FBMN annotations are compared to MetFrag candidates for each feature. In the second place, FBMN annotations are compared to the corresponding SIRIUS candidates. In the third place, the FBMN, NAP (MetFrag), and SIRIUS annotations are compared to each other to highlight those with the same candidate through the three annotation tools. The greater the number of tools giving the same annotation, the better the score and priority accorded to annotation tools based on their effectiveness in providing a relevant structural candidate (c.f. CASMI). Thus, a spectral match with a reference experimental spectrum (i.e., FBMN) will be prioritised over a predicted spectrum (i.e. MetFrag). However, de novo annotations (i.e., SIRIUS) will be ranked higher than the latter. Furthermore, the scores are better when a candidate is corroborated by NMR, unlike cases where the annotation solely relies on MS/MS tools. Consequently, the features with consistent annotation along the three mass annotation tools are scored with a Confidence_Level = 9. The features with consistent annotations between FBMN and SIRIUS are scored 10, the features with consistent annotations between FBMN and MetFrag are scored 12, and features with consistent annotations between MetFrag and SIRIUS are scored 11+. The corresponding annotation for each scored feature is then compared to the CaraMel candidates. If the MS 2 candidate is part of CaraMel annotations, the header « Is_NMR_Annotated_SU » = 1, and the corresponding molecular name is given to the header « Molecular_Name_SU » else « Is_NMR_Annotated_SU » = 0, where SU means Sum-Up. Consequently, features previously scored , also annotated by CaraMel, are respectively re-scored 1,2, 3+ or 4. Then, only the data with a PRED score = 2 are selected. The features with consistent annotations between MetFrag and SIRIUS are scored 11. The annotation is then compared to the CaraMel annotations, as previously explained. If these features are also annotated with CaraMel, the score is raised to 3. If an annotation is common to at least two MS 2 annotation tools, the third tool annotation is equally compared to the CaraMel annotations. If it matches, the corresponding molecular name is reported in the header « 3rd_Tool_SU » of the sum-up file. All the other features that do not have consistent annotations between the different MS 2 tools are equally compared to the CaraMel annotations. If the annotation from FBMN matches, Confidence_Level corresponds to 5; if one annotation candidate matches for at least the NAP workflow, Confidence Level is equal to 7. Finally, if only a candidate annotated from SIRI-US matches with a CaraMel annotation, Confidence_Level will be 6. CaraMel annotations that do not correspond to any mass annotation are scored 8. All the corresponding confidence levels are reported in Table . 2. The comparison outcomes are then written as a table in a sum-up file called « df_resume_confidence.tsv » starting with the following table column headers: « 3rd_Tool_SU, Confi-dence_Level, Feature_SU, GNPS_SU, Is_NMR_Annotated_SU, Molecular_Name, NAP_SU, Not_Matching_Tool_Annotation_SU, Rt_SU, SIRIUS_SU, m/z ». This sum-up file is then imported to the previously created network collection in Cytoscape software, and metadata are overlayed on the graph via the in-house style, as exemplified in Fig. .