It basically means the metabolite ion information detected in our LC-MS/MS conditions. The node contains the peak property, what we call 'metabolite address', including retention time [min], m/z, predicted formula-, ontology, SMILES, and InChIKey. The size reflects the maximum ion intensity among plants, which was prepared to easily know ‘which node has good MS/MS spectrum’. Basically, the quality of MS/MS spectrum is higher in larger ion peaks than lower ion peaks.

Several thousand metabolites are detected in our LC-MS/MS conditions. The carbon element count was definitely determined by means of the fully labeled 13C plant data. Of these, there are four annotation levels: structure validated, the metabolite was validated by authentic standard compounds in our laboratory; structure annotated, the metabolite was spectrometrically annotated by human curation effort in combination with spectral library, MS-FINDER, literature, and their unique ions; formula validated, the formula was identified by human curation effort with MS-FINDER; carbon shift confirmed, the metabolite was not predicted yet.

The color means that ‘this ion was detected in the plant’. This information can facilitate the literature mining for compound annotations.

Nodes are linked by means of MS/MS similarity, ontology similarity, and formula oriented bio-reactions. These details are described in our paper.

Ion features are characterized with five annotation levels.