Fig. 2: Ion identity molecular networking.

Depicted are three visualizations of the same ion identity molecular network from the post-column salt infusion experiments. a Sorting by ion identities reveals that MS² similarity edges (blue) often link sodiated ions (e.g., [M + Na]⁺ and [2 M + Na]⁺) into a subnetwork that is separated from a subnetwork of ammonium adducts with protonated species. The pie charts indicate relative abundances in different salt addition experiments (Control (H₂O), gray; Na-Acetate, yellow; NH₄-Acetate, green). The complexity and redundancy are reduced by b sorting all ions of the same molecule in a circular layout and c collapsing all IIN into representative single molecular nodes. This option reduces the complexity of this IIMN from 43 feature nodes to four molecular nodes (A–D) and 15 feature nodes (−56%). d Lists the structure of all GNPS library matches and e propagated structures for D (based on A and C) and the in-source fragments A’ to D’. This subset of structurally related compounds gives a first statistical proof for high correct annotation rates during IIN in MZmine as adduct formation responds to the corresponding salt infusion, e.g., higher [M + Na]⁺ abundances in the sodium acetate buffer infusion.