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.
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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.
Carbon shift confirmed
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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.