Table 4.

Overview on the annotated features in MAW, SIRIUS, Spectra, and MetFrag, using the standards dataset, which had in total 37 features (and 9 standards)

Annotation level	MAW	Spectra (GNPS, HMDB, MassBank)	SIRIUS	MetFrag (PubChem)
Total structural annotations	100% (37)	75.7% (28) (within MAW)	70.2% (26) (within MAW)	32.4%(12)
Chemical class prediction	97.3% (36)	–	100% (37)	–
Formula prediction	100% (37)	–	100% (37)	–

Total structural annotations refer to the percentage of annotated compounds that are the same in MAW, Spectra, and SIRIUS. Thus, 75.7% of the annotation in MAW were observed in Spectra and 70.2% of the annotations were observed in SIRIUS while some of the features had annotation sources from both Spectra and SIRIUS. We additionally ran MetFrag and among the top 100 candidates from each feature, 12 features had the same correct annotation. For the chemical classification, MAW annotated 97.3% of the features with a chemical class and all features had a molecular formula prediction. SIRIUS identified the chemical class (with CANOPUS) and molecular formula for all features, while Spectra and MetFrag did not provide these functionalities