.4.29 workspace and used directly as input for MSNovelist
MSNovelist is then run.
If a fingerprint cache exists in DATAFOLDER/fingerprint_cache.db, it is used, otherwise a new cache is created at this path
The used configuration file is deposited as DATAFOLDER/msnovelist-config-RUNID.yaml.
The MSNovelist results are stored in $DATAFOLDER/results-RUNID/decode-RUNID.csv and .pkl.

Example:

docker run -v "$(pwd)/sample-data":/msnovelist-data msnovelist predict.sh 377.mgf
(If you don't want to pollute your repository, copy the sample data somewhere else first)

Order the results by score_mod_platt, descendingly, to get the top candidate (or filter by rank_score_lim_mod_platt == 1)
Multiple spectra (in an MGF file, MS file or SIRIUS project) can be processed in one run, the first column query in the result file indicates the spectrum associated with the result