One result of the GNPS-IIMN workflow is the combined networks with IIN collapsed into single nodes. For this, all ion nodes with the same IIN ID are merged into a representative node based on the feature with the highest library match score, if available, or otherwise the feature with the maximum abundance. While all IIN edges are collapsed, MN edges of all ion identities are redirected to their representative nodes so that duplicates replace existing edges if their edge score (cosine similarity) is higher. Limiting the number of MN edges to the one with the highest cosine similarity. Furthermore, representative collapsed nodes are extended by multiple attributes, including the intensity of each ion identity and their summed intensity. This enables the direct comparison of ionization tendencies and provides new visualization options. An example with pie charts of the ion abundances is demonstrated in Supplementary Fig. 3.

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