After the analysis with MS-DIAL and patRoon, peak intensity tables were used to filter features based on the QC samples (see S1.5). The remaining features were manually checked and annotated using three different sets of criteria tailored to the three different data analysis approaches. Briefly, MS-DIAL features were annotated based on the library spectral match using the Dot product (0-100). Level 2a was assigned with Dot product ≥70, and ≥3 ion fragments matching with a known structure in the library, while Level 2b was assigned to features with the same requirements but unknown structure in library (these are spectra that are commonly detected in samples belonging to unknown structures). Level 3a was assigned to features with 50 ≤ Dot product ≤70 and ≥3 ion fragments matching, while Level 3b or Level 3c were assigned when <3 ion fragments were matching with known and unknown structures, respectively. Level 3d and 3e corresponded to features annotated via MS-FINDER, detailed in Table .