Result Export

After molecular formula annotation, you can access the result summary as demonstrated in the Quick Start session. All the top 5 formulas will be included in the results.

# retrieve the annotation result summary
results = msb_engine.get_summary()

In case you want to access all the annotation results, you can iterate through the CandidateFormula objects stored in each MetaFeature.

# retrieve all the annotation results for each metabolic feature
for meta_feature in msb_engine.data:
    for i, candidate in enumerate(meta_feature.candidate_formula_list):
        print('MetaFeature mz' + str(meta_feature.mz) + '  rt: ' + str(meta_feature.rt) + \
        '  rank: ' + str(i+1) + 'Formula: ' + candidate.formula.__str__() + \
        '  estimated FDR: ' + str(candidate.estimated_fdr))

Please see MetaFeature and CandidateFormula in Python API for more details.

Note

If you are using the command-line interface, the result summary will be automatically written in the output directory as a .tsv file. To access more detailed annotation results, you can use the -details option. See Command-line API for more details.